Functional analysis

This analysis section will calculate which functional class is overrepresented in your DNA microarray TOPHITS using the hypergeometrical distribution test. The only thing you have to do, is to select your organism and past your list of TOPHITS with their locus tags [example file]. Currently, the website supports the 5 most interesting classes; GO (Gene Ontology),  KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (cluster of orthologous groups) PFAM (Protein Families) and InterPro (integrated database of predictive protein signatures). Cite from the KEGG webserver:  KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and update history) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.

NEW: GO and InterPro Geneset enrichment analysis for more then 3000 genomes is now supported in the RNAseq analysis section: Click here

Step 1: Which organism are you studying?

Step 2: Select the class to analyse

Gene Ontology (GO)
Metabolic pathways (KEGG)
KEGG modules (KEGG-module)
KEGG BRITE orthology (BRITE)
Cluster of Orthologous Groups (COG)
COG catagories (COG-cat)
Protein FAMilies (PFAM)
Regulons [only lactis, subtilis and ecoli)

Step 3: Your list of locus tags (tophits)


Table 1;
Overrepresented classes found. Class names contain links to internet resources, hits are the number of genes from the 'toplist' present in the class, total is the number of genes of the selected organism that is present in the class. The p-value is the summation of the hypergeometrical distribution, it calculates for each CLASS, what is the chance to get the number of 'k' hits in the 'toplist' compared to a random distrubution.