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Nucleic Acids Res. 2015 Jan;43(Database issue):D82-6. doi: 10.1093/nar/gku1163. Epub 2014 Nov 11.

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

Author information

1
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
2
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan kengo@ecei.tohoku.ac.jp.

Abstract

The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased the number of microarray experiments to nine species. The increase of the number of expression data with multiple platforms could enhance the reliability of coexpression data. For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform. The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific null distribution. These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results.

PMID:
25392420
PMCID:
PMC4383961
DOI:
10.1093/nar/gku1163
[Indexed for MEDLINE]
Free PMC Article

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