Example Project Report: Differential gene expression in mouse KO fibroblasts treated with TxA and TxB

Disclaimer

This example report is for reference only. The full set of visualizations and analyses generated by analysts are decided in consultation with the researcher and based on the specific experimental questions.

The visualizations and tables shown below are a representative subset and may differ from the visualizations included in a delivered report.

1 Background

1.1 Biology

Samples are from naive T-cells isolated from wild-type or Wapl knock-out mice and treated with TxA or TxB (GSE144588). Data were analyzed with the Bioinformatics Core’s Watermelon pipeline to highlight the methods and expected deliverables for a standard RNA-seq differential expression analysis.

1.2 Samples

The following samples were analyzed:

sample	Gtype	Tx	Group
Sample_116498	wt	noTx	wt.noTx
Sample_116499	wt	noTx	wt.noTx
Sample_116500	wt	noTx	wt.noTx
Sample_116501	ko	noTx	ko.noTx
Sample_116502	ko	noTx	ko.noTx
Sample_116503	ko	noTx	ko.noTx
Sample_116504	wt	TxB	wt.TxB
Sample_116505	wt	TxB	wt.TxB
Sample_116506	wt	TxB	wt.TxB
Sample_116507	ko	TxB	ko.TxB
Sample_116508	ko	TxB	ko.TxB
Sample_116509	ko	TxB	ko.TxB
Sample_116510	wt	TxA	wt.TxA
Sample_116511	wt	TxA	wt.TxA
Sample_116512	wt	TxA	wt.TxA
Sample_116513	ko	TxA	ko.TxA
Sample_116514	ko	TxA	ko.TxA
Sample_116515	ko	TxA	ko.TxA

2 Methods

2.1 Sample preparation & sequencing

Prior tissue or cell isolation along with generation of totalRNA was performed by the researcher. Sequencing was performed by the UM AdvancedGenomics Core, with libraries constructed and subsequently sequenced on the HiSeq 4000 platform (Illumina).

2.2 Differential Expression

Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014), using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with R version 4.3.2. Annotation data from ENSEMBL 102 was used, and genes were additionally annotated with Entrez GeneIDs and text descriptions. Functional analysis, including candidate pathways activated or inhibited in comparison(s) and GO-term enrichments (Mi et al., 2019), was performed using iPathway Guide (Advaita) (iPathwayGuide), (Draghici et al., 2007).

3 Results

3.1 Boxplots

The following boxplots were selected to show the distribution of gene expression counts in the different samples.

3.1.1 Group

Figure: Box plot of raw gene expression colored by Group.

Figure: Box plot of rlog normalized gene expression colored by Group.

3.2 Clustering

Clustering is a method to visualize the similarity and difference among samples. Unsupervised clustering using complete linkage of the Euclidian distances of the gene expression profiles of pairwise samples is shown below.

Figure: Unsupervised clustering of rlog normalized expression values colored by Gtype, Tx, Group.

3.3 PCA

Principal component analysis (PCA) is another method to visualize the similarity and difference among samples. PCA was applied to the normalized gene expression profiles of the samples and the following plots were selected to highlight the expression patterns observed in the data.

3.3.1 Group

Figure: PCA plot (PC1 vs PC2) of top 100 variable genes colored by Group.

Figure: PCA plot (PC1 vs PC2) of top 500 variable genes colored by Group.

3.4 Differential Expression

The tables below summarize the setup of the differential tests with the name of the comparison, the model, and the threshold values, as well as the samples included in each comparison and the number of differentially expressed genes.

The sections that follow provide more detailed information about the differential tests, including a summary table of the top differential loci (annotated to genomic features if applicable), and a volcano plot for each comparison.

Model Name	Model	Linear fold-change	FDR
model treatment	~ Group	1.5	0.05

3.4.1 Comparisons for model treatment

Comparison	Case Samples	Ctrl Samples	Diff. Exp. Count
ko.noTx_v_wt.noTx	Sample_116501 Sample_116502 Sample_116503	Sample_116498 Sample_116499 Sample_116500	638
ko.TxA_v_ko.noTx	Sample_116513 Sample_116514 Sample_116515	Sample_116501 Sample_116502 Sample_116503	8,179
ko.TxA_v_ko.TxB	Sample_116513 Sample_116514 Sample_116515	Sample_116507 Sample_116508 Sample_116509	4,640
ko.TxA_v_wt.TxA	Sample_116513 Sample_116514 Sample_116515	Sample_116510 Sample_116511 Sample_116512	84
ko.TxB_v_ko.noTx	Sample_116507 Sample_116508 Sample_116509	Sample_116501 Sample_116502 Sample_116503	4,583
ko.TxB_v_wt.TxB	Sample_116507 Sample_116508 Sample_116509	Sample_116504 Sample_116505 Sample_116506	1,105
wt.TxA_v_wt.noTx	Sample_116510 Sample_116511 Sample_116512	Sample_116498 Sample_116499 Sample_116500	8,807
wt.TxA_v_wt.TxB	Sample_116510 Sample_116511 Sample_116512	Sample_116504 Sample_116505 Sample_116506	5,771
wt.TxB_v_wt.noTx	Sample_116504 Sample_116505 Sample_116506	Sample_116498 Sample_116499 Sample_116500	5,313

In the volcano plots below, each point is a tested locus. A gene is considered to be differentially expressed if FDR < 0.05 and | linear fold-change | > 1.5. Points are colored according to the direction of differential expression with the total number of loci indicated in the legend. The vertical lines correspond to the fold-change cutoff.

Figure: Volcano plot for ko.TxA_v_wt.TxA.

Figure: Volcano plot for ko.TxB_v_wt.TxB.

Figure: Volcano plot for ko.noTx_v_wt.noTx.

Figure: Volcano plot for ko.TxA_v_ko.TxB.

Figure: Volcano plot for ko.TxA_v_ko.noTx.

Figure: Volcano plot for ko.TxB_v_ko.noTx.

Figure: Volcano plot for wt.TxA_v_wt.TxB.

Figure: Volcano plot for wt.TxA_v_wt.noTx.

Figure: Volcano plot for wt.TxB_v_wt.noTx.

Table: Results for ko.TxA_v_wt.TxA

84 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Hist1h4m	100041230	histone cluster 1, H4m	6.438	2.0e-48
Eif2s3y	26908	eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked	8.142	1.3e-33
Ddx3y	26900	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	7.824	2.1e-31
Ifi208	100033459	interferon activated gene 208	2.149	5.4e-28
Rps3a2	NA	ribosomal protein S3A2	3.349	6.3e-23
Kdm5d	20592	lysine (K)-specific demethylase 5D	6.790	3.2e-22
Gm42427	NA	predicted gene 42427	-1.269	1.1e-21
Rps3a3	NA	ribosomal protein S3A3	3.122	8.0e-19
Gm46620	NA	predicted gene, 46620	-1.120	1.3e-17
Gm33707	NA	predicted gene, 33707	5.486	2.0e-15
Uty	22290	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	6.044	5.3e-15
Gm15446	NA	predicted gene 15446	2.225	1.8e-09
Gm42031	NA	predicted gene, 42031	-1.468	3.8e-09
Rnf43	207742	ring finger protein 43	1.022	1.0e-07
Il17rb	50905	interleukin 17 receptor B	-1.408	9.0e-07
Cnr2	12802	cannabinoid receptor 2 (macrophage)	-0.700	9.5e-06
Abca1	11303	ATP-binding cassette, sub-family A (ABC1), member 1	-1.301	1.4e-05
Tmem254b	100039257	transmembrane protein 254b	1.410	3.2e-05
Plcd3	72469	phospholipase C, delta 3	-1.651	6.8e-05
Egr3	13655	early growth response 3	-0.713	1.0e-04
Dclk2	70762	doublecortin-like kinase 2	1.099	1.1e-04
A630023P12Rik	NA	RIKEN cDNA A630023P12 gene	-1.130	1.1e-04
Tspan9	109246	tetraspanin 9	-1.426	1.2e-04
Sh3pxd2a	14218	SH3 and PX domains 2A	-0.732	1.4e-04
Rnf13	24017	ring finger protein 13	0.856	2.2e-04
Pdlim4	30794	PDZ and LIM domain 4	-1.647	4.0e-04
Gm3854	NA	predicted gene 3854	2.276	4.1e-04
Spsb1	74646	splA/ryanodine receptor domain and SOCS box containing 1	-1.297	5.6e-04
Gm7600	NA	predicted gene 7600	1.457	5.9e-04
Ecm1	13601	extracellular matrix protein 1	-1.025	6.6e-04
Trav16	NA	T cell receptor alpha variable 16	0.923	0.001
Mvb12b	72543	multivesicular body subunit 12B	-0.813	0.001
Cd1d2	12480	CD1d2 antigen	2.518	0.001
Lama5	16776	laminin, alpha 5	-1.347	0.002
Gm49980	NA	predicted gene, 49980	-0.919	0.002
Rflnb	76566	refilin B	-0.692	0.002
Adss	11566	adenylosuccinate synthetase, non muscle	0.740	0.002
Tmem181b-ps	NA	transmembrane protein 181B, pseudogene	-0.925	0.002
Rxra	20181	retinoid X receptor alpha	-0.700	0.002
Kctd12	239217	potassium channel tetramerisation domain containing 12	-0.786	0.003
Eno3	13808	enolase 3, beta muscle	0.898	0.003
Camk2b	12323	calcium/calmodulin-dependent protein kinase II, beta	-0.864	0.004
Gm46223	NA	predicted gene, 46223	-0.803	0.005
Tef	21685	thyrotroph embryonic factor	-0.697	0.005
Axin2	12006	axin 2	-0.646	0.005
B630019A10Rik	NA	RIKEN cDNA B630019A10 gene	-0.897	0.006
Plcb4	18798	phospholipase C, beta 4	2.813	0.006
Gm13408	NA	predicted gene 13408	1.673	0.007
Slc16a5	217316	solute carrier family 16 (monocarboxylic acid transporters), member 5	-1.177	0.007
Insr	16337	insulin receptor	-0.692	0.008
Pmepa1	65112	prostate transmembrane protein, androgen induced 1	-0.954	0.008
Vipr1	22354	vasoactive intestinal peptide receptor 1	-0.865	0.009
Nrn1	68404	neuritin 1	0.907	0.012
Erdr1	NA	erythroid differentiation regulator 1	1.240	0.014
Rbm44	329207	RNA binding motif protein 44	1.158	0.014
Gm15922	18722	predicted gene 15922	-2.977	0.015
Dip2c	208440	disco interacting protein 2 homolog C	-0.874	0.016
Celsr3	107934	cadherin, EGF LAG seven-pass G-type receptor 3	-1.287	0.016
5830416I19Rik	NA	RIKEN cDNA 5830416I19 gene	2.398	0.016
Gm16867	100862085	predicted gene, 16867	3.166	0.016
Bmp7	12162	bone morphogenetic protein 7	-1.010	0.018
Filip1	70598	filamin A interacting protein 1	1.043	0.018
Fndc10	230991	fibronectin type III domain containing 10	-0.875	0.019
B430306N03Rik	320148	RIKEN cDNA B430306N03 gene	-1.123	0.019
Dsel	319901	dermatan sulfate epimerase-like	-0.865	0.02
Apol9b	71898	apolipoprotein L 9b	-1.640	0.02
Rab4a	19341	RAB4A, member RAS oncogene family	-0.966	0.021
Zdhhc2	70546	zinc finger, DHHC domain containing 2	0.600	0.023
Ermn	77767	ermin, ERM-like protein	1.244	0.027
Lysmd2	70082	LysM, putative peptidoglycan-binding, domain containing 2	0.605	0.031
Sh3d19	27059	SH3 domain protein D19	0.859	0.033
Gm34680	NA	predicted gene, 34680	-1.267	0.033
Perp	64058	PERP, TP53 apoptosis effector	0.898	0.033
Egr2	13654	early growth response 2	-0.616	0.035
Mmp25	240047	matrix metallopeptidase 25	-1.400	0.036
Dclk1	13175	doublecortin-like kinase 1	1.149	0.037
Slc28a2b	381417	solute carrier family 28 member 2b	-0.817	0.038
Efna5	13640	ephrin A5	-1.936	0.038
Acvrl1	11482	activin A receptor, type II-like 1	-1.150	0.039
Nfam1	74039	Nfat activating molecule with ITAM motif 1	-1.265	0.042
Selp	20344	selectin, platelet	-1.343	0.042
Gm43305	108168162	predicted gene 43305	-0.911	0.043
6430548M08Rik	234797	RIKEN cDNA 6430548M08 gene	-1.312	0.044
Pfkfb4	270198	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	-0.661	0.048

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Table: Results for ko.TxB_v_wt.TxB

