Goseq GO-KEGG Enrichment Analysis Workflow

Inputs dataset

The workflow need the following inputs:

• The DEG file:
  • A tabular file with first column the gene symbol and second column a boolean value whether the gene is a differentially expressed gene or not.
• The gene length file:
  • A tabular file with first column the gene symbol and second column the gene length of the genes.
  • You can create this file with Gene length and GC content tool. You will need a GTF file as input.
  • If you are using featureCounts you can set Create gene-length file to yes and get gene length as separate output.
• The KEGG file:
  • A tabular file with first column the Pathway ID and second column the Pathway name like:

    • ID  Name
      01100   Metabolic pathways - mmus
      01200   Carbon metabolism - mmus 
      

  • You can get this information from the KEGG database. For example:
    • mouse: https://rest.kegg.jp/list/pathway/mmu
    • human: https://rest.kegg.jp/list/pathway/hsa
• Genome: Select one of the available genomes
• Gene ID format: Select the format of your input genes (Ensembl, Entrez, or Symbol)

Processing

• The workflow will do a simple enrichment analysis with taking into account the gene length
• The output will be 3 files GO table, Top ontology plot and DE genes in each category for Cellular Component, Biological Processes, and Molecular Function ontologies and KEGG table and DE genes in each KEGG Pathways

Contribution

@nilchia wrote the workflow and the tests.