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DGE: Output

This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

  • deseq2 - Performs differential gene expression analysis
  • gsea - Runs GSEA on the results from DESeq2

deseq2

The DESeq2 package is used for differential gene expression analysis. The pipeline produces text files and plots with the results, as well as an HTML report that contains a summary of the DGE results. This report shows

  • a PCA plot
  • for each comparison (contrast)
  • MA and volcano plots
  • a heatmap
  • a table with the names, logFCs, pvalues and box plots for the top 100 differentially expressed genes. For example:

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gsea (Gene Set Enrichment Analysis)

GSEA is used to look for enrichment of gene sets at the top or bottom of the rnaked list of genes obtained from the DGE analysis. The hallmark gene sets from MSigDB is used by default.

  • For each comparison, the pipeline produces a folder with the typical results obtained from running GSEA, as well as a plot that summarizes the results:

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