1105 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Apol11b	328563	apolipoprotein L 11b	-7.066	6.3e-71
Tmcc2	68875	transmembrane and coiled-coil domains 2	-5.939	8.5e-57
Slfn14	237890	schlafen 14	-6.776	8.3e-56
Itsn1	16443	intersectin 1 (SH3 domain protein 1A)	-3.504	3.1e-44
Fhdc1	229474	FH2 domain containing 1	-4.797	1.2e-42
Slc25a37	67712	solute carrier family 25, member 37	-3.644	4.8e-42
Epb42	13828	erythrocyte membrane protein band 4.2	-5.364	6.5e-39
Zbtb32	58206	zinc finger and BTB domain containing 32	1.581	7.5e-39
Ypel4	241525	yippee like 4	-6.107	2.4e-38
Hist1h4m	100041230	histone cluster 1, H4m	5.450	6.5e-35
Rsad2	58185	radical S-adenosyl methionine domain containing 2	-3.615	4.4e-33
Alas2	11656	aminolevulinic acid synthase 2, erythroid	-6.143	1.3e-32
Smox	228608	spermine oxidase	-2.929	1.4e-30
St3gal5	20454	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	-3.517	3.0e-29
Ube2o	217342	ubiquitin-conjugating enzyme E2O	-1.911	6.2e-29
Ube2l6	56791	ubiquitin-conjugating enzyme E2L 6	-3.184	8.5e-29
Tent5c	74645	terminal nucleotidyltransferase 5C	-1.988	2.1e-28
Cd36	12491	CD36 molecule	-5.804	2.7e-28
Ddx3y	26900	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	7.107	8.1e-28
Hba-a2	110257	hemoglobin alpha, adult chain 2	-6.425	1.0e-27
Fn3k	63828	fructosamine 3 kinase	-4.980	1.1e-27
F930017D23Rik	NA	RIKEN cDNA F930017D23 gene	-6.563	1.2e-27
Hbb-bs	NA	hemoglobin, beta adult s chain	-6.363	9.2e-27
Eif2s3y	26908	eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked	6.877	2.1e-26
Fbxo30	71865	F-box protein 30	-2.845	2.3e-26
Hbb-bt	101488143	hemoglobin, beta adult t chain	-6.264	2.3e-26
Tmod1	21916	tropomodulin 1	-4.398	5.5e-26
Xpo7	65246	exportin 7	-1.555	1.3e-25
Bpgm	12183	2,3-bisphosphoglycerate mutase	-2.076	6.7e-25
Snx22	382083	sorting nexin 22	-3.073	1.2e-24
Bsdc1	100383	BSD domain containing 1	-1.448	2.8e-24
Gm42427	NA	predicted gene 42427	-1.320	3.7e-24
Fech	14151	ferrochelatase	-2.922	3.7e-24
Fam214b	230088	family with sequence similarity 214, member B	-2.305	3.7e-24
Specc1	432572	sperm antigen with calponin homology and coiled-coil domains 1	-3.981	1.1e-23
Rps3a2	NA	ribosomal protein S3A2	3.189	2.2e-21
Apol10c-ps	NA	apolipoprotein L 10C, pseudogene	-7.111	4.8e-21
Hba-a1	15122	hemoglobin alpha, adult chain 1	-5.782	8.8e-21
Cdr2	12585	cerebellar degeneration-related 2	-2.261	1.1e-20
Rps3a3	NA	ribosomal protein S3A3	3.221	1.2e-20
Kdm5d	20592	lysine (K)-specific demethylase 5D	6.389	1.7e-20
Slc2a4	20528	solute carrier family 2 (facilitated glucose transporter), member 4	-5.495	3.5e-20
Epb41	269587	erythrocyte membrane protein band 4.1	-1.277	9.2e-20
Pdzk1ip1	67182	PDZK1 interacting protein 1	-3.744	1.2e-19
Gadd45a	13197	growth arrest and DNA-damage-inducible 45 alpha	-2.510	1.5e-19
Mkrn1	54484	makorin, ring finger protein, 1	-1.227	1.8e-19
Abcb10	56199	ATP-binding cassette, sub-family B (MDR/TAP), member 10	-3.126	2.1e-19
Apol10a	245282	apolipoprotein L 10A	-6.573	4.5e-19
Ranbp10	74334	RAN binding protein 10	-1.640	4.7e-19
Dhrs11	192970	dehydrogenase/reductase (SDR family) member 11	-2.364	6.5e-19
Slc4a1	20533	solute carrier family 4 (anion exchanger), member 1	-5.549	6.6e-19
Slc43a1	72401	solute carrier family 43, member 1	-3.230	5.1e-18
Apol11a	626615	apolipoprotein L 11a	-6.032	5.8e-18
Gm20161	NA	predicted gene, 20161	-4.618	8.4e-18
Cpeb4	67579	cytoplasmic polyadenylation element binding protein 4	-1.917	8.6e-18
Dnajb2	56812	DnaJ heat shock protein family (Hsp40) member B2	-1.952	1.7e-17
Dmtn	13829	dematin actin binding protein	-5.021	2.9e-17
Gm43864	NA	predicted gene, 43864	-6.038	3.7e-17
Ctse	13034	cathepsin E	-3.020	4.0e-17
1300017J02Rik	71775	RIKEN cDNA 1300017J02 gene	-4.503	7.7e-17
Tfdp2	211586	transcription factor Dp 2	-2.127	8.5e-17
Fam210b	67017	family with sequence similarity 210, member B	-1.886	8.9e-17
Snca	20617	synuclein, alpha	-5.612	1.6e-16
Trim10	19824	tripartite motif-containing 10	-5.034	2.8e-16
Mgst3	66447	microsomal glutathione S-transferase 3	-3.176	2.8e-16
Prokr1	58182	prokineticin receptor 1	-3.931	4.1e-16
Sowaha	237761	sosondowah ankyrin repeat domain family member A	-5.670	4.2e-16
Ackr1	13349	atypical chemokine receptor 1 (Duffy blood group)	-5.040	8.9e-16
Apol8	239552	apolipoprotein L 8	-3.481	1.7e-15
Gm37527	NA	predicted gene, 37527	-5.092	1.7e-15
Prxl2a	70564	peroxiredoxin like 2A	-2.481	1.9e-15
Hbq1b	544763	hemoglobin, theta 1B	-5.661	1.9e-15
Gypa	14934	glycophorin A	-5.287	3.1e-15
Samd11	231004	sterile alpha motif domain containing 11	-3.242	3.3e-15
Hmbs	15288	hydroxymethylbilane synthase	-2.275	3.3e-15
Dyrk3	226419	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	-3.098	3.8e-15
Map4k5	399510	mitogen-activated protein kinase kinase kinase kinase 5	-2.344	4.2e-15
Asb1	65247	ankyrin repeat and SOCS box-containing 1	-1.583	7.4e-15
Mafk	17135	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian)	-0.792	1.0e-14
Gm33707	NA	predicted gene, 33707	4.840	3.1e-14
Usp32	237898	ubiquitin specific peptidase 32	-1.312	3.1e-14
Cln8	26889	CLN8 transmembrane ER and ERGIC protein	-1.691	3.3e-14
Ccdc92b	432582	coiled-coil domain containing 92B	-5.562	3.8e-14
Slc16a10	72472	solute carrier family 16 (monocarboxylic acid transporters), member 10	-2.605	4.0e-14
Trak2	70827	trafficking protein, kinesin binding 2	-1.491	4.7e-14
Isca1	69046	iron-sulfur cluster assembly 1	-1.265	5.4e-14
Ache	11423	acetylcholinesterase	-3.723	5.7e-14
Uty	22290	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	5.703	5.9e-14
Vangl1	229658	VANGL planar cell polarity 1	-4.607	5.9e-14
Cacna1g	12291	calcium channel, voltage-dependent, T type, alpha 1G subunit	-4.889	5.9e-14
Pkd1l1	171395	polycystic kidney disease 1 like 1	-4.497	6.1e-14
Sptb	20741	spectrin beta, erythrocytic	-4.138	6.1e-14
Slc6a9	14664	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	-4.972	6.1e-14
Slc22a4	30805	solute carrier family 22 (organic cation transporter), member 4	-4.000	1.0e-13
Sox6	20679	SRY (sex determining region Y)-box 6	-4.949	1.1e-13
Marchf8	71779	membrane associated ring-CH-type finger 8	-3.927	1.7e-13
Grina	66168	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	-1.402	2.6e-13
Mgll	23945	monoglyceride lipase	-3.452	2.7e-13
Tom1l1	71943	target of myb1-like 1 (chicken)	-2.096	3.7e-13
Gm42031	NA	predicted gene, 42031	-1.680	4.2e-13
Ccdc24	381546	coiled-coil domain containing 24	-4.964	5.8e-13
Pnpo	103711	pyridoxine 5’-phosphate oxidase	-1.029	6.9e-13
Mxd1	17119	MAX dimerization protein 1	-1.304	7.4e-13
Fn3krp	238024	fructosamine 3 kinase related protein	-1.838	7.4e-13
Sh3yl1	24057	Sh3 domain YSC-like 1	-2.619	8.8e-13
Abcg2	26357	ATP binding cassette subfamily G member 2 (Junior blood group)	-2.631	9.5e-13
Foxo3	56484	forkhead box O3	-1.104	1.2e-12
Ppox	19044	protoporphyrinogen oxidase	-1.748	1.2e-12
Ppp2r5b	225849	protein phosphatase 2, regulatory subunit B’, beta	-1.308	1.2e-12
Arrb1	109689	arrestin, beta 1	-1.778	1.2e-12
Art4	109978	ADP-ribosyltransferase 4	-2.204	1.7e-12
Gm46620	NA	predicted gene, 46620	-0.925	2.2e-12
Rhou	69581	ras homolog family member U	-4.307	2.3e-12
Maats1	320214	MYCBP-associated, testis expressed 1	2.628	2.4e-12
Gm15446	NA	predicted gene 15446	2.506	5.0e-12
6430548M08Rik	234797	RIKEN cDNA 6430548M08 gene	-2.816	5.6e-12
Asprv1	67855	aspartic peptidase, retroviral-like 1	-3.825	9.7e-12
Eif2ak1	15467	eukaryotic translation initiation factor 2 alpha kinase 1	-0.988	1.0e-11
Pigq	14755	phosphatidylinositol glycan anchor biosynthesis, class Q	-1.458	1.3e-11
Narf	67608	nuclear prelamin A recognition factor	-1.292	1.4e-11
Otub2	68149	OTU domain, ubiquitin aldehyde binding 2	-1.513	1.7e-11
Marchf3	320253	membrane associated ring-CH-type finger 3	-1.889	3.0e-11
Samd4	74480	sterile alpha motif domain containing 4	-4.756	4.4e-11
Rffl	67338	ring finger and FYVE like domain containing protein	-0.968	4.7e-11
Stom	13830	stomatin	-2.793	5.2e-11
Plbd1	66857	phospholipase B domain containing 1	-3.050	5.4e-11
Mmp25	240047	matrix metallopeptidase 25	-2.812	6.7e-11
Hs6st1	50785	heparan sulfate 6-O-sulfotransferase 1	-1.110	7.3e-11
Anxa1	16952	annexin A1	-2.486	7.9e-11
Cpox	12892	coproporphyrinogen oxidase	-1.762	8.6e-11
Cadm3	94332	cell adhesion molecule 3	-3.723	9.3e-11
C1qa	12259	complement component 1, q subcomponent, alpha polypeptide	-4.575	1.2e-10
Syt14	329324	synaptotagmin XIV	-3.265	1.7e-10
Septin5	18951	septin 5	-2.571	2.1e-10
Dusp8	18218	dual specificity phosphatase 8	-3.760	2.5e-10
Dcaf6	74106	DDB1 and CUL4 associated factor 6	-0.989	2.9e-10
Spta1	20739	spectrin alpha, erythrocytic 1	-4.201	3.0e-10
Slc11a1	18173	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1	-3.232	3.0e-10
Ctsf	56464	cathepsin F	-3.031	3.1e-10
Stradb	227154	STE20-related kinase adaptor beta	-1.412	3.2e-10
Dclk1	13175	doublecortin-like kinase 1	2.404	3.3e-10
Ptafr	19204	platelet-activating factor receptor	-3.704	4.1e-10
Btn1a1	12231	butyrophilin, subfamily 1, member A1	-4.565	4.3e-10
Gm29438	NA	predicted gene 29438	-3.284	4.4e-10
Crat	12908	carnitine acetyltransferase	-1.829	5.4e-10
Mboat2	67216	membrane bound O-acyltransferase domain containing 2	-3.140	5.5e-10
Ank1	11733	ankyrin 1, erythroid	-3.681	5.7e-10
Tarm1	245126	T cell-interacting, activating receptor on myeloid cells 1	-4.243	6.9e-10
Havcr2	171285	hepatitis A virus cellular receptor 2	1.696	6.9e-10
Gm16793	NA	predicted gene, 16793	-2.998	7.0e-10
Slc6a20a	102680	solute carrier family 6 (neurotransmitter transporter), member 20A	-4.183	7.3e-10
Synj2	20975	synaptojanin 2	1.279	8.0e-10
Arhgef12	69632	Rho guanine nucleotide exchange factor (GEF) 12	-1.830	8.1e-10
Rab30	75985	RAB30, member RAS oncogene family	-3.785	8.3e-10
Hemgn	93966	hemogen	-3.509	9.0e-10
Gypc	71683	glycophorin C	-1.538	1.1e-09
Slc25a51	230125	solute carrier family 25, member 51	-0.856	1.1e-09
Btnl10	192194	butyrophilin-like 10	-4.182	1.2e-09
Marchf2	224703	membrane associated ring-CH-type finger 2	-1.050	1.6e-09
Slc66a2	66943	solute carrier family 66 member 2	-1.520	1.6e-09
Adcy6	11512	adenylate cyclase 6	-1.601	1.6e-09
Cdkl1	71091	cyclin-dependent kinase-like 1 (CDC2-related kinase)	-4.811	1.7e-09
Ankrd36	76389	ankyrin repeat domain 36	-4.384	2.1e-09
Tfrc	22042	transferrin receptor	-2.016	2.5e-09
Erdr1	NA	erythroid differentiation regulator 1	2.054	2.7e-09
Kel	23925	Kell blood group	-4.254	2.8e-09
Ulk1	22241	unc-51 like kinase 1	-0.883	3.1e-09
Lipg	16891	lipase, endothelial	-2.996	3.9e-09
Cd24a	12484	CD24a antigen	-3.462	4.1e-09
Ptdss2	27388	phosphatidylserine synthase 2	-1.740	4.5e-09
Sertad2	58172	SERTA domain containing 2	-0.890	4.6e-09
Tspan8	216350	tetraspanin 8	-3.747	5.3e-09
Hagh	14651	hydroxyacyl glutathione hydrolase	-1.609	5.4e-09
Nfe2	18022	nuclear factor, erythroid derived 2	-2.611	6.2e-09
Iba57	216792	IBA57 homolog, iron-sulfur cluster assembly	-0.830	6.2e-09
Plek2	27260	pleckstrin 2	-2.861	6.2e-09
Hcar2	80885	hydroxycarboxylic acid receptor 2	-4.866	6.6e-09
Denn2b	76954	DENN domain containing 2B	-2.050	7.2e-09
Yod1	226418	YOD1 deubiquitinase	-1.267	8.6e-09
Fnip2	329679	folliculin interacting protein 2	-2.115	9.0e-09
Ubac1	98766	ubiquitin associated domain containing 1	-1.353	9.8e-09
Mxi1	17859	MAX interactor 1, dimerization protein	-1.147	1.0e-08
Clec4a2	26888	C-type lectin domain family 4, member a2	-4.596	1.0e-08
Ncoa4	27057	nuclear receptor coactivator 4	-0.635	1.2e-08
Gm867	333670	predicted gene 867	-3.838	1.2e-08
Fcna	14133	ficolin A	-4.917	1.2e-08
Padi4	18602	peptidyl arginine deiminase, type IV	-2.802	1.4e-08
Btrc	12234	beta-transducin repeat containing protein	-1.156	1.5e-08
Tmem120b	330189	transmembrane protein 120B	-1.226	1.6e-08
Hectd4	269700	HECT domain E3 ubiquitin protein ligase 4	-1.284	1.7e-08
Pip5k1b	18719	phosphatidylinositol-4-phosphate 5-kinase, type 1 beta	-2.520	1.9e-08
2310022B05Rik	69551	RIKEN cDNA 2310022B05 gene	-1.277	2.1e-08
Gm47173	NA	predicted gene, 47173	-4.808	2.1e-08
Brpf3	268936	bromodomain and PHD finger containing, 3	-1.265	2.3e-08
Gm47252	NA	predicted gene, 47252	-4.484	2.3e-08
Il1b	16176	interleukin 1 beta	-4.555	2.8e-08
Gzmk	14945	granzyme K	1.855	2.9e-08
Nxpe2	78252	neurexophilin and PC-esterase domain family, member 2	-3.877	2.9e-08
Rab3il1	74760	RAB3A interacting protein (rabin3)-like 1	-4.051	2.9e-08
Cd59a	12509	CD59a antigen	-3.565	2.9e-08

