Episode 07 outline

Episode 07 functional enrichment

1. Gene Ontology

1.1 Route Arabidopsis (Fred)

Panther
GO table of results
custom code for the dot-plot

1.2 Non-model species with a GO annotation (Fred)

ID conversion with biomartr followed by Panther etc.

1.3 Non-model species without a GO (Tijs)

diff genes identifiers -> fasta file of mRNAs -> HMMER2GO

2. KEGG

2.1 Route Arabidopsis (Marc)

(Arabidopsis) Convert AGI numbers to Entrez gene id

2.2 Route non-model species (Marc)

(Tomato) Convert Ensembl gene identifiers to Entrez gene id Enrich KEGG
Outputs = dot-plot and table of ORA

2.3 Non-model species without any annotation (Tijs)

BlastKOALA = BLAST-based KO annotation and KEGG mapping
KofamKOALA = HMM profile-based KO annotation and KEGG mapping