Bactome II Analyzing Gene List for Gene Ontology Over Representation.

Citation: Ling, MHT. 2011. Bactome II: Analyzing Gene List for Gene Ontology Over-Representation. The Python Papers Source Codes 3: 3.

Link to [Abstract], [PDF] and [Zipped Codes].

Here is a permanent link to this [PDF] and [Zipped codes] in my own archive.

Microarray is an experimental tool that allows for the screening of several thousand genes in a single experiment and the analysis of which often requires mapping onto biological processes. This allows for the examination of processes that are over-represented. A number of tools have been developed but each differed in terms of organisms that can be analyzed. Gene Ontology website has a list of up-to-date annotation files for different organisms that can be used for over-representation analysis. Each file maps each gene of the organism to its ontological terms. It is a simple tool that allows users to use the up-to-date annotation files to generate the expected and observed counts for each GO identifier (GO ID) from a given gene list for further statistical analyses.