Table: Results for ko.noTx_v_wt.noTx

638 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Hist1h4m	100041230	histone cluster 1, H4m	5.958	3.6e-40
Ddx3y	26900	DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked	7.855	9.1e-34
Gm33707	NA	predicted gene, 33707	7.379	1.1e-30
Eif2s3y	26908	eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked	7.180	3.2e-29
Xist	NA	inactive X specific transcripts	-6.352	1.4e-28
Rps3a2	NA	ribosomal protein S3A2	3.523	1.1e-25
Kdm5d	20592	lysine (K)-specific demethylase 5D	7.011	1.9e-24
Icosl	50723	icos ligand	0.917	9.2e-24
Ajuba	16475	ajuba LIM protein	2.785	1.9e-22
Rps3a3	NA	ribosomal protein S3A3	3.314	1.9e-22
Chrm4	12672	cholinergic receptor, muscarinic 4	2.225	4.8e-20
Gm42427	NA	predicted gene 42427	-1.223	5.2e-20
Slc7a8	50934	solute carrier family 7 (cationic amino acid transporter, y+ system), member 8	4.513	1.6e-19
Gm49980	NA	predicted gene, 49980	-2.046	9.1e-19
Ly6d	17068	lymphocyte antigen 6 complex, locus D	4.169	8.2e-18
Uty	22290	ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome	6.466	1.2e-17
Anxa4	11746	annexin A4	1.519	2.7e-17
Cdh24	239096	cadherin-like 24	2.133	3.6e-17
Synj2	20975	synaptojanin 2	1.563	1.6e-14
Trip10	106628	thyroid hormone receptor interactor 10	1.622	1.8e-14
Emp1	13730	epithelial membrane protein 1	1.836	9.0e-14
Pkd1l1	171395	polycystic kidney disease 1 like 1	-4.814	2.3e-13
Pak6	214230	p21 (RAC1) activated kinase 6	1.996	7.2e-13
Arhgef5	54324	Rho guanine nucleotide exchange factor (GEF) 5	1.474	1.2e-12
Aqp9	64008	aquaporin 9	1.825	1.3e-12
Zbtb32	58206	zinc finger and BTB domain containing 32	0.995	3.3e-12
Tnfsf14	50930	tumor necrosis factor (ligand) superfamily, member 14	1.153	3.3e-12
Gm15446	NA	predicted gene 15446	2.465	4.4e-12
Axl	26362	AXL receptor tyrosine kinase	1.520	1.0e-11
Styk1	243659	serine/threonine/tyrosine kinase 1	3.455	1.6e-11
Gm26992	NA	predicted gene, 26992	-4.829	3.8e-11
Plek	56193	pleckstrin	1.253	7.9e-11
Nrn1	68404	neuritin 1	1.618	1.6e-10
Cd22	12483	CD22 antigen	1.398	2.1e-10
Cdkn1a	12575	cyclin-dependent kinase inhibitor 1A (P21)	2.161	3.8e-10
Rnf43	207742	ring finger protein 43	1.080	4.7e-10
Misp3	70134	MISP family member 3	3.222	5.8e-10
Sytl3	83672	synaptotagmin-like 3	0.956	8.1e-10
Gm46620	NA	predicted gene, 46620	-0.830	2.4e-09
Plxnd1	67784	plexin D1	1.424	3.5e-09
Ccr5	12774	chemokine (C-C motif) receptor 5	1.145	4.7e-09
St14	19143	suppression of tumorigenicity 14 (colon carcinoma)	1.140	5.0e-09
Lrrc3b	218763	leucine rich repeat containing 3B	3.148	7.5e-09
Myo1f	17916	myosin IF	0.628	2.0e-08
Zdhhc2	70546	zinc finger, DHHC domain containing 2	1.090	2.4e-08
Entpd4	67464	ectonucleoside triphosphate diphosphohydrolase 4	0.805	2.4e-08
Bspry	192120	B-box and SPRY domain containing	1.414	3.6e-08
Naip2	17948	NLR family, apoptosis inhibitory protein 2	1.181	3.8e-08
Penk	18619	preproenkephalin	2.250	4.2e-08
Tmem254b	100039257	transmembrane protein 254b	1.661	4.5e-08
Pcgf2	22658	polycomb group ring finger 2	1.386	4.5e-08
Erdr1	NA	erythroid differentiation regulator 1	1.969	5.2e-08
Stk32c	57740	serine/threonine kinase 32C	2.304	8.0e-08
Ms4a6d	68774	membrane-spanning 4-domains, subfamily A, member 6D	1.523	9.7e-08
Serpina3g	20715	serine (or cysteine) peptidase inhibitor, clade A, member 3G	1.537	1.1e-07
Samd3	268288	sterile alpha motif domain containing 3	1.005	1.2e-07
Cxcr3	12766	chemokine (C-X-C motif) receptor 3	1.057	1.2e-07
Gm38326	NA	predicted gene, 38326	4.340	1.4e-07
Serpina3f	238393	serine (or cysteine) peptidase inhibitor, clade A, member 3F	1.949	2.4e-07
Myo6	17920	myosin VI	1.212	2.4e-07
Dclk2	70762	doublecortin-like kinase 2	1.301	2.4e-07
Col16a1	107581	collagen, type XVI, alpha 1	3.789	3.2e-07
Osbpl3	71720	oxysterol binding protein-like 3	0.941	4.0e-07
Lynx1	23936	Ly6/neurotoxin 1	1.507	4.2e-07
Entpd4b	100862375	ectonucleoside triphosphate diphosphohydrolase 4B	0.810	4.6e-07
Pik3ap1	83490	phosphoinositide-3-kinase adaptor protein 1	1.412	5.5e-07
Slc35g1	240660	solute carrier family 35, member G1	-0.600	5.7e-07
Edaradd	171211	EDAR (ectodysplasin-A receptor)-associated death domain	1.194	6.4e-07
Ccn4	22402	cellular communication network factor 4	2.247	7.1e-07
Cd1d2	12480	CD1d2 antigen	2.699	1.0e-06
Enc1	13803	ectodermal-neural cortex 1	-0.863	1.1e-06
Bhlhe40	20893	basic helix-loop-helix family, member e40	1.793	1.1e-06
Il18r1	16182	interleukin 18 receptor 1	1.014	1.2e-06
Kcnk5	16529	potassium channel, subfamily K, member 5	0.934	1.2e-06
Arrdc4	66412	arrestin domain containing 4	1.096	1.2e-06
Gm42031	NA	predicted gene, 42031	-1.259	1.2e-06
Itga6	16403	integrin alpha 6	-0.590	1.2e-06
Gdf11	14561	growth differentiation factor 11	0.682	1.3e-06
Gpc1	14733	glypican 1	0.968	1.7e-06
Raph1	77300	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1.152	1.7e-06
Slc6a8	102857	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	1.393	1.7e-06
BC106179	NA	cDNA sequence BC106179	-0.850	1.7e-06
Gm7600	NA	predicted gene 7600	1.604	1.9e-06
Drc1	381738	dynein regulatory complex subunit 1	1.324	2.0e-06
5830416I19Rik	NA	RIKEN cDNA 5830416I19 gene	3.390	2.0e-06
Tmem159	233806	transmembrane protein 159	1.563	2.1e-06
Dlg5	71228	discs large MAGUK scaffold protein 5	2.150	2.6e-06
Zfp683	NA	zinc finger protein 683	0.823	2.6e-06
Gzmm	16904	granzyme M (lymphocyte met-ase 1)	1.335	2.7e-06
Cd44	12505	CD44 antigen	0.702	2.8e-06
Ephb6	13848	Eph receptor B6	0.735	3.0e-06
Cd38	12494	CD38 antigen	0.958	3.0e-06
Cep97	74201	centrosomal protein 97	-0.588	3.4e-06
2410018L13Rik	NA	RIKEN cDNA 2410018L13 gene	2.302	3.5e-06
Gm6637	NA	predicted gene 6637	1.493	3.5e-06
Irf4	16364	interferon regulatory factor 4	0.765	3.8e-06
S100a6	20200	S100 calcium binding protein A6 (calcyclin)	1.494	4.0e-06
Tjp3	27375	tight junction protein 3	0.840	4.7e-06
Il18rap	16174	interleukin 18 receptor accessory protein	0.883	5.0e-06
Dtl	76843	denticleless E3 ubiquitin protein ligase	0.746	5.0e-06
5430427O19Rik	71398	RIKEN cDNA 5430427O19 gene	1.163	5.1e-06
Slc15a3	65221	solute carrier family 15, member 3	1.781	5.1e-06
Nccrp1	233038	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	2.199	6.4e-06
Tbx21	57765	T-box 21	0.986	6.4e-06
Gm47577	NA	predicted gene, 47577	-3.527	6.6e-06
Itpripl2	319622	inositol 1,4,5-triphosphate receptor interacting protein-like 2	1.341	6.6e-06
Gm5541	NA	predicted gene 5541	2.283	6.8e-06
Plekhg3	263406	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	0.797	7.4e-06
Itgax	16411	integrin alpha X	1.583	7.4e-06
Slamf7	75345	SLAM family member 7	0.644	8.6e-06
Anxa2	12306	annexin A2	0.929	1.1e-05
Lsr	54135	lipolysis stimulated lipoprotein receptor	0.916	1.1e-05
Scn1b	20266	sodium channel, voltage-gated, type I, beta	2.351	1.1e-05
Gm49339	NA	predicted gene, 49339	2.012	1.1e-05
Gm5575	NA	predicted gene 5575	-3.380	1.2e-05
Dapk2	13143	death-associated protein kinase 2	1.468	1.3e-05
Dkkl1	50722	dickkopf-like 1	1.372	1.5e-05
Perp	64058	PERP, TP53 apoptosis effector	2.069	1.5e-05
Camk2b	12323	calcium/calmodulin-dependent protein kinase II, beta	-1.049	1.5e-05
Ccdc136	232664	coiled-coil domain containing 136	2.722	1.7e-05
Dscam	13508	DS cell adhesion molecule	2.092	1.8e-05
F2r	14062	coagulation factor II (thrombin) receptor	0.739	2.0e-05
Plcb1	18795	phospholipase C, beta 1	3.959	2.0e-05
Rab4a	19341	RAB4A, member RAS oncogene family	-1.327	2.0e-05
Casp1	12362	caspase 1	1.229	2.2e-05
Nid2	18074	nidogen 2	1.462	2.3e-05
Klrg1	50928	killer cell lectin-like receptor subfamily G, member 1	1.383	2.3e-05
Prr13	66151	proline rich 13	0.695	2.4e-05
Gng2	14702	guanine nucleotide binding protein (G protein), gamma 2	0.658	2.6e-05
Kcnk6	52150	potassium inwardly-rectifying channel, subfamily K, member 6	1.135	2.6e-05
Trim46	360213	tripartite motif-containing 46	1.240	2.8e-05
Fam129a	63913	family with sequence similarity 129, member A	0.708	3.1e-05
Mid1-ps1	NA	midline 1, pseudogene 1	-3.592	3.1e-05
Fam131b	76156	family with sequence similarity 131, member B	1.943	3.1e-05
Adap1	231821	ArfGAP with dual PH domains 1	0.896	3.4e-05
Ebi3	50498	Epstein-Barr virus induced gene 3	1.576	3.5e-05
Csf1	12977	colony stimulating factor 1 (macrophage)	1.537	3.5e-05
Slco4a1	108115	solute carrier organic anion transporter family, member 4a1	1.268	3.6e-05
Capn11	268958	calpain 11	3.917	3.6e-05
Phlda3	27280	pleckstrin homology like domain, family A, member 3	1.345	3.7e-05
Tigit	100043314	T cell immunoreceptor with Ig and ITIM domains	1.522	3.7e-05
Setbp1	240427	SET binding protein 1	1.371	3.7e-05
Pmaip1	58801	phorbol-12-myristate-13-acetate-induced protein 1	1.057	3.7e-05
Cdh1	12550	cadherin 1	1.876	3.7e-05
Nbea	26422	neurobeachin	-2.600	3.8e-05
Chst11	58250	carbohydrate sulfotransferase 11	1.087	4.1e-05
Rnf157	217340	ring finger protein 157	1.052	4.1e-05
Gas7	14457	growth arrest specific 7	1.348	4.3e-05
Aplp1	11803	amyloid beta (A4) precursor-like protein 1	0.909	4.4e-05
Gna15	14676	guanine nucleotide binding protein, alpha 15	0.792	5.3e-05
Ccl1	20290	chemokine (C-C motif) ligand 1	1.992	5.3e-05
Hip1	215114	huntingtin interacting protein 1	1.117	6.5e-05
Marcksl1	17357	MARCKS-like 1	1.118	6.7e-05
Cysltr2	70086	cysteinyl leukotriene receptor 2	1.098	7.4e-05
Cdc42ep1	104445	CDC42 effector protein (Rho GTPase binding) 1	2.338	7.4e-05
Lrrk1	233328	leucine-rich repeat kinase 1	1.328	7.5e-05
Acot7	70025	acyl-CoA thioesterase 7	1.087	7.6e-05
Tnfrsf8	21941	tumor necrosis factor receptor superfamily, member 8	1.446	8.8e-05
Bcl2a1d	12047	B cell leukemia/lymphoma 2 related protein A1d	1.206	9.0e-05
Pdzk1ip1	67182	PDZK1 interacting protein 1	1.963	9.1e-05
Rell1	100532	RELT-like 1	1.321	1.1e-04
Lgals1	16852	lectin, galactose binding, soluble 1	1.165	1.2e-04
Dclk1	13175	doublecortin-like kinase 1	2.267	1.2e-04
Asb2	65256	ankyrin repeat and SOCS box-containing 2	1.459	1.3e-04
Podnl1	244550	podocan-like 1	0.643	1.3e-04
Gm35279	NA	predicted gene, 35279	-3.609	1.3e-04
Gm28875	NA	predicted gene 28875	0.859	1.4e-04
Tmem254c	100039192	transmembrane protein 254c	1.537	1.4e-04
Plp2	18824	proteolipid protein 2	0.682	1.4e-04
Fgl2	14190	fibrinogen-like protein 2	1.274	1.5e-04
Gpr162	14788	G protein-coupled receptor 162	1.461	1.5e-04
Sp6	83395	trans-acting transcription factor 6	1.121	1.5e-04
Nlrp1b	637515	NLR family, pyrin domain containing 1B	1.101	1.6e-04
Uhrf1	18140	ubiquitin-like, containing PHD and RING finger domains, 1	0.798	1.7e-04
Egln3	112407	egl-9 family hypoxia-inducible factor 3	1.203	1.7e-04
Lgalsl	216551	lectin, galactoside binding-like	0.914	1.8e-04
Il1r2	16178	interleukin 1 receptor, type II	1.942	1.8e-04
Mdfic	16543	MyoD family inhibitor domain containing	0.869	2.0e-04
Cebpb	12608	CCAAT/enhancer binding protein (C/EBP), beta	1.034	2.0e-04
9930014A18Rik	NA	RIKEN cDNA 9930014A18 gene	0.674	2.2e-04
Mmp15	17388	matrix metallopeptidase 15	-1.055	2.2e-04
Ptpn13	19249	protein tyrosine phosphatase, non-receptor type 13	1.190	2.2e-04
Ly6a	110454	lymphocyte antigen 6 complex, locus A	1.127	2.5e-04
E2f1	13555	E2F transcription factor 1	0.752	2.5e-04
Pvrig	102640920	poliovirus receptor related immunoglobulin domain containing	1.363	2.5e-04
Il2rb	16185	interleukin 2 receptor, beta chain	0.643	2.8e-04
Atp2b2	11941	ATPase, Ca++ transporting, plasma membrane 2	2.478	2.8e-04
Ryk	20187	receptor-like tyrosine kinase	1.404	2.8e-04
Txlnb	378431	taxilin beta	1.028	2.9e-04
Pls3	102866	plastin 3 (T-isoform)	2.015	3.0e-04
Fat4	329628	FAT atypical cadherin 4	3.228	3.4e-04
Socs2	216233	suppressor of cytokine signaling 2	1.041	3.4e-04
Cdkl5	382253	cyclin-dependent kinase-like 5	-0.945	3.4e-04
Hist1h4n	319161	histone cluster 1, H4n	-1.221	3.4e-04
Tspan31	67125	tetraspanin 31	0.885	3.5e-04
Rps4l	NA	ribosomal protein S4-like	1.505	3.7e-04
Gnb4	14696	guanine nucleotide binding protein (G protein), beta 4	-0.769	3.9e-04
Abcb1a	18671	ATP-binding cassette, sub-family B (MDR/TAP), member 1A	0.797	4.1e-04
Psrc1	56742	proline/serine-rich coiled-coil 1	1.064	4.1e-04
Utf1	22286	undifferentiated embryonic cell transcription factor 1	1.070	4.1e-04

Table: Results for ko.TxA_v_ko.TxB

4640 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Sh3pxd2a	14218	SH3 and PX domains 2A	-4.975	0.0e+00
Cnr2	12802	cannabinoid receptor 2 (macrophage)	-2.985	4.1e-137
Nedd4l	83814	neural precursor cell expressed, developmentally down-regulated gene 4-like	-3.204	1.5e-120
Nrp2	18187	neuropilin 2	-4.241	1.9e-114
Epas1	13819	endothelial PAS domain protein 1	4.045	9.4e-113
Ubash3b	72828	ubiquitin associated and SH3 domain containing, B	1.721	2.7e-106
Sell	20343	selectin, lymphocyte	-3.361	7.6e-106
Ccr7	12775	chemokine (C-C motif) receptor 7	-4.307	6.9e-100
Il6ra	16194	interleukin 6 receptor, alpha	-3.372	6.8e-94
Samd3	268288	sterile alpha motif domain containing 3	-3.428	3.2e-92
Slc16a5	217316	solute carrier family 16 (monocarboxylic acid transporters), member 5	-5.498	2.7e-91
Ncald	52589	neurocalcin delta	2.891	2.3e-89
1700025G04Rik	69399	RIKEN cDNA 1700025G04 gene	-2.666	3.8e-88
Hip1r	29816	huntingtin interacting protein 1 related	1.918	3.2e-86
L1cam	16728	L1 cell adhesion molecule	2.625	2.2e-84
Gldc	104174	glycine decarboxylase	6.315	5.4e-84
Sema4b	20352	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	-1.703	6.7e-84
Chst15	77590	carbohydrate sulfotransferase 15	-2.849	1.1e-82
Id2	15902	inhibitor of DNA binding 2	2.078	8.0e-82
Ildr1	106347	immunoglobulin-like domain containing receptor 1	2.589	1.6e-80
Dsp	109620	desmoplakin	4.196	2.5e-80
Klrb1b	80782	killer cell lectin-like receptor subfamily B member 1B	8.198	1.3e-79
Ptms	69202	parathymosin	2.313	6.0e-79
Tbc1d16	207592	TBC1 domain family, member 16	-3.151	1.7e-78
Adamts14	237360	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 14	4.359	1.5e-77
Vipr1	22354	vasoactive intestinal peptide receptor 1	-3.822	3.8e-74
Dlg4	13385	discs large MAGUK scaffold protein 4	-2.311	3.7e-72
Plekha1	101476	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	-2.086	1.3e-71
Serpinb6b	20708	serine (or cysteine) peptidase inhibitor, clade B, member 6b	3.446	1.8e-70
Tdrp	72148	testis development related protein	-3.958	4.1e-70
Irak3	73914	interleukin-1 receptor-associated kinase 3	4.074	1.4e-69
Rapgef4	56508	Rap guanine nucleotide exchange factor (GEF) 4	-3.843	1.9e-69
Zbtb32	58206	zinc finger and BTB domain containing 32	1.932	5.9e-68
Icos	54167	inducible T cell co-stimulator	1.998	4.2e-66
Sipa1l2	244668	signal-induced proliferation-associated 1 like 2	-2.521	1.1e-65
Slc2a3	20527	solute carrier family 2 (facilitated glucose transporter), member 3	1.403	1.5e-65
Drc1	381738	dynein regulatory complex subunit 1	-3.984	4.8e-65
Ttc28	209683	tetratricopeptide repeat domain 28	-3.113	6.0e-65
St14	19143	suppression of tumorigenicity 14 (colon carcinoma)	2.720	6.1e-65
Trim30c	434219	tripartite motif-containing 30C	-4.659	1.6e-64
Atp1b1	11931	ATPase, Na+/K+ transporting, beta 1 polypeptide	-3.898	1.3e-63
Marveld2	218518	MARVEL (membrane-associating) domain containing 2	2.529	3.5e-63
Crmp1	12933	collapsin response mediator protein 1	2.241	3.5e-63
Nsg2	18197	neuron specific gene family member 2	-3.435	4.7e-63
Pakap	677884	paralemmin A kinase anchor protein	-3.704	5.5e-63
Galnt3	14425	polypeptide N-acetylgalactosaminyltransferase 3	2.821	1.1e-62
Kcna2	16490	potassium voltage-gated channel, shaker-related subfamily, member 2	-4.229	3.5e-62
Slc6a19	74338	solute carrier family 6 (neurotransmitter transporter), member 19	-5.169	8.2e-62
Tmem108	81907	transmembrane protein 108	-4.802	5.1e-60
AA467197	433470	expressed sequence AA467197	4.127	6.8e-60
Lgals3	16854	lectin, galactose binding, soluble 3	3.958	7.7e-60
Gna15	14676	guanine nucleotide binding protein, alpha 15	2.539	1.5e-59
Adam8	11501	a disintegrin and metallopeptidase domain 8	3.776	1.7e-59
Adgrg5	382045	adhesion G protein-coupled receptor G5	-3.133	4.0e-59
Itga3	16400	integrin alpha 3	3.276	4.7e-59
Syde1	71709	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	-3.471	6.9e-59
Parp8	52552	poly (ADP-ribose) polymerase family, member 8	-2.070	2.5e-57
Zbtb18	30928	zinc finger and BTB domain containing 18	-1.929	1.3e-56
Tet1	52463	tet methylcytosine dioxygenase 1	-3.474	1.7e-56
Dntt	21673	deoxynucleotidyltransferase, terminal	-5.864	2.0e-54
Dapl1	76747	death associated protein-like 1	-4.409	3.0e-54
Fgf13	14168	fibroblast growth factor 13	-2.212	2.3e-53
Slc28a2b	381417	solute carrier family 28 member 2b	-3.402	3.2e-53
Sorcs2	81840	sortilin-related VPS10 domain containing receptor 2	-4.244	5.6e-53
Itih5	209378	inter-alpha (globulin) inhibitor H5	2.297	1.4e-52
Ifnar2	15976	interferon (alpha and beta) receptor 2	-1.372	3.0e-52
Mgst2	211666	microsomal glutathione S-transferase 2	-2.023	3.8e-52
Treml2	328833	triggering receptor expressed on myeloid cells-like 2	-2.417	9.8e-52
Cd2ap	12488	CD2-associated protein	-1.407	1.1e-51
Acvr1b	11479	activin A receptor, type 1B	-1.704	3.4e-51
Gpr55	227326	G protein-coupled receptor 55	2.507	4.8e-50
Igfbp4	16010	insulin-like growth factor binding protein 4	-4.632	5.2e-49
Cacna2d4	319734	calcium channel, voltage-dependent, alpha 2/delta subunit 4	-2.952	1.2e-48
Scmh1	29871	sex comb on midleg homolog 1	-2.212	3.4e-48
Serpinb9	20723	serine (or cysteine) peptidase inhibitor, clade B, member 9	2.853	9.7e-48
Tanc1	66860	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	-1.911	1.6e-47
Csf1	12977	colony stimulating factor 1 (macrophage)	4.389	1.6e-46
Ms4a4c	64380	membrane-spanning 4-domains, subfamily A, member 4C	-2.926	1.3e-45
Plekhb2	226971	pleckstrin homology domain containing, family B (evectins) member 2	1.382	1.9e-45
Ajuba	16475	ajuba LIM protein	3.576	4.3e-45
5830411N06Rik	244234	RIKEN cDNA 5830411N06 gene	-4.267	7.9e-45
Pdk1	228026	pyruvate dehydrogenase kinase, isoenzyme 1	-2.409	8.3e-45
Prf1	18646	perforin 1 (pore forming protein)	2.535	1.9e-44
Dgkh	380921	diacylglycerol kinase, eta	2.431	2.3e-44
Xdh	22436	xanthine dehydrogenase	1.562	2.5e-44
Plekha6	240753	pleckstrin homology domain containing, family A member 6	-3.849	2.6e-44
Whrn	73750	whirlin	-2.272	5.0e-44
Spock2	94214	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	3.934	5.0e-44
Cul9	78309	cullin 9	-2.781	7.0e-44
Hhat	226861	hedgehog acyltransferase	1.874	8.4e-44
Furin	18550	furin (paired basic amino acid cleaving enzyme)	1.772	2.5e-42
Havcr2	171285	hepatitis A virus cellular receptor 2	3.351	5.0e-42
Tlr7	170743	toll-like receptor 7	-2.625	1.8e-41
P2ry12	70839	purinergic receptor P2Y, G-protein coupled 12	4.646	2.4e-41
Pmepa1	65112	prostate transmembrane protein, androgen induced 1	-3.041	3.2e-41
Ifitm1	68713	interferon induced transmembrane protein 1	4.090	9.8e-41
Trio	223435	triple functional domain (PTPRF interacting)	-1.792	3.8e-40
Serpinb9b	20706	serine (or cysteine) peptidase inhibitor, clade B, member 9b	5.294	7.7e-40
Nrgn	64011	neurogranin	3.297	8.5e-40
Muc20	224116	mucin 20	4.120	8.8e-40
Itgax	16411	integrin alpha X	3.816	9.7e-40
Gm1043	381634	predicted gene 1043	-3.283	1.3e-39
Gpr68	238377	G protein-coupled receptor 68	1.617	1.6e-39
Aqp9	64008	aquaporin 9	-3.105	2.7e-39
Lrig1	16206	leucine-rich repeats and immunoglobulin-like domains 1	-2.799	2.9e-39
Pqlc3	217430	PQ loop repeat containing	1.330	3.2e-39
Serpinb1b	282663	serine (or cysteine) peptidase inhibitor, clade B, member 1b	5.397	4.2e-39
Dubr	NA	Dppa2 upstream binding RNA	1.393	4.6e-39
Osbpl3	71720	oxysterol binding protein-like 3	2.030	5.2e-39
Il1rl1	17082	interleukin 1 receptor-like 1	3.686	6.4e-39
Zbtb38	245007	zinc finger and BTB domain containing 38	1.284	7.7e-39
Farp1	223254	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	2.175	1.9e-38
Rhoc	11853	ras homolog family member C	3.050	2.1e-38
Erc2	238988	ELKS/RAB6-interacting/CAST family member 2	6.400	2.1e-38
Efhd2	27984	EF hand domain containing 2	1.397	2.5e-38
AC161757.1	NA	toll-like receptor 1 (Tlr1) pseudogene	-2.096	3.0e-38
Lsr	54135	lipolysis stimulated lipoprotein receptor	2.064	4.1e-38
Cdr2l	237988	cerebellar degeneration-related protein 2-like	-4.241	5.0e-38
Sytl2	83671	synaptotagmin-like 2	1.300	5.6e-38
Cxxc5	67393	CXXC finger 5	-2.650	5.7e-38
Zfp395	380912	zinc finger protein 395	-1.646	8.0e-38
Bach2	12014	BTB and CNC homology, basic leucine zipper transcription factor 2	-2.936	1.7e-37
A630014C17Rik	NA	RIKEN cDNA A630014C17 gene	-2.665	1.9e-37
Ccnd2	12444	cyclin D2	-1.596	3.6e-37
Ssbp2	66970	single-stranded DNA binding protein 2	-2.473	1.4e-36
Cd80	12519	CD80 antigen	2.759	1.8e-36
Prex1	277360	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1.399	2.3e-36
Irak2	108960	interleukin-1 receptor-associated kinase 2	1.515	4.3e-36
Lpcat4	99010	lysophosphatidylcholine acyltransferase 4	1.567	5.0e-36
Nacc2	67991	nucleus accumbens associated 2, BEN and BTB (POZ) domain containing	-3.236	5.9e-36
Il6st	16195	interleukin 6 signal transducer	-1.804	6.0e-36
Rab27a	11891	RAB27A, member RAS oncogene family	1.645	7.7e-36
Slc14a1	108052	solute carrier family 14 (urea transporter), member 1	-2.214	8.3e-36
Stx2	13852	syntaxin 2	-1.851	1.0e-35
Chit1	71884	chitinase 1 (chitotriosidase)	4.717	1.2e-35
Lta	16992	lymphotoxin A	-2.338	1.3e-35
Dzip1	66573	DAZ interacting protein 1	-2.009	1.6e-35
4921525O09Rik	NA	RIKEN cDNA 4921525O09 gene	-4.040	1.8e-35
Rbl2	19651	RB transcriptional corepressor like 2	1.100	2.0e-35
Spn	20737	sialophorin	1.226	2.1e-35
Il12rb2	16162	interleukin 12 receptor, beta 2	2.841	2.9e-35
H2-Ob	15002	histocompatibility 2, O region beta locus	-2.756	3.9e-35
Plekhg5	269608	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	2.012	4.7e-35
Popdc2	64082	popeye domain containing 2	3.039	4.8e-35
Ttpal	76080	tocopherol (alpha) transfer protein-like	0.907	4.8e-35
Igf2bp3	140488	insulin-like growth factor 2 mRNA binding protein 3	1.907	5.9e-35
Nsmf	56876	NMDA receptor synaptonuclear signaling and neuronal migration factor	1.044	6.1e-35
Ddc	13195	dopa decarboxylase	-4.947	7.1e-35
Smad1	17125	SMAD family member 1	-1.912	9.1e-35
Rps6ka2	20112	ribosomal protein S6 kinase, polypeptide 2	-2.419	1.9e-34
Lypd6b	71897	LY6/PLAUR domain containing 6B	-4.870	2.2e-34
Gm20696	NA	predicted gene 20696	-3.732	2.6e-34
Cxcr6	80901	chemokine (C-X-C motif) receptor 6	2.942	2.8e-34
Lrp12	239393	low density lipoprotein-related protein 12	-2.195	2.8e-34
Gzma	14938	granzyme A	5.342	2.8e-34
Il4ra	16190	interleukin 4 receptor, alpha	-1.515	3.1e-34
Gpld1	14756	glycosylphosphatidylinositol specific phospholipase D1	3.819	3.1e-34
Pdcd1	18566	programmed cell death 1	3.403	4.0e-34
Zscan12	22758	zinc finger and SCAN domain containing 12	-1.574	4.9e-34
Tmem163	72160	transmembrane protein 163	1.601	5.4e-34
Filip1	70598	filamin A interacting protein 1	4.485	5.5e-34
Actg2	11468	actin, gamma 2, smooth muscle, enteric	-4.212	5.7e-34
Arap2	212285	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1.136	6.0e-34
Macrod1	107227	mono-ADP ribosylhydrolase 1	-2.983	7.4e-34
Klhl3	100503085	kelch-like 3	-2.113	1.2e-33
Rnf122	68867	ring finger protein 122	-2.586	1.7e-33
Ifngr2	15980	interferon gamma receptor 2	-2.432	2.2e-33
Slc25a24	229731	solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24	1.873	3.0e-33
Cx3cr1	13051	chemokine (C-X3-C motif) receptor 1	4.256	3.6e-33
Dnajc27	217378	DnaJ heat shock protein family (Hsp40) member C27	-1.253	4.8e-33
Cnksr3	215748	Cnksr family member 3	-2.570	6.5e-33
Rgmb	68799	repulsive guidance molecule family member B	-2.815	7.4e-33
Rasgrf2	19418	RAS protein-specific guanine nucleotide-releasing factor 2	-2.562	8.1e-33
Ak3	56248	adenylate kinase 3	1.005	1.2e-32
Apbb1	11785	amyloid beta (A4) precursor protein-binding, family B, member 1	2.435	1.5e-32
Patj	12695	PATJ, crumbs cell polarity complex component	-1.649	2.1e-32
1810006J02Rik	NA	RIKEN cDNA 1810006J02 gene	-4.117	2.8e-32
Abi3	66610	ABI gene family, member 3	-1.522	2.9e-32
Ptpn11	19247	protein tyrosine phosphatase, non-receptor type 11	1.273	4.0e-32
St8sia1	20449	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	-1.988	4.5e-32
Pam	18484	peptidylglycine alpha-amidating monooxygenase	-2.467	7.5e-32
Tmem154	320782	transmembrane protein 154	1.346	1.8e-31
Slc52a3	69698	solute carrier protein family 52, member 3	1.971	3.0e-31
Rflnb	76566	refilin B	-1.813	3.2e-31
Lrmp	16970	lymphoid-restricted membrane protein	0.962	4.6e-31
Gm42809	NA	predicted gene 42809	-3.753	5.9e-31
Eml2	72205	echinoderm microtubule associated protein like 2	1.285	1.3e-30
Rnf144a	108089	ring finger protein 144A	-1.777	1.7e-30
Slc2a8	56017	solute carrier family 2, (facilitated glucose transporter), member 8	2.057	1.9e-30
Tns2	209039	tensin 2	2.773	2.0e-30
Icosl	50723	icos ligand	0.951	2.6e-30
Cd68	12514	CD68 antigen	2.219	2.7e-30
Pik3cg	30955	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	1.105	3.3e-30
Pglyrp1	21946	peptidoglycan recognition protein 1	2.414	4.0e-30
She	214547	src homology 2 domain-containing transforming protein E	-4.702	4.3e-30
Lrrc75b	192734	leucine rich repeat containing 75B	-2.485	4.6e-30
Chsy1	269941	chondroitin sulfate synthase 1	1.170	4.6e-30
Btbd11	74007	BTB (POZ) domain containing 11	-1.670	4.6e-30
Cuedc1	103841	CUE domain containing 1	-1.525	5.3e-30
Ermn	77767	ermin, ERM-like protein	4.135	7.4e-30

