This article is part of the supplement: Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge

Open Access Proceedings

PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries

Hui Huang1,2†, Xiaogang Wu1,2,3†, Madhankumar Sonachalam2†, Sammed N Mandape1, Ragini Pandey2, Karl F MacDorman1, Ping Wan4* and Jake Y Chen1,2,3*

1 School of Informatics, Indiana University, Indianapolis, IN 46202, USA

2 Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA

3 MedeoLinx, LLC, Indianapolis, IN 46280, USA

4 Capital Normal University, Beijing, 100048, China

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BMC Bioinformatics 2012, 13(Suppl 15):S2 doi:10.1186/1471-2105-13-S15-S2

Published: 11 September 2012

Additional files

Additional file 1:

Change of similarity score with different α in Equation I. The frequency on the y-axis refers to the count of all gene set pairs falling into the category of a particular similarity range on the x-axis. Different α in Equation I have been used to calculate the similarity score. When α approaches 0, the distribution skewed to right with many false positive high similarity scores; when α approach 1, the distribution is too left-skewed failing to differentiate those low similarity scores apart.

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