Transit - Annotation Files to use for Pathway Enrichment

• associations file: ORF id -> pathway id
• pathways file: pathway id -> name/description
• FET,GSEA,ONT: which enrichment methods can each pathway set be used for? (e.g. "-M FET" flag in transit pathway_enrichment command)
  • FET=Fisher's Exact Test, GSEA=Gene Set Enrichment Analysis (Subramaniam 2004, PMID 16199517); ONT=Ontologizer (Bauer 2008, PMID 18511468)
• Sanger roles: from (Cole 1997, PMID 9634230) (unique to Mtb)
• COG gene and pathway counts exclude "General Function Only" and "Function Unknown"
• the Genbank accession number should be used to obtain the genome seq for mapping reads using TPP
• the corresponding prot_table (see genomes page?) should be used for runnning resampling so the genes have the conventional ORF ids for pathway analysis
• For counts of genes with COG pathway assignments in the tables below, we exclude the following large but meaningless pathways:
  • R - General function prediction only
  • S - Function unknown
• For counts of genes with Sanger pathways assignments in the tables below, we exclude the following large but meaningless pathways:
  • V - Conserved hypotheticals
  • VI - Unknowns

Mycobacterium tuberculosis H37Rv (NC_000962.3) (total ORFs=4019)

Mycobacterium smegmatis mc2 155 (NC_008596.1) (total ORFs=6719)

Mycobacterium abscessus ATCC 19977 (NC_010397.1) (total ORFs = 4920)

annotation	FET	GSEA	ONT	associations file	pathways file	pathways with >=1 gene	genes with >=1 pathway
KEGG	Yes	Yes	No	Mab.KEGG.associations.txt	Mab.KEGG.pathway_names.txt	196	2025
COG	Yes	Yes	No	Mab_COG_roles.dat	COG_roles.dat	19	2948

Mycobacterium avium 104 (NC_008595.1) (total ORFs = 5120)

annotation	FET	GSEA	ONT	associations file	pathways file	pathways with >=1 gene	genes with >=1 pathway
KEGG	Yes	Yes	No	avium.KEGG.associations.txt	avium.KEGG.pathway_names.txt	206	2199

Note: if you would like to request pathway files for other organisms, please email me at ioerger@cs.tamu.edu.