Table: Results for ko.TxA_v_ko.noTx

8179 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Sh3pxd2a	14218	SH3 and PX domains 2A	-5.297	0.0e+00
Ncald	52589	neurocalcin delta	4.812	4.9e-217
Zbtb32	58206	zinc finger and BTB domain containing 32	3.521	2.1e-205
Havcr2	171285	hepatitis A virus cellular receptor 2	7.515	1.3e-169
Lgals3	16854	lectin, galactose binding, soluble 3	6.740	1.7e-168
Cnr2	12802	cannabinoid receptor 2 (macrophage)	-3.230	3.4e-162
Ccr7	12775	chemokine (C-C motif) receptor 7	-5.429	1.1e-159
Ifitm1	68713	interferon induced transmembrane protein 1	8.926	1.6e-151
Nedd4l	83814	neural precursor cell expressed, developmentally down-regulated gene 4-like	-3.541	4.2e-149
Tmem163	72160	transmembrane protein 163	3.719	8.0e-146
Sema4b	20352	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	-2.229	8.5e-146
Galnt3	14425	polypeptide N-acetylgalactosaminyltransferase 3	6.133	3.5e-144
Il6ra	16194	interleukin 6 receptor, alpha	-4.141	1.0e-142
Chsy1	269941	chondroitin sulfate synthase 1	2.514	3.3e-137
Tdrp	72148	testis development related protein	-5.488	4.9e-136
Ttc28	209683	tetratricopeptide repeat domain 28	-4.427	1.0e-132
Vipr1	22354	vasoactive intestinal peptide receptor 1	-5.038	7.5e-130
Acvr1b	11479	activin A receptor, type 1B	-2.671	5.2e-129
Top2a	21973	topoisomerase (DNA) II alpha	4.172	4.1e-128
Serpinb6b	20708	serine (or cysteine) peptidase inhibitor, clade B, member 6b	4.630	9.4e-127
Gzmb	14939	granzyme B	7.557	2.7e-126
Chst15	77590	carbohydrate sulfotransferase 15	-3.450	2.5e-123
Kif11	16551	kinesin family member 11	4.440	4.1e-123
Spag5	54141	sperm associated antigen 5	4.586	2.4e-122
Patj	12695	PATJ, crumbs cell polarity complex component	-3.147	3.3e-120
Ehd4	98878	EH-domain containing 4	2.505	4.3e-120
2610318N02Rik	70458	RIKEN cDNA 2610318N02 gene	3.942	5.8e-119
Bub1b	12236	BUB1B, mitotic checkpoint serine/threonine kinase	4.180	1.5e-118
Ncaph	215387	non-SMC condensin I complex, subunit H	4.092	1.5e-117
Rflnb	76566	refilin B	-3.489	1.5e-116
Kcna2	16490	potassium voltage-gated channel, shaker-related subfamily, member 2	-5.705	3.5e-115
Hells	15201	helicase, lymphoid specific	2.780	2.5e-114
Sell	20343	selectin, lymphocyte	-3.474	7.4e-114
Osbpl3	71720	oxysterol binding protein-like 3	3.484	1.7e-113
Plekha1	101476	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	-2.596	2.9e-113
Tpx2	72119	TPX2, microtubule-associated	4.517	2.4e-111
Prr11	270906	proline rich 11	4.945	3.0e-110
Cdca2	108912	cell division cycle associated 2	4.158	5.5e-110
Lrig1	16206	leucine-rich repeats and immunoglobulin-like domains 1	-4.640	1.4e-109
Ccna2	12428	cyclin A2	4.763	3.7e-109
Prc1	233406	protein regulator of cytokinesis 1	4.248	3.8e-109
Plek	56193	pleckstrin	3.749	4.3e-109
Birc5	11799	baculoviral IAP repeat-containing 5	4.569	1.6e-105
Slc16a5	217316	solute carrier family 16 (monocarboxylic acid transporters), member 5	-5.853	2.1e-104
St14	19143	suppression of tumorigenicity 14 (colon carcinoma)	3.480	2.4e-104
1500009L16Rik	69784	RIKEN cDNA 1500009L16 gene	5.423	2.6e-104
AA467197	433470	expressed sequence AA467197	7.337	2.6e-104
Kcnk5	16529	potassium channel, subfamily K, member 5	3.323	5.6e-104
Shcbp1	20419	Shc SH2-domain binding protein 1	4.666	1.2e-103
Dsp	109620	desmoplakin	4.990	1.8e-103
Plk1	18817	polo like kinase 1	4.853	1.1e-102
Peg13	NA	paternally expressed 13	-3.819	1.1e-102
Id2	15902	inhibitor of DNA binding 2	2.311	9.5e-102
Aurkb	20877	aurora kinase B	4.493	9.5e-102
Dtl	76843	denticleless E3 ubiquitin protein ligase	2.740	4.7e-101
Kif20a	19348	kinesin family member 20A	4.088	6.1e-101
Myo1f	17916	myosin IF	2.026	4.2e-99
Tbc1d16	207592	TBC1 domain family, member 16	-3.510	6.5e-99
Cep55	74107	centrosomal protein 55	4.178	6.6e-99
Kif18b	70218	kinesin family member 18B	4.689	9.5e-99
Hip1r	29816	huntingtin interacting protein 1 related	2.034	8.5e-98
Kif15	209737	kinesin family member 15	3.966	1.3e-97
Kif2c	73804	kinesin family member 2C	4.635	4.1e-97
Nuf2	66977	NUF2, NDC80 kinetochore complex component	4.622	4.6e-96
Pif1	208084	PIF1 5’-to-3’ DNA helicase	4.812	7.3e-96
Atp1b1	11931	ATPase, Na+/K+ transporting, beta 1 polypeptide	-4.760	8.1e-96
Adam8	11501	a disintegrin and metallopeptidase domain 8	4.829	8.1e-96
Crmp1	12933	collapsin response mediator protein 1	2.767	2.0e-95
Mcm10	70024	minichromosome maintenance 10 replication initiation factor	3.992	2.3e-95
Trio	223435	triple functional domain (PTPRF interacting)	-2.738	2.8e-95
Ildr1	106347	immunoglobulin-like domain containing receptor 1	2.815	3.5e-95
Epas1	13819	endothelial PAS domain protein 1	3.679	4.4e-95
Kif22	110033	kinesin family member 22	3.706	7.5e-95
Hmmr	15366	hyaluronan mediated motility receptor (RHAMM)	4.869	8.2e-95
Ncapg2	76044	non-SMC condensin II complex, subunit G2	3.820	2.3e-94
Lmnb1	16906	lamin B1	2.896	3.4e-94
H2-Ob	15002	histocompatibility 2, O region beta locus	-4.441	4.5e-93
Rad51	19361	RAD51 recombinase	3.637	2.9e-92
Mis18bp1	217653	MIS18 binding protein 1	4.154	2.9e-92
Serpinb9	20723	serine (or cysteine) peptidase inhibitor, clade B, member 9	3.963	5.7e-92
Zwilch	68014	zwilch kinetochore protein	3.025	7.3e-92
Ube2c	68612	ubiquitin-conjugating enzyme E2C	4.964	1.1e-91
Kif4	16571	kinesin family member 4	4.379	2.1e-91
Gldc	104174	glycine decarboxylase	7.347	4.2e-91
Cdca3	14793	cell division cycle associated 3	4.160	7.8e-91
Paqr4	76498	progestin and adipoQ receptor family member IV	3.181	8.2e-91
Cdca8	52276	cell division cycle associated 8	4.009	1.3e-90
Cd2ap	12488	CD2-associated protein	-1.840	8.3e-90
Parpbp	75317	PARP1 binding protein	4.287	1.6e-89
Brip1	237911	BRCA1 interacting protein C-terminal helicase 1	3.459	2.1e-89
Stil	20460	Scl/Tal1 interrupting locus	4.323	4.4e-89
Sipa1l2	244668	signal-induced proliferation-associated 1 like 2	-2.911	4.8e-89
Ckap2l	70466	cytoskeleton associated protein 2-like	4.573	5.7e-89
Nek2	18005	NIMA (never in mitosis gene a)-related expressed kinase 2	4.704	6.1e-89
Cdk1	12534	cyclin-dependent kinase 1	4.667	6.4e-89
Clspn	269582	claspin	3.968	1.0e-88
Prr5	109270	proline rich 5 (renal)	6.726	1.6e-88
Bard1	12021	BRCA1 associated RING domain 1	3.055	3.5e-88
Slc6a19	74338	solute carrier family 6 (neurotransmitter transporter), member 19	-6.133	4.4e-88
Rbm47	245945	RNA binding motif protein 47	5.331	7.8e-88
St8sia1	20449	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	-3.267	1.2e-87
Anxa2	12306	annexin A2	3.425	2.4e-87
Znrf1	170737	zinc and ring finger 1	-2.241	2.1e-86
Ncapg	54392	non-SMC condensin I complex, subunit G	4.297	3.7e-86
Syde1	71709	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	-4.145	3.8e-86
Cdc45	12544	cell division cycle 45	3.314	4.7e-86
Sgo2a	68549	shugoshin 2A	4.401	6.6e-86
Whrn	73750	whirlin	-3.100	6.6e-86
Adap1	231821	ArfGAP with dual PH domains 1	3.346	1.8e-85
Dlg4	13385	discs large MAGUK scaffold protein 4	-2.499	2.2e-85
Fam129b	227737	family with sequence similarity 129, member B	3.384	3.0e-85
Ifngr2	15980	interferon gamma receptor 2	-3.836	6.3e-85
Cacna2d4	319734	calcium channel, voltage-dependent, alpha 2/delta subunit 4	-3.829	9.8e-84
Tacc3	21335	transforming, acidic coiled-coil containing protein 3	3.664	2.1e-83
Slamf7	75345	SLAM family member 7	2.273	2.8e-83
Pakap	677884	paralemmin A kinase anchor protein	-4.230	2.8e-83
Rad54b	623474	RAD54 homolog B (S. cerevisiae)	3.638	6.8e-83
Cnksr3	215748	Cnksr family member 3	-3.979	8.6e-83
Igf2bp3	140488	insulin-like growth factor 2 mRNA binding protein 3	3.076	1.5e-82
Ect2	13605	ect2 oncogene	3.713	4.2e-82
Nusap1	108907	nucleolar and spindle associated protein 1	4.348	7.0e-82
Slc28a2b	381417	solute carrier family 28 member 2b	-4.177	2.4e-81
Rrm2	20135	ribonucleotide reductase M2	3.935	2.8e-81
Mybl2	17865	myeloblastosis oncogene-like 2	4.027	5.7e-81
Cdca5	67849	cell division cycle associated 5	4.041	5.8e-81
Aspm	12316	abnormal spindle microtubule assembly	4.574	6.8e-81
Rapgef4	56508	Rap guanine nucleotide exchange factor (GEF) 4	-4.122	7.2e-81
Rad54l	19366	RAD54 like (S. cerevisiae)	3.419	8.6e-81
Kif14	381293	kinesin family member 14	4.604	1.2e-80
Efhd2	27984	EF hand domain containing 2	2.023	1.2e-80
Cenpe	229841	centromere protein E	4.566	2.3e-80
Parp8	52552	poly (ADP-ribose) polymerase family, member 8	-2.433	2.6e-80
Cdc6	23834	cell division cycle 6	3.545	4.6e-80
Rbbp8	225182	retinoblastoma binding protein 8, endonuclease	2.222	5.4e-80
Arhgap11a	228482	Rho GTPase activating protein 11A	3.375	1.4e-79
Dna2	327762	DNA replication helicase/nuclease 2	3.829	3.6e-79
Ncapd2	68298	non-SMC condensin I complex, subunit D2	2.783	3.9e-79
BC106179	NA	cDNA sequence BC106179	-4.611	3.9e-79
Otud1	71198	OTU domain containing 1	-3.113	4.2e-79
Fkbp5	14229	FK506 binding protein 5	2.541	7.6e-79
Scmh1	29871	sex comb on midleg homolog 1	-2.790	8.2e-79
Troap	78733	trophinin associated protein	4.430	1.1e-78
Ccnb2	12442	cyclin B2	4.444	1.4e-78
Casp3	12367	caspase 3	2.981	2.7e-78
Klhl3	100503085	kelch-like 3	-3.177	3.2e-78
Hip1	215114	huntingtin interacting protein 1	4.149	3.3e-78
Cdc20	107995	cell division cycle 20	3.873	3.3e-78
Popdc2	64082	popeye domain containing 2	4.938	3.6e-78
Cip2a	224171	cell proliferation regulating inhibitor of protein phosphatase 2A	3.792	3.8e-78
Cenpn	72155	centromere protein N	3.368	1.7e-77
Bub1	12235	BUB1, mitotic checkpoint serine/threonine kinase	4.772	1.7e-77
Nrp2	18187	neuropilin 2	-3.487	1.9e-77
Ldlrap1	100017	low density lipoprotein receptor adaptor protein 1	-1.838	2.7e-77
Cenpa	12615	centromere protein A	2.567	3.8e-77
Cenpi	102920	centromere protein I	4.062	4.5e-77
Fhl2	14200	four and a half LIM domains 2	3.555	5.3e-77
Xdh	22436	xanthine dehydrogenase	2.054	5.9e-77
Pclaf	68026	PCNA clamp associated factor	4.249	1.0e-76
Iqgap3	404710	IQ motif containing GTPase activating protein 3	4.353	1.3e-76
Pmepa1	65112	prostate transmembrane protein, androgen induced 1	-4.088	1.5e-76
Esco2	71988	establishment of sister chromatid cohesion N-acetyltransferase 2	4.354	3.5e-76
Mki67	17345	antigen identified by monoclonal antibody Ki 67	4.457	5.0e-76
Dlgap5	218977	DLG associated protein 5	3.521	7.7e-76
Exo1	26909	exonuclease 1	3.260	1.3e-75
Kntc1	208628	kinetochore associated 1	3.507	1.6e-75
Gna15	14676	guanine nucleotide binding protein, alpha 15	2.851	1.8e-75
Uhrf1	18140	ubiquitin-like, containing PHD and RING finger domains, 1	3.059	4.4e-75
Il6st	16195	interleukin 6 signal transducer	-2.590	9.4e-75
Knl1	76464	kinetochore scaffold 1	4.224	1.2e-74
Bspry	192120	B-box and SPRY domain containing	3.746	1.4e-74
Cenpf	108000	centromere protein F	5.020	1.8e-74
Melk	17279	maternal embryonic leucine zipper kinase	3.774	1.8e-74
Kdm5b	75605	lysine (K)-specific demethylase 5B	-1.761	3.4e-74
Sapcd2	72080	suppressor APC domain containing 2	4.559	1.7e-73
Neil3	234258	nei like 3 (E. coli)	4.041	2.1e-73
A630014C17Rik	NA	RIKEN cDNA A630014C17 gene	-3.645	3.2e-73
Ska3	219114	spindle and kinetochore associated complex subunit 3	3.663	3.6e-73
Sema7a	20361	sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A	3.596	3.9e-73
Cdc25c	12532	cell division cycle 25C	5.233	7.5e-73
Zfp831	100043757	zinc finger protein 831	-2.592	9.2e-73
Nr1d2	353187	nuclear receptor subfamily 1, group D, member 2	-2.412	9.4e-73
Nsg2	18197	neuron specific gene family member 2	-3.671	9.6e-73
Xkrx	331524	X-linked Kx blood group related, X-linked	-4.846	1.1e-72
Scml4	268297	Scm polycomb group protein like 4	-2.070	1.4e-72
Zbtb4	75580	zinc finger and BTB domain containing 4	-2.213	6.0e-72
Ticrr	77011	TOPBP1-interacting checkpoint and replication regulator	3.918	7.7e-72
Ubash3b	72828	ubiquitin associated and SH3 domain containing, B	1.395	1.2e-71
Foxm1	14235	forkhead box M1	3.747	1.6e-71
Knstrn	51944	kinetochore-localized astrin/SPAG5 binding	3.047	2.4e-71
Gzmk	14945	granzyme K	5.328	1.8e-70
Ccne1	12447	cyclin E1	2.430	2.5e-70
Arsb	11881	arylsulfatase B	2.589	4.1e-70
Espl1	105988	extra spindle pole bodies 1, separase	4.456	7.8e-70
Hmgb2	97165	high mobility group box 2	2.899	9.7e-70
Treml2	328833	triggering receptor expressed on myeloid cells-like 2	-2.776	5.7e-69
Ccnb1	268697	cyclin B1	4.820	7.2e-69
Ephb6	13848	Eph receptor B6	-2.355	8.2e-69
Arhgap19	71085	Rho GTPase activating protein 19	3.818	1.4e-68
Gm4739	NA	predicted gene 4739	3.220	2.2e-68
Igfbp4	16010	insulin-like growth factor binding protein 4	-5.437	3.2e-68

