Module 12: DE Annotations & Downsteam applications

Objectives

• Understand advantages of using gene ids when analyzing RNA-seq data.
• Given a list of ENSEMBL gene ids, add gene symbols and Entrez accessions.
• Generate common visualizations for differential expression comparisons
• Understand choosing thresholds for calling differentially expressed genes
• Discuss options for functional enrichments

Differential Expression Workflow

Here we will generate summary figures for our results and annotate our DE tables.

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Adding genome annotations

Since, gene symbols can change over time or be ambiguous we use, and recommend, using the EMSEMBL reference genome and ENSEMBL IDs for alignments and we’ve been working with tables and data where all genes are labeled only by their long ENSEMBL ID. However, this can make it difficult to quickly look for genes of interest.

Luckily, Bioconductor provides many tools and resources to facilitate access to genomic annotation resources.

To start, we will first load the biomaRt library and choose what reference we want to access. For a more detailed walk through of using biomaRt, this training module might be useful, including what to do when annotations are not 1:1 mappings.

We’ll start by loading the biomaRt library and calling the useEnsembl() function to select the database we’ll use to extract the information we need. This will download the mapping of ENSEMBL IDs to gene symbols, enabling us to eventually add the gene symbol column we want.

library('biomaRt')
ensembl = useEnsembl(dataset = 'mmusculus_gene_ensembl', biomart='ensembl')

Note - this process takes some time and will take up a larger amount of working memory so proceed with caution if you try to run these commands on a laptop with less than 4G of memory

To identify possible filters to restrict our data, we can use the listFilters function. To identify the attributes we want to retrive, we can use the listAttributes function. The best approach is to use list or search functions to help narrow down the available options.

head(listFilters(mart = ensembl), n = 20)
head(listAttributes(ensembl), n = 30)

We can access additional genomic annotations using the bioMart package. To identify we’ll structure our ‘query’ or search of the bioMart resources to use the ENSEMBL id from our alignment to add the gene symbols and gene description for each gene.

id_mapping = getBM(attributes=c('ensembl_gene_id', 'external_gene_name'),
      filters = 'ensembl_gene_id',
      values = row.names(assay(dds_fitted)),
      mart = ensembl)
# will take some time to run

# Preview the result
head(id_mapping)

     ensembl_gene_id external_gene_name
1 ENSMUSG00000000001              Gnai3
2 ENSMUSG00000000028              Cdc45
3 ENSMUSG00000000031                H19
4 ENSMUSG00000000037              Scml2
5 ENSMUSG00000000049               Apoh
6 ENSMUSG00000000056               Narf

Now that we have the ENSEMBL information and a gene symbol to match to our results, we can proceed in the smaller groups. As with the previous exercise, we have broken it into small steps with hints as needed.

Note: For additional information regarding bioMart, please consult the ENSEMBL bioMart vignette or the broader Bioconductor Annotation Resources vignette.

Look at the two data frames that are going to be needed: id_mapping and results_minus_vs_plus.

head(id_mapping)

     ensembl_gene_id external_gene_name
1 ENSMUSG00000000001              Gnai3
2 ENSMUSG00000000028              Cdc45
3 ENSMUSG00000000031                H19
4 ENSMUSG00000000037              Scml2
5 ENSMUSG00000000049               Apoh
6 ENSMUSG00000000056               Narf

head(results_minus_vs_plus)

log2 fold change (MLE): condition minus vs plus 
Wald test p-value: condition minus vs plus 
DataFrame with 6 rows and 7 columns
                      baseMean log2FoldChange     lfcSE      stat    pvalue      padj     call
                     <numeric>      <numeric> <numeric> <numeric> <numeric> <numeric> <factor>
ENSMUSG00000000001  1489.83039       0.297760  0.210310  1.415815  0.156830  0.868573       NS
ENSMUSG00000000028  1748.93544       0.226421  0.176795  1.280695  0.200301  0.902900       NS
ENSMUSG00000000031  2151.87715       0.457635  0.764579  0.598545  0.549476  0.995391       NS
ENSMUSG00000000037    24.91672       0.579130  0.561259  1.031840  0.302147  0.950613       NS
ENSMUSG00000000049     7.78377      -0.899483  1.553063 -0.579167  0.562476  0.998043       NS
ENSMUSG00000000056 19653.54030      -0.174048  0.203529 -0.855151  0.392468  0.982479       NS

We want to match the id column of results_minus_vs_plus to the ensembl_gene_id column of id_mapping, and once that match is found, we want to extract the external_gene_name column of id_mapping to get the gene symbol. Next, look at the documentation for dplyr::left_join() and merge the id_mapping table into the results_minus_vs_plus table on the columns ensembl_gene_id and external_gene_name.

results_minus_vs_plus_annotated = as_tibble(results_minus_vs_plus, rownames = "id") %>%
    left_join(id_mapping, by = c('id' = 'ensembl_gene_id'))
head(results_minus_vs_plus_annotated)

