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BMCBI
2004

Comparing functional annotation analyses with Catmap

9 years 1 months ago
Comparing functional annotation analyses with Catmap
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-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we...
Thomas Breslin, Patrik Edén, Morten Krogh
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Thomas Breslin, Patrik Edén, Morten Krogh
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