Table: Results for ko.TxB_v_ko.noTx

4583 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Dtl	76843	denticleless E3 ubiquitin protein ligase	3.031	2.3e-122
Top2a	21973	topoisomerase (DNA) II alpha	4.045	2.1e-119
Hells	15201	helicase, lymphoid specific	2.761	1.3e-111
Spag5	54141	sperm associated antigen 5	4.117	1.7e-97
Kif11	16551	kinesin family member 11	3.963	3.6e-97
Bub1b	12236	BUB1B, mitotic checkpoint serine/threonine kinase	3.799	4.8e-97
Mcm10	70024	minichromosome maintenance 10 replication initiation factor	4.045	6.1e-97
Zwilch	68014	zwilch kinetochore protein	3.052	1.7e-92
Cdc6	23834	cell division cycle 6	3.800	4.7e-91
Ncaph	215387	non-SMC condensin I complex, subunit H	3.564	2.8e-88
Ncapg2	76044	non-SMC condensin II complex, subunit G2	3.693	2.7e-87
Uhrf1	18140	ubiquitin-like, containing PHD and RING finger domains, 1	3.286	1.4e-85
Tpx2	72119	TPX2, microtubule-associated	3.959	7.8e-85
Kif15	209737	kinesin family member 15	3.701	3.0e-84
Clspn	269582	claspin	3.876	7.7e-84
Aurkb	20877	aurora kinase B	4.073	7.0e-83
Shcbp1	20419	Shc SH2-domain binding protein 1	4.189	1.3e-82
Prc1	233406	protein regulator of cytokinesis 1	3.710	1.3e-82
Plk1	18817	polo like kinase 1	4.365	1.9e-82
Rad51	19361	RAD51 recombinase	3.444	5.3e-82
Ccna2	12428	cyclin A2	4.094	4.2e-80
Kif20a	19348	kinesin family member 20A	3.655	4.5e-80
Kntc1	208628	kinetochore associated 1	3.629	4.5e-80
E2f1	13555	E2F transcription factor 1	2.896	8.9e-80
Kif18b	70218	kinesin family member 18B	4.229	9.8e-80
Iqgap3	404710	IQ motif containing GTPase activating protein 3	4.453	1.9e-79
2610318N02Rik	70458	RIKEN cDNA 2610318N02 gene	3.246	4.0e-79
Cdca2	108912	cell division cycle associated 2	3.537	5.3e-79
Rad54b	623474	RAD54 homolog B (S. cerevisiae)	3.563	1.1e-78
Exo1	26909	exonuclease 1	3.324	6.3e-78
Cdc45	12544	cell division cycle 45	3.165	8.5e-78
Brip1	237911	BRCA1 interacting protein C-terminal helicase 1	3.222	6.2e-77
Mis18bp1	217653	MIS18 binding protein 1	3.755	1.3e-74
Prr11	270906	proline rich 11	4.078	1.9e-74
Mybl2	17865	myeloblastosis oncogene-like 2	3.833	9.6e-73
Bard1	12021	BRCA1 associated RING domain 1	2.771	6.7e-72
Pask	269224	PAS domain containing serine/threonine kinase	3.398	6.7e-72
Birc5	11799	baculoviral IAP repeat-containing 5	3.780	9.0e-72
Kif2c	73804	kinesin family member 2C	3.997	1.0e-71
Esco2	71988	establishment of sister chromatid cohesion N-acetyltransferase 2	4.244	1.0e-71
Stil	20460	Scl/Tal1 interrupting locus	3.882	3.1e-71
Rrm2	20135	ribonucleotide reductase M2	3.696	3.2e-71
Kif4	16571	kinesin family member 4	3.870	6.7e-71
Cdk1	12534	cyclin-dependent kinase 1	4.180	7.4e-71
Kif14	381293	kinesin family member 14	4.303	6.3e-70
Nuf2	66977	NUF2, NDC80 kinetochore complex component	3.941	2.5e-69
Hmmr	15366	hyaluronan mediated motility receptor (RHAMM)	4.169	5.0e-69
Kif22	110033	kinesin family member 22	3.166	8.9e-69
Cdca3	14793	cell division cycle associated 3	3.631	9.3e-69
Neil3	234258	nei like 3 (E. coli)	3.927	1.1e-68
Ncapg	54392	non-SMC condensin I complex, subunit G	3.846	1.7e-68
Sgo2a	68549	shugoshin 2A	3.939	3.0e-68
Rad54l	19366	RAD54 like (S. cerevisiae)	3.155	3.0e-68
Cdca8	52276	cell division cycle associated 8	3.490	3.2e-68
Cep55	74107	centrosomal protein 55	3.477	6.3e-68
Pole	18973	polymerase (DNA directed), epsilon	2.785	6.6e-68
Cdca5	67849	cell division cycle associated 5	3.710	1.0e-67
Ube2c	68612	ubiquitin-conjugating enzyme E2C	4.273	1.4e-67
Dna2	327762	DNA replication helicase/nuclease 2	3.540	4.0e-67
Nusap1	108907	nucleolar and spindle associated protein 1	3.949	4.1e-67
Ckap2l	70466	cytoskeleton associated protein 2-like	3.979	6.2e-67
Pif1	208084	PIF1 5’-to-3’ DNA helicase	4.032	9.7e-67
Nek2	18005	NIMA (never in mitosis gene a)-related expressed kinase 2	4.072	3.0e-66
Lmnb1	16906	lamin B1	2.410	6.4e-65
Cenpn	72155	centromere protein N	3.099	6.8e-65
Cenpi	102920	centromere protein I	3.748	6.8e-65
Kdm5b	75605	lysine (K)-specific demethylase 5B	-1.649	8.7e-65
Ticrr	77011	TOPBP1-interacting checkpoint and replication regulator	3.706	8.5e-64
Troap	78733	trophinin associated protein	3.999	1.7e-63
Melk	17279	maternal embryonic leucine zipper kinase	3.498	1.8e-63
Chek1	12649	checkpoint kinase 1	3.072	2.5e-63
Mki67	17345	antigen identified by monoclonal antibody Ki 67	4.064	7.7e-63
Cenpf	108000	centromere protein F	4.615	1.6e-62
Wee1	22390	WEE 1 homolog 1 (S. pombe)	2.607	1.6e-62
Arhgap11a	228482	Rho GTPase activating protein 11A	3.000	1.7e-62
Anln	68743	anillin, actin binding protein	3.892	1.8e-62
Espl1	105988	extra spindle pole bodies 1, separase	4.224	2.4e-62
Tacc3	21335	transforming, acidic coiled-coil containing protein 3	3.167	6.0e-62
Hrob	217216	homologous recombination factor with OB-fold	4.145	6.7e-62
Knl1	76464	kinetochore scaffold 1	3.853	1.0e-61
Parpbp	75317	PARP1 binding protein	3.562	3.3e-61
Bub1	12235	BUB1, mitotic checkpoint serine/threonine kinase	4.250	5.1e-61
Cenpe	229841	centromere protein E	3.984	7.5e-61
Fanca	14087	Fanconi anemia, complementation group A	3.360	7.6e-61
Foxm1	14235	forkhead box M1	3.467	7.7e-61
Nsl1	381318	NSL1, MIS12 kinetochore complex component	3.047	3.3e-60
Aspm	12316	abnormal spindle microtubule assembly	3.953	3.9e-60
Ncapd2	68298	non-SMC condensin I complex, subunit D2	2.432	4.0e-60
Kif23	71819	kinesin family member 23	2.790	6.8e-59
Phf19	74016	PHD finger protein 19	2.770	1.1e-58
Pclaf	68026	PCNA clamp associated factor	3.727	1.1e-58
Ect2	13605	ect2 oncogene	3.148	1.3e-58
Rad51ap1	19362	RAD51 associated protein 1	3.561	1.5e-58
Cip2a	224171	cell proliferation regulating inhibitor of protein phosphatase 2A	3.291	2.2e-58
Lig1	16881	ligase I, DNA, ATP-dependent	2.513	2.7e-58
Ccne1	12447	cyclin E1	2.220	3.3e-58
Brca1	12189	breast cancer 1, early onset	2.978	5.2e-58
Sapcd2	72080	suppressor APC domain containing 2	4.057	1.1e-57
E2f8	108961	E2F transcription factor 8	4.013	1.4e-57
Chaf1a	27221	chromatin assembly factor 1, subunit A (p150)	3.118	1.9e-57
Cdc20	107995	cell division cycle 20	3.328	2.0e-57
Cit	12704	citron	3.671	2.8e-56
Dscc1	72107	DNA replication and sister chromatid cohesion 1	2.974	1.0e-55
Fignl1	60530	fidgetin-like 1	3.360	2.9e-55
Eme1	268465	essential meiotic structure-specific endonuclease 1	2.848	6.6e-55
Chtf18	214901	CTF18, chromosome transmission fidelity factor 18	2.568	9.2e-55
Pimreg	109212	PICALM interacting mitotic regulator	3.877	9.2e-55
Arhgap19	71085	Rho GTPase activating protein 19	3.418	1.3e-54
Tcf19	106795	transcription factor 19	2.592	1.9e-54
Gtse1	29870	G two S phase expressed protein 1	3.443	2.1e-54
H3c15	97114	H3 clustered histone 15	4.095	3.3e-54
Spc24	67629	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	3.698	4.2e-54
Fancd2	211651	Fanconi anemia, complementation group D2	3.434	8.2e-54
Dlgap5	218977	DLG associated protein 5	2.937	2.1e-52
H2ac10	319173	H2A clustered histone 10	3.720	1.2e-51
Havcr2	171285	hepatitis A virus cellular receptor 2	4.164	1.2e-51
Pola1	18968	polymerase (DNA directed), alpha 1	2.456	3.8e-51
Ttk	22137	Ttk protein kinase	4.058	3.9e-51
Incenp	16319	inner centromere protein	2.450	6.4e-51
Ska3	219114	spindle and kinetochore associated complex subunit 3	3.072	7.2e-51
Asf1b	66929	anti-silencing function 1B histone chaperone	2.824	1.3e-50
Ccnf	12449	cyclin F	3.506	2.3e-50
Tk1	21877	thymidine kinase 1	2.752	6.5e-50
Ccnb1	268697	cyclin B1	4.112	7.6e-50
Cdc25c	12532	cell division cycle 25C	4.351	8.1e-50
Depdc1b	218581	DEP domain containing 1B	2.916	9.9e-50
E2f7	52679	E2F transcription factor 7	3.973	1.1e-49
Trip13	69716	thyroid hormone receptor interactor 13	3.252	1.1e-48
Spc25	66442	SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)	3.678	1.2e-48
Traip	22036	TRAF-interacting protein	2.561	2.1e-48
Atad5	237877	ATPase family, AAA domain containing 5	2.361	3.0e-48
Tfdp1	21781	transcription factor Dp 1	2.093	3.1e-48
Ccnb2	12442	cyclin B2	3.487	3.9e-48
Chaf1b	110749	chromatin assembly factor 1, subunit B (p60)	1.725	5.9e-48
Mms22l	212377	MMS22-like, DNA repair protein	1.938	2.7e-47
Tyms	22171	thymidylate synthase	2.737	7.4e-47
Rbbp8	225182	retinoblastoma binding protein 8, endonuclease	1.703	2.0e-46
Ckap2	80986	cytoskeleton associated protein 2	3.508	2.0e-46
Pbk	52033	PDZ binding kinase	3.949	2.1e-46
Zfp367	238673	zinc finger protein 367	1.818	2.7e-46
Enkd1	102124	enkurin domain containing 1	2.364	8.3e-46
Mtfr2	71804	mitochondrial fission regulator 2	3.741	1.3e-45
Tmem163	72160	transmembrane protein 163	2.118	2.6e-45
Nsd2	107823	nuclear receptor binding SET domain protein 2	2.048	4.8e-45
Smc2	14211	structural maintenance of chromosomes 2	2.308	1.8e-44
Diaph3	56419	diaphanous related formin 3	3.065	2.1e-44
Ephb6	13848	Eph receptor B6	-1.879	3.0e-44
Ifitm1	68713	interferon induced transmembrane protein 1	4.836	3.0e-44
Ezh2	14056	enhancer of zeste 2 polycomb repressive complex 2 subunit	2.022	5.7e-44
Mxd3	17121	Max dimerization protein 3	3.050	1.5e-43
E2f2	242705	E2F transcription factor 2	2.051	5.4e-43
H2bc9	319182	H2B clustered histone 9	3.412	1.0e-42
H2bc14	319186	H2B clustered histone 14	3.595	2.3e-42
Nxpe3	385658	neurexophilin and PC-esterase domain family, member 3	-1.443	2.4e-42
Ska1	66468	spindle and kinetochore associated complex subunit 1	4.075	1.0e-41
Neurl1b	240055	neuralized E3 ubiquitin protein ligase 1B	4.232	1.2e-41
Ehd4	98878	EH-domain containing 4	1.483	2.0e-41
Knstrn	51944	kinetochore-localized astrin/SPAG5 binding	2.330	2.6e-41
Ndc80	67052	NDC80 kinetochore complex component	2.331	3.3e-41
Orc1	18392	origin recognition complex, subunit 1	3.146	7.6e-41
Sgo1	72415	shugoshin 1	2.925	1.2e-40
H2bc13	319185	H2B clustered histone 13	3.483	1.4e-40
Mcm5	17218	minichromosome maintenance complex component 5	2.243	2.2e-40
Zbtb32	58206	zinc finger and BTB domain containing 32	1.588	2.4e-40
Aurka	20878	aurora kinase A	3.148	2.8e-40
H2ac15	319169	H2A clustered histone 15	3.188	3.2e-40
Galnt3	14425	polypeptide N-acetylgalactosaminyltransferase 3	3.312	6.5e-40
Mastl	67121	microtubule associated serine/threonine kinase-like	2.968	7.4e-40
Tedc1	104732	tubulin epsilon and delta complex 1	2.161	9.5e-40
Kif20b	240641	kinesin family member 20B	2.192	1.5e-39
Dhfr	13361	dihydrofolate reductase	2.424	2.0e-39
Mcm6	17219	minichromosome maintenance complex component 6	1.693	2.9e-39
Cdc7	12545	cell division cycle 7 (S. cerevisiae)	1.754	3.0e-39
Chsy1	269941	chondroitin sulfate synthase 1	1.344	3.5e-39
H1f5	56702	H1.5 linker histone, cluster member	3.672	4.5e-39
H2ac4	319172	H2A clustered histone 4	3.517	5.6e-39
BC106179	NA	cDNA sequence BC106179	-2.289	5.7e-39
Gzmb	14939	granzyme B	4.190	6.6e-39
Cenph	26886	centromere protein H	3.552	9.9e-39
Sp6	83395	trans-acting transcription factor 6	-3.310	1.3e-38
Fam129b	227737	family with sequence similarity 129, member B	2.296	1.5e-38
Fbxo5	67141	F-box protein 5	2.404	6.3e-38
H3c8	97908	H3 clustered histone 8	3.643	7.5e-38
Cenpm	66570	centromere protein M	3.234	8.2e-38
Ccne2	12448	cyclin E2	2.921	9.7e-38
H2bc11	319183	H2B clustered histone 11	3.396	1.0e-37
Recql4	79456	RecQ protein-like 4	2.607	1.3e-37
Cdca7l	217946	cell division cycle associated 7 like	1.340	1.5e-37
Cdca7	66953	cell division cycle associated 7	2.389	1.8e-37
Aunip	69885	aurora kinase A and ninein interacting protein	3.387	2.0e-37
H2bc3	319178	H2B clustered histone 3	3.500	2.2e-37
Cdkn2c	12580	cyclin dependent kinase inhibitor 2C	2.706	3.1e-37
Atad2	70472	ATPase family, AAA domain containing 2	1.557	9.0e-37
H2ac11	319167	H2A clustered histone 11	3.243	9.4e-37
Plk4	20873	polo like kinase 4	2.173	2.9e-36
Gm4739	NA	predicted gene 4739	2.340	6.0e-36
Hmgb2	97165	high mobility group box 2	2.084	6.6e-36
Cks2	66197	CDC28 protein kinase regulatory subunit 2	2.639	8.5e-36
Gins2	272551	GINS complex subunit 2 (Psf2 homolog)	1.753	1.2e-35
Stmn1	16765	stathmin 1	2.740	1.3e-35