# A tibble: 6 × 9
  id                 baseMean log2FoldChange lfcSE   stat pvalue  padj call  external_gene_name
  <chr>                 <dbl>          <dbl> <dbl>  <dbl>  <dbl> <dbl> <fct> <chr>             
1 ENSMUSG00000000001  1490.            0.298 0.210  1.42   0.157 0.869 NS    Gnai3             
2 ENSMUSG00000000028  1749.            0.226 0.177  1.28   0.200 0.903 NS    Cdc45             
3 ENSMUSG00000000031  2152.            0.458 0.765  0.599  0.549 0.995 NS    H19               
4 ENSMUSG00000000037    24.9           0.579 0.561  1.03   0.302 0.951 NS    Scml2             
5 ENSMUSG00000000049     7.78         -0.899 1.55  -0.579  0.562 0.998 NS    Apoh              
6 ENSMUSG00000000056 19654.           -0.174 0.204 -0.855  0.392 0.982 NS    Narf              

We can use some of the tidyverse functions we’ve encountered previously to rename the external_gene_name column to symbol and to move it into the second column position? Hint: Because of the order of the packages we may have loaded, we’ll use dplyr::rename() and dplyr::select() instead of just the select() function. We can discuss this in a moment.

results_minus_vs_plus_annotated = results_minus_vs_plus_annotated %>%
    dplyr::rename('symbol' = 'external_gene_name') %>%
    dplyr::select(id, symbol, everything())
results_minus_vs_plus_annotated

# A tibble: 16,249 × 9
   id                 symbol baseMean log2FoldChange lfcSE   stat pvalue  padj call 
   <chr>              <chr>     <dbl>          <dbl> <dbl>  <dbl>  <dbl> <dbl> <fct>
 1 ENSMUSG00000000001 Gnai3   1490.            0.298 0.210  1.42   0.157 0.869 NS   
 2 ENSMUSG00000000028 Cdc45   1749.            0.226 0.177  1.28   0.200 0.903 NS   
 3 ENSMUSG00000000031 H19     2152.            0.458 0.765  0.599  0.549 0.995 NS   
 4 ENSMUSG00000000037 Scml2     24.9           0.579 0.561  1.03   0.302 0.951 NS   
 5 ENSMUSG00000000049 Apoh       7.78         -0.899 1.55  -0.579  0.562 0.998 NS   
 6 ENSMUSG00000000056 Narf   19654.           -0.174 0.204 -0.855  0.392 0.982 NS   
 7 ENSMUSG00000000078 Klf6     951.           -0.145 0.222 -0.652  0.515 0.992 NS   
 8 ENSMUSG00000000085 Scmh1    727.            0.265 0.275  0.964  0.335 0.966 NS   
 9 ENSMUSG00000000088 Cox5a   1427.           -0.272 0.212 -1.28   0.199 0.903 NS   
10 ENSMUSG00000000093 Tbx2      15.2           0.542 0.687  0.788  0.430 0.985 NS   
# … with 16,239 more rows

And now we have our differential expression results annotated with gene symbols, which can help in the interpretation of the results, and can be used in downstream analysis such as functional analysis.

Outputting results to file

A key aspect of our analysis is preserving the relevant datasets for both our records and for downstream applications, such as functional enrichments.

DE results table

We’ll write out our DE results, now that we’ve added information to the table to help us or our collaborators interpret the results.

write.csv(results_minus_vs_plus,
          row.names = FALSE,
          na = ".",
          file="outputs/tables/DE_results_minus_vs_plus.csv")

R session data

In addition to the individual RObj(s) we saved earlier, we can capture a snapshot our entire session using the save.image function. This can be loaded in the same manner as an individual Robj.

First, we’ll save our session info so we can reference the packages and versions used to generate these data.

session_summary <- sessionInfo()

save.image(file = "outputs/Robjs/DE_iron.RData")

Summary

In this section, we:

• Generated a volcano plot for our differential expression results
• Summarized our differential expression results
• Discussed choosing thresholds
• Annotated our tables of results to map gene IDs to gene symbols
• Saved our results to file

Overall takeaways

We’ve run through most of the building blocks needed to run a differential expression analysis and hopefully built up a better understanding of how differential expression comparisons work, particularly how experimental design can impact our results.

What to consider moving forward:

• How can I control for technical variation in my experimental design?
• How much variation is expected with a treatment group?
• What is my RNA quality, and how can that be optimized?
• Are there quality concerns for my sequencing data?
• What comparisons are relevant to my biological question?
• Are there covariates that should be considered?
• What will a differential expression analysis tell me?

Let’s pause here for general questions

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But how do we make sense of large numbers of DE genes?

A way to determine possible broader biological interpretations from the observed DE results, is functional enrichments. There are many options, such as some included in this discussion thread. Other common functional enrichments approaches are gene set enrichment analysis, aka GSEA, Database for Annotation, Visualization and Integrated Discovery, aka DAVID, Ingenity, and iPathway Guide

The University of Michigan has license and support for additional tools, such as Cytoscape, so we recommend reaching out to staff with Taubman Library to learn more about resources that might be application toyour research.

