3.3 Differential expression analyses with DESeq2
3.3.1 VNN1 High VS Low
In the following subsections, samples were divided into two groups of same size (±1):
- High: those with VNN1 signal above median
- Low: those with VNN1 signal below median
Upregulated genes are those following VNN1 signal.
3.3.1.1 Projects subsets
3.3.1.1.1 TCGA-SARC
For the whole TCGA-SARC dataset, the differential expression analysis is done either considering only gender as covariate, or both gender and primary diagnosis.
3.3.1.1.1.1 Gender covariate
.](_main_files/figure-html/resultsDeseq2Vnn1HighVsLowProjectIdTcgaSarcGenderCovKnitPostDeseq2TemplatePlotVolcanoDeseq2-1.png)
Figure 3.179: Volcano plot. 1072 significant genes according to Pvalue < 0.05 and |log2FoldChange| > 2 are highlighted in red and available in this table.
- Enrichr results for all deregulated genes are available here
- Enrichr results for upregulated genes are available here
- Enrichr results for downregulated genes are available here
- g:Profiler results for all deregulated genes are available here
- g:Profiler results for all upregulated genes are available here
- g:Profiler results for all downregulated genes are available here
- g:Profiler results for comparison of the three queries above are available here