Table: Results for wt.TxA_v_wt.TxB

5771 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Sh3pxd2a	14218	SH3 and PX domains 2A	-4.400	4.8e-287
Epas1	13819	endothelial PAS domain protein 1	4.882	4.4e-163
Zbtb32	58206	zinc finger and BTB domain containing 32	3.114	6.5e-161
Hip1r	29816	huntingtin interacting protein 1 related	2.333	1.8e-127
Ptms	69202	parathymosin	2.931	2.1e-125
Id2	15902	inhibitor of DNA binding 2	2.534	1.1e-121
Nedd4l	83814	neural precursor cell expressed, developmentally down-regulated gene 4-like	-3.104	1.1e-120
Nrp2	18187	neuropilin 2	-4.162	2.9e-117
Ubash3b	72828	ubiquitin associated and SH3 domain containing, B	1.762	1.1e-111
Samd3	268288	sterile alpha motif domain containing 3	-3.676	6.5e-108
St14	19143	suppression of tumorigenicity 14 (colon carcinoma)	3.541	2.4e-106
Ncald	52589	neurocalcin delta	3.136	1.1e-103
Icos	54167	inducible T cell co-stimulator	2.488	1.7e-102
Crmp1	12933	collapsin response mediator protein 1	2.890	1.7e-102
Dsp	109620	desmoplakin	5.136	1.8e-101
Ildr1	106347	immunoglobulin-like domain containing receptor 1	2.948	5.9e-101
Galnt3	14425	polypeptide N-acetylgalactosaminyltransferase 3	3.787	6.5e-101
Sell	20343	selectin, lymphocyte	-3.234	1.7e-98
Tmcc2	68875	transmembrane and coiled-coil domains 2	-7.813	2.3e-96
Il6ra	16194	interleukin 6 receptor, alpha	-3.320	6.9e-93
Cnr2	12802	cannabinoid receptor 2 (macrophage)	-2.317	4.9e-91
1700025G04Rik	69399	RIKEN cDNA 1700025G04 gene	-2.674	6.4e-91
Sema4b	20352	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	-1.730	1.1e-90
Plekha1	101476	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	-2.245	5.1e-88
Ccr7	12775	chemokine (C-C motif) receptor 7	-3.896	1.4e-83
Ajuba	16475	ajuba LIM protein	5.206	2.8e-83
Adamts14	237360	a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 14	4.454	3.5e-81
Havcr2	171285	hepatitis A virus cellular receptor 2	4.714	1.2e-80
Igf2bp3	140488	insulin-like growth factor 2 mRNA binding protein 3	2.989	1.3e-80
Gna15	14676	guanine nucleotide binding protein, alpha 15	2.959	2.7e-80
L1cam	16728	L1 cell adhesion molecule	2.532	2.3e-79
Lgals3	16854	lectin, galactose binding, soluble 3	4.544	1.3e-78
Apol11b	328563	apolipoprotein L 11b	-7.264	1.8e-77
Zbtb18	30928	zinc finger and BTB domain containing 18	-2.188	5.2e-77
Chst15	77590	carbohydrate sulfotransferase 15	-2.618	6.1e-77
Gldc	104174	glycine decarboxylase	5.734	8.1e-77
Drc1	381738	dynein regulatory complex subunit 1	-4.314	1.0e-75
Tbc1d16	207592	TBC1 domain family, member 16	-2.947	1.5e-74
Rapgef4	56508	Rap guanine nucleotide exchange factor (GEF) 4	-3.871	4.8e-74
Stx2	13852	syntaxin 2	-2.630	5.0e-74
Marveld2	218518	MARVEL (membrane-associating) domain containing 2	2.682	4.6e-73
Dlg4	13385	discs large MAGUK scaffold protein 4	-2.293	4.9e-73
Slc16a5	217316	solute carrier family 16 (monocarboxylic acid transporters), member 5	-4.478	9.2e-73
Slc2a3	20527	solute carrier family 2 (facilitated glucose transporter), member 3	1.472	1.3e-72
Podnl1	244550	podocan-like 1	2.393	4.2e-72
Tdrp	72148	testis development related protein	-3.885	1.4e-70
Slfn14	237890	schlafen 14	-8.521	4.3e-70
Parp8	52552	poly (ADP-ribose) polymerase family, member 8	-2.253	9.3e-69
Sipa1l2	244668	signal-induced proliferation-associated 1 like 2	-2.515	1.2e-68
Dapl1	76747	death associated protein-like 1	-4.991	1.9e-68
Atp1b1	11931	ATPase, Na+/K+ transporting, beta 1 polypeptide	-3.911	4.6e-67
Serpinb6b	20708	serine (or cysteine) peptidase inhibitor, clade B, member 6b	3.328	8.2e-66
Nsmf	56876	NMDA receptor synaptonuclear signaling and neuronal migration factor	1.413	1.4e-65
Cd2ap	12488	CD2-associated protein	-1.560	1.4e-65
Xdh	22436	xanthine dehydrogenase	1.895	1.9e-65
Adam8	11501	a disintegrin and metallopeptidase domain 8	3.945	2.5e-65
Trim30c	434219	tripartite motif-containing 30C	-4.384	2.4e-64
Vipr1	22354	vasoactive intestinal peptide receptor 1	-3.444	1.4e-63
Pakap	677884	paralemmin A kinase anchor protein	-3.593	2.7e-62
Efhd2	27984	EF hand domain containing 2	1.770	1.9e-61
Klrb1b	80782	killer cell lectin-like receptor subfamily B member 1B	6.521	5.2e-61
Hhat	226861	hedgehog acyltransferase	2.218	2.0e-60
Nrgn	64011	neurogranin	4.164	2.0e-60
Ifnar2	15976	interferon (alpha and beta) receptor 2	-1.468	2.0e-60
Ptpn3	545622	protein tyrosine phosphatase, non-receptor type 3	2.619	2.7e-59
Itih5	209378	inter-alpha (globulin) inhibitor H5	2.422	1.2e-58
Sytl2	83671	synaptotagmin-like 2	1.595	1.9e-57
Art4	109978	ADP-ribosyltransferase 4	-5.099	3.5e-57
Csf1	12977	colony stimulating factor 1 (macrophage)	4.823	1.6e-56
Epb42	13828	erythrocyte membrane protein band 4.2	-6.436	2.5e-56
Lsr	54135	lipolysis stimulated lipoprotein receptor	2.564	7.0e-56
Spock2	94214	sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2	4.450	7.7e-56
Adgrg5	382045	adhesion G protein-coupled receptor G5	-3.027	1.1e-55
Farp1	223254	FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived)	2.616	1.3e-55
Itga3	16400	integrin alpha 3	3.118	5.3e-55
Fhdc1	229474	FH2 domain containing 1	-5.391	6.8e-55
Sorcs2	81840	sortilin-related VPS10 domain containing receptor 2	-4.114	1.6e-54
Tmem108	81907	transmembrane protein 108	-4.429	1.7e-54
Mapre2	212307	microtubule-associated protein, RP/EB family, member 2	1.397	2.1e-54
Ms4a4c	64380	membrane-spanning 4-domains, subfamily A, member 4C	-3.202	2.1e-54
Tmem154	320782	transmembrane protein 154	1.770	2.2e-54
Pdcd1	18566	programmed cell death 1	4.298	5.4e-54
Dntt	21673	deoxynucleotidyltransferase, terminal	-5.243	1.1e-53
Ttc28	209683	tetratricopeptide repeat domain 28	-2.768	1.2e-53
Mgst2	211666	microsomal glutathione S-transferase 2	-2.009	1.4e-53
Icosl	50723	icos ligand	1.233	1.9e-53
Gpr55	227326	G protein-coupled receptor 55	2.579	5.4e-53
Nsg2	18197	neuron specific gene family member 2	-3.120	1.4e-52
Ifi208	100033459	interferon activated gene 208	-2.854	2.9e-52
Zfp395	380912	zinc finger protein 395	-1.925	3.7e-52
Plekhb2	226971	pleckstrin homology domain containing, family B (evectins) member 2	1.472	1.3e-51
Kcna2	16490	potassium voltage-gated channel, shaker-related subfamily, member 2	-3.442	2.5e-51
Whrn	73750	whirlin	-2.459	2.8e-51
Tmem163	72160	transmembrane protein 163	1.995	3.6e-51
Ypel4	241525	yippee like 4	-7.221	3.7e-51
Tet1	52463	tet methylcytosine dioxygenase 1	-3.197	5.0e-51
Serpinb9	20723	serine (or cysteine) peptidase inhibitor, clade B, member 9	2.945	6.8e-51
Slc6a19	74338	solute carrier family 6 (neurotransmitter transporter), member 19	-4.471	9.9e-51
Ttpal	76080	tocopherol (alpha) transfer protein-like	1.085	1.9e-50
Slc25a37	67712	solute carrier family 25, member 37	-3.925	2.8e-50
Car5b	56078	carbonic anhydrase 5b, mitochondrial	3.630	3.1e-50
Osbpl3	71720	oxysterol binding protein-like 3	2.298	6.0e-50
H2-Ob	15002	histocompatibility 2, O region beta locus	-3.293	1.8e-49
Muc20	224116	mucin 20	4.703	1.9e-49
Spn	20737	sialophorin	1.440	6.3e-49
Gpr68	238377	G protein-coupled receptor 68	1.790	1.3e-48
Hip1	215114	huntingtin interacting protein 1	3.261	1.5e-48
Fkbp5	14229	FK506 binding protein 5	1.988	3.2e-48
Rsad2	58185	radical S-adenosyl methionine domain containing 2	-4.296	4.0e-48
Txk	22165	TXK tyrosine kinase	-1.839	5.5e-48
Cacna2d4	319734	calcium channel, voltage-dependent, alpha 2/delta subunit 4	-2.802	6.2e-48
Syde1	71709	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	-2.992	8.1e-48
Eml2	72205	echinoderm microtubule associated protein like 2	1.604	1.1e-47
Myo1g	246177	myosin IG	1.265	1.8e-47
AA467197	433470	expressed sequence AA467197	3.589	2.3e-47
Slc52a3	69698	solute carrier protein family 52, member 3	2.424	2.7e-47
Cd80	12519	CD80 antigen	3.169	3.4e-47
B4galnt4	330671	beta-1,4-N-acetyl-galactosaminyl transferase 4	3.677	4.1e-47
Cnksr3	215748	Cnksr family member 3	-2.963	7.0e-47
Fgf13	14168	fibroblast growth factor 13	-2.041	1.7e-46
Dnajb2	56812	DnaJ heat shock protein family (Hsp40) member B2	-3.156	3.3e-46
Alas2	11656	aminolevulinic acid synthase 2, erythroid	-7.184	1.0e-45
Plekha6	240753	pleckstrin homology domain containing, family A member 6	-3.808	1.0e-45
Igfbp4	16010	insulin-like growth factor binding protein 4	-4.436	2.4e-45
Serpinb9b	20706	serine (or cysteine) peptidase inhibitor, clade B, member 9b	5.805	3.7e-45
Dgkh	380921	diacylglycerol kinase, eta	2.449	3.8e-45
Lrig1	16206	leucine-rich repeats and immunoglobulin-like domains 1	-2.953	3.9e-45
Mtmr1	53332	myotubularin related protein 1	1.243	4.6e-45
Slc2a8	56017	solute carrier family 2, (facilitated glucose transporter), member 8	2.478	9.8e-45
Auts2	319974	autism susceptibility candidate 2	-5.062	1.8e-44
Nrp1	18186	neuropilin 1	2.850	3.5e-44
Rhoc	11853	ras homolog family member C	3.286	4.0e-44
Lpcat4	99010	lysophosphatidylcholine acyltransferase 4	1.731	4.5e-44
Lag3	16768	lymphocyte-activation gene 3	4.437	4.7e-44
Pqlc3	217430	PQ loop repeat containing	1.397	8.2e-44
Il12rb2	16162	interleukin 12 receptor, beta 2	3.162	1.4e-43
Rab27a	11891	RAB27A, member RAS oncogene family	1.809	1.8e-43
Ahr	11622	aryl-hydrocarbon receptor	3.062	2.1e-43
1500009L16Rik	69784	RIKEN cDNA 1500009L16 gene	3.256	5.6e-43
Ak3	56248	adenylate kinase 3	1.150	8.5e-43
Arap2	212285	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1.273	8.6e-43
Zbtb38	245007	zinc finger and BTB domain containing 38	1.337	1.6e-42
Tlr7	170743	toll-like receptor 7	-2.525	1.7e-42
Trim36	28105	tripartite motif-containing 36	2.094	1.8e-42
Tigit	100043314	T cell immunoreceptor with Ig and ITIM domains	4.137	1.9e-42
Tanc1	66860	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	-1.789	2.6e-42
Bach2	12014	BTB and CNC homology, basic leucine zipper transcription factor 2	-3.094	4.3e-42
Hbb-bs	15129100503605	hemoglobin, beta adult s chain	-7.843	4.4e-42
Tns2	209039	tensin 2	3.250	1.3e-41
Pcbp4	59092	poly(rC) binding protein 4	2.005	1.4e-41
Ptpn11	19247	protein tyrosine phosphatase, non-receptor type 11	1.446	1.7e-41
Ggta1	14594	glycoprotein galactosyltransferase alpha 1, 3	1.334	2.1e-41
A630014C17Rik	NA	RIKEN cDNA A630014C17 gene	-2.550	2.9e-41
Tmod1	21916	tropomodulin 1	-5.584	3.6e-41
Slc14a1	108052	solute carrier family 14 (urea transporter), member 1	-2.346	5.4e-41
Pdk1	228026	pyruvate dehydrogenase kinase, isoenzyme 1	-2.290	6.3e-41
5830411N06Rik	244234	RIKEN cDNA 5830411N06 gene	-4.002	6.7e-41
Irak3	73914	interleukin-1 receptor-associated kinase 3	2.990	1.2e-40
Maats1	320214	MYCBP-associated, testis expressed 1	4.519	1.3e-40
Prf1	18646	perforin 1 (pore forming protein)	2.418	1.3e-40
Vax2	24113	ventral anterior homeobox 2	5.240	1.3e-40
Hba-a2	110257	hemoglobin alpha, adult chain 2	-7.626	1.8e-40
Marchf3	320253	membrane associated ring-CH-type finger 3	-3.609	1.9e-40
Prr5	109270	proline rich 5 (renal)	3.890	2.0e-40
Trpm6	225997	transient receptor potential cation channel, subfamily M, member 6	4.592	2.1e-40
Klra13-ps	NA	killer cell lectin-like receptor subfamily A, member 13, pseudogene	-7.345	2.6e-40
Usp28	235323	ubiquitin specific peptidase 28	-1.583	3.1e-40
Furin	18550	furin (paired basic amino acid cleaving enzyme)	1.719	3.4e-40
Lamc1	226519	laminin, gamma 1	3.210	3.9e-40
Fam129a	63913	family with sequence similarity 129, member A	1.854	5.3e-40
Irak2	108960	interleukin-1 receptor-associated kinase 2	1.582	9.0e-40
Slc28a2b	381417	solute carrier family 28 member 2b	-2.822	9.3e-40
Treml2	328833	triggering receptor expressed on myeloid cells-like 2	-2.100	1.2e-39
Anxa4	11746	annexin A4	1.994	3.3e-39
Rbl2	19651	RB transcriptional corepressor like 2	1.154	3.3e-39
Mob3b	214944	MOB kinase activator 3B	-1.625	4.3e-39
Apobec2	11811	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 2	1.960	5.7e-39
Itgax	16411	integrin alpha X	3.765	6.1e-39
Clcn5	12728	chloride channel, voltage-sensitive 5	1.691	7.2e-39
Prdm1	12142	PR domain containing 1, with ZNF domain	2.788	1.3e-38
Gabrr2	14409	gamma-aminobutyric acid (GABA) C receptor, subunit rho 2	-3.872	1.3e-38
Cul9	78309	cullin 9	-2.530	2.4e-38
Pdcd1lg2	58205	programmed cell death 1 ligand 2	2.442	2.9e-38
Poglut3	68304	protein O-glucosyltransferase 3	2.580	3.6e-38
Acvr1b	11479	activin A receptor, type 1B	-1.415	4.6e-38
Kcnk5	16529	potassium channel, subfamily K, member 5	1.955	1.1e-37
Prex1	277360	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1.419	1.4e-37
Lrmp	16970	lymphoid-restricted membrane protein	1.057	1.4e-37
Il6st	16195	interleukin 6 signal transducer	-1.836	1.7e-37
Dubr	NA	Dppa2 upstream binding RNA	1.347	2.9e-37
Erc2	238988	ELKS/RAB6-interacting/CAST family member 2	7.479	3.3e-37
Dzip1	66573	DAZ interacting protein 1	-2.027	5.1e-37
Gm20696	NA	predicted gene 20696	-3.803	7.8e-37
P2ry12	70839	purinergic receptor P2Y, G-protein coupled 12	3.868	9.0e-37
Maf	17132	avian musculoaponeurotic fibrosarcoma oncogene homolog	2.930	1.1e-36
Trpv2	22368	transient receptor potential cation channel, subfamily V, member 2	1.192	1.1e-36
AC161757.1	NA	toll-like receptor 1 (Tlr1) pseudogene	-1.936	2.4e-36
Ttc3	22129	tetratricopeptide repeat domain 3	-1.219	2.5e-36
Cdr2l	237988	cerebellar degeneration-related protein 2-like	-3.759	2.7e-36
Arhgap29	214137	Rho GTPase activating protein 29	-3.745	2.8e-36

