## Pathways / Hypergeometric test for KEGG or PFAM

### Description

Searches for over- or under-represented genes for KEGG or PFAM categories.

### Parameters

- P value threshold (0-1) [0.05]
- Search for over- or under-represented genes (under, over) [over]
- Which ontology to test (KEGG, PFAM) [KEGG]

### Details

This tool takes the filtered data set, and goes through all KEGG or PFAM categories. For every category, a hypergeometric test is calculated, and the categories that acquire a p-value smaller than the user-specified threshold, are reported.

### Output

Output is an HTML-file with a list of significant categories. If you would like to know what are the genes listed as "observed", you can run the tool "Annotation/ Add annotations to data" on your original data set, followed by the tool "Preprocessing/ Filter using column term". Please note that this can sometimes yield a higher number of rows than the gene number indicated in the hypergeomteric test result. This is because there are several probes/probesets for one gene, and they are treated as one gene in the hypergeometric test.