Comparing functional annotation analyses with Catmap.

ABSTRACT:

Background

Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis.

Results

We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap), to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-base

SUBMITTER: Breslin T 

PROVIDER: S-EPMC543458 | biostudies-literature | 2004 Dec

REPOSITORIES: biostudies-literature