Table: Results for wt.TxA_v_wt.noTx

8807 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Sh3pxd2a	14218	SH3 and PX domains 2A	-4.914	0.0e+00
Zbtb32	58206	zinc finger and BTB domain containing 32	4.117	1.0e-253
Ncald	52589	neurocalcin delta	5.175	1.7e-236
Chsy1	269941	chondroitin sulfate synthase 1	2.934	4.8e-186
Lgals3	16854	lectin, galactose binding, soluble 3	7.042	2.4e-182
Havcr2	171285	hepatitis A virus cellular receptor 2	8.114	3.4e-174
Plek	56193	pleckstrin	4.731	6.7e-171
Nedd4l	83814	neural precursor cell expressed, developmentally down-regulated gene 4-like	-3.610	3.8e-165
Tmem163	72160	transmembrane protein 163	4.112	1.1e-163
Osbpl3	71720	oxysterol binding protein-like 3	4.196	1.2e-161
Kcnk5	16529	potassium channel, subfamily K, member 5	4.237	1.3e-161
St14	19143	suppression of tumorigenicity 14 (colon carcinoma)	4.422	1.3e-158
Ifitm1	68713	interferon induced transmembrane protein 1	8.898	4.9e-152
Gzmb	14939	granzyme B	8.333	8.5e-152
Hip1r	29816	huntingtin interacting protein 1 related	2.537	1.8e-151
Id2	15902	inhibitor of DNA binding 2	2.783	2.0e-147
Ehd4	98878	EH-domain containing 4	2.793	3.3e-146
Ccr7	12775	chemokine (C-C motif) receptor 7	-5.120	4.4e-145
Myo1f	17916	myosin IF	2.436	1.4e-142
Adam8	11501	a disintegrin and metallopeptidase domain 8	5.939	1.5e-141
Spag5	54141	sperm associated antigen 5	4.949	7.9e-139
Bub1b	12236	BUB1B, mitotic checkpoint serine/threonine kinase	4.547	3.1e-138
Tdrp	72148	testis development related protein	-5.403	1.5e-137
Il6ra	16194	interleukin 6 receptor, alpha	-4.013	1.9e-136
Dtl	76843	denticleless E3 ubiquitin protein ligase	3.245	4.6e-136
Serpinb6b	20708	serine (or cysteine) peptidase inhibitor, clade B, member 6b	4.806	8.9e-136
Kif11	16551	kinesin family member 11	4.680	2.0e-135
Icosl	50723	icos ligand	2.043	3.2e-135
Slamf7	75345	SLAM family member 7	2.881	5.6e-132
Top2a	21973	topoisomerase (DNA) II alpha	4.208	2.4e-130
Ncaph	215387	non-SMC condensin I complex, subunit H	4.313	9.6e-129
Ttc28	209683	tetratricopeptide repeat domain 28	-4.244	3.3e-127
Hip1	215114	huntingtin interacting protein 1	5.339	8.4e-127
BC106179	NA	cDNA sequence BC106179	-5.004	1.4e-126
Tpx2	72119	TPX2, microtubule-associated	4.814	3.2e-125
Prr11	270906	proline rich 11	5.338	1.4e-123
Patj	12695	PATJ, crumbs cell polarity complex component	-3.114	6.6e-122
Sell	20343	selectin, lymphocyte	-3.572	8.7e-121
Efhd2	27984	EF hand domain containing 2	2.480	1.1e-120
Galnt3	14425	polypeptide N-acetylgalactosaminyltransferase 3	7.656	8.0e-119
Tbc1d16	207592	TBC1 domain family, member 16	-3.680	1.3e-118
Plekha1	101476	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	-2.585	1.6e-118
Ccna2	12428	cyclin A2	4.972	5.1e-118
2610318N02Rik	70458	RIKEN cDNA 2610318N02 gene	3.840	2.2e-117
Sytl3	83672	synaptotagmin-like 3	3.122	4.9e-117
Kif15	209737	kinesin family member 15	4.401	5.1e-117
Anxa2	12306	annexin A2	3.958	6.0e-116
1500009L16Rik	69784	RIKEN cDNA 1500009L16 gene	5.972	2.8e-115
Il18rap	16174	interleukin 18 receptor accessory protein	3.643	3.5e-115
Xdh	22436	xanthine dehydrogenase	2.514	5.4e-115
Gna15	14676	guanine nucleotide binding protein, alpha 15	3.554	6.3e-115
Adap1	231821	ArfGAP with dual PH domains 1	3.929	7.6e-115
Vipr1	22354	vasoactive intestinal peptide receptor 1	-4.598	3.7e-114
Aurkb	20877	aurora kinase B	4.810	6.0e-114
Cdca8	52276	cell division cycle associated 8	4.559	9.7e-114
Fkbp5	14229	FK506 binding protein 5	3.050	2.4e-113
Dsp	109620	desmoplakin	5.531	2.5e-112
Birc5	11799	baculoviral IAP repeat-containing 5	4.745	3.4e-112
Xkrx	331524	X-linked Kx blood group related, X-linked	-6.061	5.3e-112
Bspry	192120	B-box and SPRY domain containing	4.812	5.6e-112
Cep55	74107	centrosomal protein 55	4.560	6.5e-112
Kif4	16571	kinesin family member 4	4.907	7.5e-112
Cdca2	108912	cell division cycle associated 2	4.182	9.5e-111
Crmp1	12933	collapsin response mediator protein 1	2.988	1.4e-110
Kif20a	19348	kinesin family member 20A	4.272	1.4e-109
Nsmf	56876	NMDA receptor synaptonuclear signaling and neuronal migration factor	1.858	4.2e-109
Sema7a	20361	sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A	4.453	2.9e-108
Pif1	208084	PIF1 5’-to-3’ DNA helicase	5.266	3.4e-108
Chst15	77590	carbohydrate sulfotransferase 15	-3.082	3.8e-108
Atp1b1	11931	ATPase, Na+/K+ transporting, beta 1 polypeptide	-4.937	7.3e-108
Acvr1b	11479	activin A receptor, type 1B	-2.358	8.6e-108
Mcm10	70024	minichromosome maintenance 10 replication initiation factor	4.332	9.8e-108
Kif18b	70218	kinesin family member 18B	4.932	1.0e-107
Hells	15201	helicase, lymphoid specific	2.714	1.6e-107
Fam129b	227737	family with sequence similarity 129, member B	3.846	1.6e-107
Kcna2	16490	potassium voltage-gated channel, shaker-related subfamily, member 2	-4.919	7.6e-107
Stil	20460	Scl/Tal1 interrupting locus	4.821	2.6e-106
Kif2c	73804	kinesin family member 2C	4.892	3.5e-106
H2-Ob	15002	histocompatibility 2, O region beta locus	-4.766	1.7e-105
AA467197	433470	expressed sequence AA467197	7.644	1.1e-104
Epas1	13819	endothelial PAS domain protein 1	3.837	3.2e-104
Paqr4	76498	progestin and adipoQ receptor family member IV	3.409	3.7e-104
Rad51	19361	RAD51 recombinase	3.941	3.8e-104
Itgax	16411	integrin alpha X	6.272	4.1e-104
Rapgef4	56508	Rap guanine nucleotide exchange factor (GEF) 4	-4.563	4.6e-104
Uhrf1	18140	ubiquitin-like, containing PHD and RING finger domains, 1	3.612	9.5e-104
Clspn	269582	claspin	4.313	1.7e-103
Mapre2	212307	microtubule-associated protein, RP/EB family, member 2	1.928	2.1e-103
Usp28	235323	ubiquitin specific peptidase 28	-2.510	1.8e-102
Cnr2	12802	cannabinoid receptor 2 (macrophage)	-2.441	3.4e-102
Ncapg2	76044	non-SMC condensin II complex, subunit G2	3.983	6.7e-102
Il6st	16195	interleukin 6 signal transducer	-3.021	6.8e-102
Cdca3	14793	cell division cycle associated 3	4.423	1.2e-101
Lrig1	16206	leucine-rich repeats and immunoglobulin-like domains 1	-4.369	5.6e-100
Nek2	18005	NIMA (never in mitosis gene a)-related expressed kinase 2	5.022	1.1e-99
Prc1	233406	protein regulator of cytokinesis 1	4.050	1.1e-99
Ifitm2	80876	interferon induced transmembrane protein 2	7.314	1.3e-99
Dna2	327762	DNA replication helicase/nuclease 2	4.394	1.8e-99
St8sia1	20449	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	-3.438	2.2e-99
Slc16a5	217316	solute carrier family 16 (monocarboxylic acid transporters), member 5	-5.206	2.7e-99
Rflnb	76566	refilin B	-3.169	1.5e-98
Cnksr3	215748	Cnksr family member 3	-4.217	1.8e-98
Shcbp1	20419	Shc SH2-domain binding protein 1	4.584	2.2e-98
Hmmr	15366	hyaluronan mediated motility receptor (RHAMM)	4.948	2.0e-96
Ckap2l	70466	cytoskeleton associated protein 2-like	4.796	2.2e-96
Cdc6	23834	cell division cycle 6	3.926	2.8e-96
Fhl2	14200	four and a half LIM domains 2	4.117	5.3e-96
Serpinb9	20723	serine (or cysteine) peptidase inhibitor, clade B, member 9	4.050	6.6e-96
Nuf2	66977	NUF2, NDC80 kinetochore complex component	4.651	2.3e-95
Ube2c	68612	ubiquitin-conjugating enzyme E2C	5.075	4.1e-95
Mis18bp1	217653	MIS18 binding protein 1	4.249	2.1e-94
Lmnb1	16906	lamin B1	2.896	2.8e-94
Ildr1	106347	immunoglobulin-like domain containing receptor 1	2.784	3.9e-93
Rrm2	20135	ribonucleotide reductase M2	4.225	4.3e-93
Aspm	12316	abnormal spindle microtubule assembly	4.918	1.7e-92
Tacc3	21335	transforming, acidic coiled-coil containing protein 3	3.853	9.5e-92
Arsb	11881	arylsulfatase B	2.963	1.2e-91
Cdc45	12544	cell division cycle 45	3.454	1.4e-91
Parp8	52552	poly (ADP-ribose) polymerase family, member 8	-2.581	2.0e-91
Ccnb2	12442	cyclin B2	4.816	2.1e-91
Ncapg	54392	non-SMC condensin I complex, subunit G	4.474	3.5e-91
Sema4b	20352	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	-1.722	1.2e-90
Gldc	104174	glycine decarboxylase	7.154	1.5e-90
Cacna2d4	319734	calcium channel, voltage-dependent, alpha 2/delta subunit 4	-3.813	1.6e-90
Kif14	381293	kinesin family member 14	4.909	2.0e-90
Sapcd2	72080	suppressor APC domain containing 2	5.314	1.4e-89
Plk1	18817	polo like kinase 1	4.514	1.9e-89
Ncapd2	68298	non-SMC condensin I complex, subunit D2	2.957	2.4e-89
Mybl2	17865	myeloblastosis oncogene-like 2	4.234	7.3e-89
Runx2	12393	runt related transcription factor 2	3.450	7.6e-89
Neil3	234258	nei like 3 (E. coli)	4.580	8.5e-89
Kntc1	208628	kinetochore associated 1	3.861	9.7e-89
A630014C17Rik	NA	RIKEN cDNA A630014C17 gene	-3.665	1.1e-88
Iqgap3	404710	IQ motif containing GTPase activating protein 3	4.803	1.1e-88
Troap	78733	trophinin associated protein	4.779	3.2e-88
Cdca5	67849	cell division cycle associated 5	4.256	5.8e-88
Mki67	17345	antigen identified by monoclonal antibody Ki 67	4.791	9.3e-88
Rbm47	245945	RNA binding motif protein 47	5.146	1.2e-87
Zwilch	68014	zwilch kinetochore protein	2.954	4.9e-87
Cdk1	12534	cyclin-dependent kinase 1	4.637	5.4e-87
Cenpe	229841	centromere protein E	4.757	7.8e-87
Peg13	NA	paternally expressed 13	-3.475	1.0e-86
Ptms	69202	parathymosin	2.409	1.1e-86
Vim	22352	vimentin	2.634	1.3e-86
Casp3	12367	caspase 3	3.142	1.4e-86
Rad54b	623474	RAD54 homolog B (S. cerevisiae)	4.029	1.6e-86
Ptpn3	545622	protein tyrosine phosphatase, non-receptor type 3	3.202	3.4e-86
Prr5	109270	proline rich 5 (renal)	7.024	3.6e-86
Anxa4	11746	annexin A4	3.156	5.7e-86
Pclaf	68026	PCNA clamp associated factor	4.522	6.8e-86
Ajuba	16475	ajuba LIM protein	5.202	7.9e-86
Popdc2	64082	popeye domain containing 2	5.263	2.6e-85
Zfp395	380912	zinc finger protein 395	-2.442	2.9e-85
Ift80	68259	intraflagellar transport 80	-2.984	4.6e-85
Pik3ap1	83490	phosphoinositide-3-kinase adaptor protein 1	4.607	4.8e-85
E2f1	13555	E2F transcription factor 1	3.032	3.0e-84
Pmaip1	58801	phorbol-12-myristate-13-acetate-induced protein 1	3.951	3.5e-84
Sgo2a	68549	shugoshin 2A	4.364	3.9e-84
Scml4	268297	Scm polycomb group protein like 4	-2.218	5.0e-84
Parpbp	75317	PARP1 binding protein	4.193	5.7e-84
Cd2ap	12488	CD2-associated protein	-1.753	8.0e-84
AI506816	NA	expressed sequence AI506816	2.209	1.1e-83
Mgst2	211666	microsomal glutathione S-transferase 2	-2.485	1.6e-83
Klrc1	16641	killer cell lectin-like receptor subfamily C, member 1	5.138	2.8e-83
Gprc5b	64297	G protein-coupled receptor, family C, group 5, member B	-6.657	4.2e-83
Pakap	677884	paralemmin A kinase anchor protein	-4.118	5.3e-83
Cenpn	72155	centromere protein N	3.529	5.8e-83
Mob3b	214944	MOB kinase activator 3B	-2.309	7.9e-83
Exo1	26909	exonuclease 1	3.468	8.7e-83
Kcnh2	16511	potassium voltage-gated channel, subfamily H (eag-related), member 2	-4.019	9.0e-83
Podnl1	244550	podocan-like 1	2.552	1.2e-82
Cdc20	107995	cell division cycle 20	3.987	1.2e-82
Melk	17279	maternal embryonic leucine zipper kinase	4.033	1.3e-82
Nusap1	108907	nucleolar and spindle associated protein 1	4.374	1.5e-82
Nrp2	18187	neuropilin 2	-3.489	1.7e-82
Igf2bp3	140488	insulin-like growth factor 2 mRNA binding protein 3	2.977	3.7e-82
Cit	12704	citron	4.398	9.5e-81
E2f2	242705	E2F transcription factor 2	2.803	1.1e-80
Ska3	219114	spindle and kinetochore associated complex subunit 3	3.902	1.3e-80
Slco4a1	108115	solute carrier organic anion transporter family, member 4a1	4.621	1.9e-80
Bard1	12021	BRCA1 associated RING domain 1	2.915	1.9e-80
Syde1	71709	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	-3.807	3.4e-80
Slc2a3	20527	solute carrier family 2 (facilitated glucose transporter), member 3	1.538	4.1e-80
Litaf	56722	LPS-induced TN factor	3.254	1.7e-79
Bach2	12014	BTB and CNC homology, basic leucine zipper transcription factor 2	-4.232	2.5e-79
Ttc3	22129	tetratricopeptide repeat domain 3	-1.792	2.8e-79
Pimreg	109212	PICALM interacting mitotic regulator	4.738	4.7e-79
Ifi208	100033459	interferon activated gene 208	-3.492	5.3e-79
Il12rb2	16162	interleukin 12 receptor, beta 2	4.291	6.8e-79
Hk2	15277	hexokinase 2	3.319	8.0e-79
Trip13	69716	thyroid hormone receptor interactor 13	4.230	9.2e-79
Whrn	73750	whirlin	-2.989	9.7e-79
Kif22	110033	kinesin family member 22	3.356	9.8e-79
Knl1	76464	kinetochore scaffold 1	4.357	1.2e-78
Brip1	237911	BRCA1 interacting protein C-terminal helicase 1	3.231	1.2e-78
Slc28a2b	381417	solute carrier family 28 member 2b	-3.944	1.4e-78
Ifitm3	66141	interferon induced transmembrane protein 3	6.597	1.6e-78
Ggt5	23887	gamma-glutamyltransferase 5	-3.596	2.1e-78
Hrob	217216	homologous recombination factor with OB-fold	4.883	2.4e-78
Sipa1l2	244668	signal-induced proliferation-associated 1 like 2	-2.666	3.2e-78

Table: Results for wt.TxB_v_wt.noTx

5313 differentially expressed genes. View limited to maximum of 200 rows in html report.