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Sources

• HBC DGE training module, part 1: https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html
• HBC DGE training module, part 2: https://hbctraining.github.io/DGE_workshop/lessons/05_DGE_DESeq2_analysis2.html
• DESeq2 vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#differential-expression-analysis
• Bioconductor Genomic Annotation resources: http://bioconductor.org/packages/devel/workflows/vignettes/annotation/inst/doc/Annotation_Resources.html
• BioMart vignette: https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html

Additional Resources

• MIDAS Reproduciblity Hub: https://midas.umich.edu/reproducibility-overview/
• ARC resources: https://arc-ts.umich.edu/
• Gene Set Enrichment Resources from Bioconductor: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/RNASeq2018/html/06_Gene_set_testing.nb.html
• Using HTSeq data with DESeq2: https://angus.readthedocs.io/en/2019/diff-ex-and-viz.html
• Detailed RNA-seq analysis paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096346/
• Overview of RNA-seq analysis considerations: https://academic-oup-com.proxy.lib.umich.edu/bfg/article/14/2/130/257370
• Alternative overview of DESeq2, including visualizations and functional enrichments: http://dputhier.github.io/jgb71e-polytech-bioinfo-app/practical/rna-seq_R/rnaseq_diff_Snf2.html

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Session Info

sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.52.0              knitr_1.41                  rmarkdown_2.18             
 [4] data.table_1.14.6           RColorBrewer_1.1-3          pheatmap_1.0.12            
 [7] ggrepel_0.9.2               DESeq2_1.36.0               SummarizedExperiment_1.26.1
[10] Biobase_2.56.0              MatrixGenerics_1.8.1        matrixStats_0.63.0         
[13] GenomicRanges_1.48.0        GenomeInfoDb_1.32.4         IRanges_2.30.1             
[16] S4Vectors_0.34.0            BiocGenerics_0.42.0         forcats_0.5.2              
[19] stringr_1.5.0               dplyr_1.0.10                purrr_0.3.5                
[22] readr_2.1.3                 tidyr_1.2.1                 tibble_3.1.8               
[25] ggplot2_3.4.0               tidyverse_1.3.2            

loaded via a namespace (and not attached):
 [1] googledrive_2.0.0      colorspace_2.0-3       ellipsis_0.3.2         XVector_0.36.0        
 [5] fs_1.5.2               rstudioapi_0.14        farver_2.1.1           bit64_4.0.5           
 [9] AnnotationDbi_1.58.0   fansi_1.0.3            lubridate_1.9.0        xml2_1.3.3            
[13] codetools_0.2-18       splines_4.2.0          cachem_1.0.6           geneplotter_1.74.0    
[17] jsonlite_1.8.3         broom_1.0.1            annotate_1.74.0        dbplyr_2.2.1          
[21] png_0.1-8              compiler_4.2.0         httr_1.4.4             backports_1.4.1       
[25] assertthat_0.2.1       Matrix_1.5-3           fastmap_1.1.0          gargle_1.2.1          
[29] cli_3.4.1              prettyunits_1.1.1      htmltools_0.5.3        tools_4.2.0           
[33] gtable_0.3.1           glue_1.6.2             GenomeInfoDbData_1.2.8 rappdirs_0.3.3        
[37] Rcpp_1.0.9             cellranger_1.1.0       jquerylib_0.1.4        vctrs_0.5.1           
[41] Biostrings_2.64.1      xfun_0.35              rvest_1.0.3            timechange_0.1.1      
[45] lifecycle_1.0.3        XML_3.99-0.13          googlesheets4_1.0.1    zlibbioc_1.42.0       
[49] scales_1.2.1           vroom_1.6.0            hms_1.1.2              parallel_4.2.0        
[53] curl_4.3.3             yaml_2.3.6             memoise_2.0.1          sass_0.4.4            
[57] stringi_1.7.8          RSQLite_2.2.19         highr_0.9              genefilter_1.78.0     
[61] filelock_1.0.2         BiocParallel_1.30.4    rlang_1.0.6            pkgconfig_2.0.3       
[65] bitops_1.0-7           evaluate_0.18          lattice_0.20-45        labeling_0.4.2        
[69] bit_4.0.5              tidyselect_1.2.0       magrittr_2.0.3         R6_2.5.1              
[73] generics_0.1.3         DelayedArray_0.22.0    DBI_1.1.3              pillar_1.8.1          
[77] haven_2.5.1            withr_2.5.0            survival_3.4-0         KEGGREST_1.36.3       
[81] RCurl_1.98-1.9         modelr_0.1.10          crayon_1.5.2           utf8_1.2.2            
[85] BiocFileCache_2.4.0    tzdb_0.3.0             progress_1.2.2         locfit_1.5-9.6        
[89] grid_4.2.0             readxl_1.4.1           blob_1.2.3             reprex_2.0.2          
[93] digest_0.6.30          xtable_1.8-4           munsell_0.5.0          bslib_0.4.1           

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