Gene	entrezgene_id	description	log2 (FC)	q-val
Dtl	76843	denticleless E3 ubiquitin protein ligase	3.738	5.1e-180
Top2a	21973	topoisomerase (DNA) II alpha	4.318	4.1e-136
Spag5	54141	sperm associated antigen 5	4.754	4.4e-127
Kif11	16551	kinesin family member 11	4.547	6.2e-127
Cdc6	23834	cell division cycle 6	4.518	1.5e-126
Kntc1	208628	kinetochore associated 1	4.536	1.7e-121
E2f1	13555	E2F transcription factor 1	3.582	8.8e-117
Bub1b	12236	BUB1B, mitotic checkpoint serine/threonine kinase	4.184	2.7e-116
Uhrf1	18140	ubiquitin-like, containing PHD and RING finger domains, 1	3.836	4.4e-116
Mcm10	70024	minichromosome maintenance 10 replication initiation factor	4.511	4.9e-116
Kif15	209737	kinesin family member 15	4.370	1.2e-114
Hells	15201	helicase, lymphoid specific	2.783	3.5e-112
Ncapg2	76044	non-SMC condensin II complex, subunit G2	4.156	3.8e-110
Clspn	269582	claspin	4.345	2.9e-104
Ccna2	12428	cyclin A2	4.680	5.8e-104
Tpx2	72119	TPX2, microtubule-associated	4.389	1.6e-103
Ncaph	215387	non-SMC condensin I complex, subunit H	3.858	2.4e-102
Stil	20460	Scl/Tal1 interrupting locus	4.721	3.7e-101
Iqgap3	404710	IQ motif containing GTPase activating protein 3	5.148	3.7e-101
Rad54b	623474	RAD54 homolog B (S. cerevisiae)	4.355	1.5e-100
Neil3	234258	nei like 3 (E. coli)	4.861	2.3e-99
Rad51	19361	RAD51 recombinase	3.854	7.2e-99
Rrm2	20135	ribonucleotide reductase M2	4.353	3.9e-98
Mki67	17345	antigen identified by monoclonal antibody Ki 67	5.069	1.6e-97
Kif18b	70218	kinesin family member 18B	4.705	2.1e-97
Aurkb	20877	aurora kinase B	4.457	2.7e-97
Kif4	16571	kinesin family member 4	4.589	2.7e-97
Prc1	233406	protein regulator of cytokinesis 1	3.957	1.5e-94
Zwilch	68014	zwilch kinetochore protein	3.081	6.8e-94
Cdca8	52276	cell division cycle associated 8	4.150	1.1e-93
E2f2	242705	E2F transcription factor 2	3.025	2.9e-93
Birc5	11799	baculoviral IAP repeat-containing 5	4.327	8.8e-93
Exo1	26909	exonuclease 1	3.650	4.5e-91
Cdc45	12544	cell division cycle 45	3.455	5.3e-91
Dna2	327762	DNA replication helicase/nuclease 2	4.208	1.5e-90
Mis18bp1	217653	MIS18 binding protein 1	4.174	2.2e-90
Apol11b	328563	apolipoprotein L 11b	10.913	5.3e-89
Prr11	270906	proline rich 11	4.534	1.2e-88
Esco2	71988	establishment of sister chromatid cohesion N-acetyltransferase 2	4.759	1.0e-87
Pask	269224	PAS domain containing serine/threonine kinase	3.762	1.7e-86
Ncapg	54392	non-SMC condensin I complex, subunit G	4.355	8.3e-86
Anln	68743	anillin, actin binding protein	4.555	1.7e-85
Mybl2	17865	myeloblastosis oncogene-like 2	4.163	2.2e-85
Kif14	381293	kinesin family member 14	4.771	6.9e-85
E2f8	108961	E2F transcription factor 8	4.909	7.2e-85
Cdca3	14793	cell division cycle associated 3	4.031	6.4e-84
Chek1	12649	checkpoint kinase 1	3.649	1.5e-83
Shcbp1	20419	Shc SH2-domain binding protein 1	4.239	2.1e-83
Hmmr	15366	hyaluronan mediated motility receptor (RHAMM)	4.600	7.8e-83
Ube2c	68612	ubiquitin-conjugating enzyme E2C	4.738	1.9e-82
Kif20a	19348	kinesin family member 20A	3.715	1.9e-82
Cdca2	108912	cell division cycle associated 2	3.620	1.9e-82
Hba-a2	110257	hemoglobin alpha, adult chain 2	10.888	2.8e-81
Nuf2	66977	NUF2, NDC80 kinetochore complex component	4.306	3.1e-81
Zfp367	238673	zinc finger protein 367	2.398	3.8e-81
Cd22	12483	CD22 antigen	3.694	4.6e-81
Knl1	76464	kinetochore scaffold 1	4.436	5.1e-81
Aspm	12316	abnormal spindle microtubule assembly	4.614	5.1e-81
Pif1	208084	PIF1 5’-to-3’ DNA helicase	4.545	5.7e-80
Brip1	237911	BRCA1 interacting protein C-terminal helicase 1	3.267	7.9e-80
Nusap1	108907	nucleolar and spindle associated protein 1	4.292	5.5e-79
Cdk1	12534	cyclin-dependent kinase 1	4.429	6.4e-79
Ckap2l	70466	cytoskeleton associated protein 2-like	4.348	8.6e-79
Cit	12704	citron	4.347	2.1e-78
Cdca5	67849	cell division cycle associated 5	4.031	2.2e-78
Hbb-bs	15129100503605	hemoglobin, beta adult s chain	10.757	2.5e-78
Hbb-bt	101488143	hemoglobin, beta adult t chain	10.837	1.4e-77
Brca1	12189	breast cancer 1, early onset	3.435	2.5e-77
Pole	18973	polymerase (DNA directed), epsilon	2.959	1.3e-76
Kif2c	73804	kinesin family member 2C	4.162	2.0e-76
Cenpe	229841	centromere protein E	4.448	1.6e-75
Bard1	12021	BRCA1 associated RING domain 1	2.822	7.8e-75
Fignl1	60530	fidgetin-like 1	3.955	9.3e-75
Cenpi	102920	centromere protein I	4.051	1.2e-74
Nek2	18005	NIMA (never in mitosis gene a)-related expressed kinase 2	4.352	1.8e-74
Tmcc2	68875	transmembrane and coiled-coil domains 2	6.731	2.0e-74
Ticrr	77011	TOPBP1-interacting checkpoint and replication regulator	3.997	5.5e-74
Hrob	217216	homologous recombination factor with OB-fold	4.751	1.4e-73
Cep55	74107	centrosomal protein 55	3.713	1.5e-73
Wee1	22390	WEE 1 homolog 1 (S. pombe)	2.835	2.6e-73
Cenpn	72155	centromere protein N	3.324	7.4e-73
Cenpf	108000	centromere protein F	4.959	1.8e-72
Troap	78733	trophinin associated protein	4.338	4.4e-72
Sgo2a	68549	shugoshin 2A	4.007	2.1e-70
Rad51ap1	19362	RAD51 associated protein 1	3.966	2.7e-70
Espl1	105988	extra spindle pole bodies 1, separase	4.494	2.7e-70
Rad54l	19366	RAD54 like (S. cerevisiae)	3.186	3.5e-70
Lig1	16881	ligase I, DNA, ATP-dependent	2.758	5.0e-70
Tacc3	21335	transforming, acidic coiled-coil containing protein 3	3.366	1.1e-69
Plk1	18817	polo like kinase 1	3.981	3.0e-69
E2f7	52679	E2F transcription factor 7	4.780	4.4e-69
Slfn14	237890	schlafen 14	9.010	6.4e-69
Slc4a1	20533	solute carrier family 4 (anion exchanger), member 1	10.493	4.5e-68
Ect2	13605	ect2 oncogene	3.393	5.5e-68
Bub1	12235	BUB1, mitotic checkpoint serine/threonine kinase	4.499	6.8e-68
Ncapd2	68298	non-SMC condensin I complex, subunit D2	2.582	7.4e-68
Chsy1	269941	chondroitin sulfate synthase 1	1.770	1.3e-67
H2ac10	319173	H2A clustered histone 10	4.262	1.5e-67
Chaf1a	27221	chromatin assembly factor 1, subunit A (p150)	3.368	7.7e-67
Parpbp	75317	PARP1 binding protein	3.755	9.6e-67
Nsl1	381318	NSL1, MIS12 kinetochore complex component	3.218	1.1e-66
Foxm1	14235	forkhead box M1	3.623	1.6e-66
Fancd2	211651	Fanconi anemia, complementation group D2	3.840	1.8e-66
Epb42	13828	erythrocyte membrane protein band 4.2	7.102	1.9e-66
Fanca	14087	Fanconi anemia, complementation group A	3.506	2.0e-66
Ccne2	12448	cyclin E2	3.974	2.5e-66
Hba-a1	15122	hemoglobin alpha, adult chain 1	10.217	4.6e-66
Melk	17279	maternal embryonic leucine zipper kinase	3.612	9.9e-66
Tcf19	106795	transcription factor 19	2.844	4.4e-65
Ccne1	12447	cyclin E1	2.330	5.2e-65
Pbk	52033	PDZ binding kinase	4.794	6.7e-65
Tk1	21877	thymidine kinase 1	3.138	1.4e-64
Asf1b	66929	anti-silencing function 1B histone chaperone	3.198	2.7e-64
Pclaf	68026	PCNA clamp associated factor	3.918	3.2e-64
Ccr5	12774	chemokine (C-C motif) receptor 5	2.871	4.9e-64
Ccnf	12449	cyclin F	3.948	1.3e-63
Cip2a	224171	cell proliferation regulating inhibitor of protein phosphatase 2A	3.438	2.4e-63
Dlgap5	218977	DLG associated protein 5	3.232	3.0e-63
Map3k8	26410	mitogen-activated protein kinase kinase kinase 8	1.889	6.6e-63
Spc25	66442	SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)	4.224	2.0e-62
Orc1	18392	origin recognition complex, subunit 1	3.960	2.1e-62
H3c15	97114	H3 clustered histone 15	4.386	3.0e-62
Atad5	237877	ATPase family, AAA domain containing 5	2.677	3.3e-62
Drc1	381738	dynein regulatory complex subunit 1	3.799	3.0e-61
Kif23	71819	kinesin family member 23	2.832	4.2e-61
Ccnb2	12442	cyclin B2	3.939	6.2e-61
Alas2	11656	aminolevulinic acid synthase 2, erythroid	8.372	1.5e-60
Arhgap11a	228482	Rho GTPase activating protein 11A	2.940	1.6e-60
Ube2l6	56791	ubiquitin-conjugating enzyme E2L 6	4.577	3.8e-60
Ska3	219114	spindle and kinetochore associated complex subunit 3	3.382	7.0e-60
Ttk	22137	Ttk protein kinase	4.500	1.7e-59
Diaph3	56419	diaphanous related formin 3	3.541	3.7e-59
Chtf18	214901	CTF18, chromosome transmission fidelity factor 18	2.670	6.5e-59
2610318N02Rik	70458	RIKEN cDNA 2610318N02 gene	2.754	1.1e-58
Spc24	67629	SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)	3.907	1.2e-58
Ypel4	241525	yippee like 4	8.514	7.4e-58
AC160336.1	NA	novel transcript	-1.809	1.0e-57
Phf19	74016	PHD finger protein 19	2.743	2.1e-57
Kif22	110033	kinesin family member 22	2.866	4.2e-57
Pimreg	109212	PICALM interacting mitotic regulator	4.044	4.7e-57
Lmnb1	16906	lamin B1	2.251	7.8e-57
Tyms	22171	thymidylate synthase	3.023	1.1e-56
Specc1	432572	sperm antigen with calponin homology and coiled-coil domains 1	6.137	4.2e-56
Sapcd2	72080	suppressor APC domain containing 2	4.222	6.8e-56
Plek	56193	pleckstrin	2.704	7.3e-56
Gtse1	29870	G two S phase expressed protein 1	3.497	1.1e-55
Cdc25c	12532	cell division cycle 25C	4.641	1.1e-55
Enkd1	102124	enkurin domain containing 1	2.711	1.7e-55
St3gal5	20454	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	4.835	2.2e-55
BC106179	NA	cDNA sequence BC106179	-2.513	4.1e-55
Nsd2	107823	nuclear receptor binding SET domain protein 2	2.264	4.6e-55
Slc43a3	58207	solute carrier family 43, member 3	4.219	5.1e-55
Cks2	66197	CDC28 protein kinase regulatory subunit 2	3.337	1.0e-54
Mms22l	212377	MMS22-like, DNA repair protein	2.071	1.6e-54
Arhgap19	71085	Rho GTPase activating protein 19	3.400	2.1e-54
Traip	22036	TRAF-interacting protein	2.737	2.3e-54
Cdc20	107995	cell division cycle 20	3.219	1.3e-53
Sgo1	72415	shugoshin 1	3.343	1.9e-53
H2bc9	319182	H2B clustered histone 9	3.812	2.9e-53
H2ac4	319172	H2A clustered histone 4	4.074	2.9e-52
Ckap2	80986	cytoskeleton associated protein 2	3.734	4.6e-52
Mxd3	17121	Max dimerization protein 3	3.358	5.9e-52
Trip13	69716	thyroid hormone receptor interactor 13	3.448	1.0e-51
Incenp	16319	inner centromere protein	2.465	1.2e-51
Smc2	14211	structural maintenance of chromosomes 2	2.480	1.6e-51
Ccnb1	268697	cyclin B1	4.160	5.8e-51
Bcl2l1	12048	BCL2-like 1	1.856	9.0e-51
Ehd4	98878	EH-domain containing 4	1.661	1.0e-50
Samd3	268288	sterile alpha motif domain containing 3	2.423	1.0e-50
Apol8	239552	apolipoprotein L 8	6.687	1.8e-50
H2ac15	319169	H2A clustered histone 15	3.543	1.2e-49
Pola1	18968	polymerase (DNA directed), alpha 1	2.409	1.7e-49
Ifitm1	68713	interferon induced transmembrane protein 1	5.084	1.8e-49
Rbbp8	225182	retinoblastoma binding protein 8, endonuclease	1.742	4.1e-49
H2bc14	319186	H2B clustered histone 14	3.872	4.1e-49
H2ac11	319167	H2A clustered histone 11	3.744	6.9e-49
Depdc1b	218581	DEP domain containing 1B	2.854	1.6e-48
Rsad2	58185	radical S-adenosyl methionine domain containing 2	4.304	1.7e-48
Itsn1	16443	intersectin 1 (SH3 domain protein 1A)	3.575	3.3e-48
Kdm5b	75605	lysine (K)-specific demethylase 5B	-1.410	4.5e-48
Myo1f	17916	myosin IF	1.414	4.9e-48
Fhdc1	229474	FH2 domain containing 1	4.979	7.4e-48
Spta1	20739	spectrin alpha, erythrocytic 1	9.138	1.2e-47
Trim10	19824	tripartite motif-containing 10	9.091	1.4e-47
Eme1	268465	essential meiotic structure-specific endonuclease 1	2.653	1.7e-47
Slc25a37	67712	solute carrier family 25, member 37	3.804	1.8e-47
Ska1	66468	spindle and kinetochore associated complex subunit 1	4.583	2.3e-47
Hemgn	93966	hemogen	7.751	2.9e-47
Dapk2	13143	death-associated protein kinase 2	3.929	3.1e-47
Dhfr	13361	dihydrofolate reductase	2.670	3.7e-47
Dscc1	72107	DNA replication and sister chromatid cohesion 1	2.622	7.5e-47
Psrc1	56742	proline/serine-rich coiled-coil 1	3.214	8.1e-47
Gypa	14934	glycophorin A	9.745	1.0e-46
H2bc13	319185	H2B clustered histone 13	3.738	1.1e-46
Mtfr2	71804	mitochondrial fission regulator 2	3.882	1.2e-46
H2bc11	319183	H2B clustered histone 11	3.778	1.2e-46
Wdhd1	218973	WD repeat and HMG-box DNA binding protein 1	2.057	2.5e-46
Kcnk5	16529	potassium channel, subfamily K, member 5	2.282	3.4e-46
Stom	13830	stomatin	5.666	5.4e-46
Dyrk3	226419	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	5.767	8.9e-46

4 Follow-Up

We are happy to answer any questions you may have and/or set-up a meeting to go over the results of your experiment.

In addition, if you would like more detailed output (e.g. FastQC and/or DESeq2 detailed output, etc.) please let us know. For information on the RNA-seq workflows and a comparison between available differential expression tools, please refer to (Zhang et al., 2014).

• Bioinformatics Core bioinformatics@umich.edu

5 Acknowledgement for Publication

It is important to document use of each Biomedical Research Core Facility by investigators in publications. This facilitates efforts to obtain funding for our Cores and their continued functioning. Please recognize the core’s contribution in the Acknowledgment section of your publications.

“We acknowledge support from the Bioinformatics Core of the University of Michigan Medical School’s Biomedical Research Core Facilities (RRID:SCR_019168).”

If core staff have added scientific value to your project — made intellectual contributions in design, analysis and interpretation of data and/or manuscript writing, then please consider including them as co-authors in your publications.

6 Appendices

6.1 Differential Expression Files

6.1.1 DESeq2 Counts

These are counts extracted from the DESeq2 object after filtering / normalization.

counts/deseq2_raw_counts.txt

raw_counts are the counts used in DESeq2, exactly as they are in the DESeq2 object (after filtering low/nonexpressed genes).

counts/deseq2_depth_normalized_counts.txt

These are the counts from above normalized to the sequencing depth by DESeq2.

counts/deseq2_rlog_normalized_counts.txt

Same as above, but normalized using the DESeq2’s regularized log transformation to normalize.

counts/deseq2_rlog_normalized_counts.annot.txt

Rlog normalized counts as described above, with additional annotation columns

6.1.2 Count-Level QC

These use the count data in various plots to illustrate the count-level QC. The plots are color-labeled based on phonotype / characteristic information from the experimental design. The versions with different color labels will each reside in their own folder.

plots_labeled_by_pheno/{phenotype}/BoxPlot_raw.{pdf,png}

BoxPlot of count data for each sample in the experiment.

plots_labeled_by_pheno/{phenotype}/BoxPlot_rlog.{pdf,png}

Boxplot of count data for each sample after rlog transformation.

plots_labeled_by_pheno/Heatmap_TopExp.{pdf,png}

Heatmap of count data, with data from up to 500 of the most highly expressed genes. Rows represent genes, columns represent samples.

plots_labeled_by_pheno/Heatmap_TopVar.{pdf,png}

Heatmap of count data, with data from up to 500 of the most variably expressed genes (across the samples). Rows represent genes, columns represent samples.

plots_labeled_by_pheno/{phenotype}/PCAplot_{pcs}_top{ngenes}.{pdf,png}

PCA plots of count data. {pcs} represents the principal components plotted 1 & 2 or 2 & 3. Top {ngenes} represents the number of highly expressed genes used in the PCA.

plots_labeled_by_pheno/SampleHeatmap.{pdf,png}

Heatmap of the euclidian distance between samples, based on the aggregated count data.

plots_labeled_by_pheno/{phenotype}/ScreePlot_top{ngenes}.{pdf,png}

Scree plots of the count data. Top {ngenes} represents the number of highly expressed genes used in the plot.

6.1.3 DESeq2 Differential Expression Results

diffex_{model_name}/{comparison}.annot.txt

Output from DESeq2 differential expression analysis for a particular comparison, in plain tab-separated format, with additional annotations from BiomaRt

diffex_{model_name}/{comparison}.annot.xlsx

Output from DESeq2 differential expression analysis for a particular comparison, in xlsx format, with additional annotations from BiomaRt and hyperlinks to NCBI.

volcano_plots/VolcanoPlot_{comparison}.{pdf,png}

Volcano plots summarizing differential expression data for a particular comparison.

6.1.4 DESeq2 Summary

summary/deseq2_summary.txt

Summarized information from the different comparisons performed with DESeq2.

summary/deseq2_summary.xlsx

An Excel spreadsheet containing the same information as above, with an additional column of entrezgeneID hyperlinks when possible

References

Draghici,S. et al. (2007) A systems biology approach for pathway level analysis. Genome Research, 17, 1537–1545.

iPathwayGuide.

Love,M.I. et al. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 1–21.

Mi,H. et al. (2019) PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Research, 47, D419–D426.

Zhang,Z.H. et al. (2014) A comparative study of techniques for differential expression analysis on RNA-seq data. PLoS ONE, 9.