COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.
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.
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Yasunobu
Y
Okamura
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Yuichi
Y
Aoki
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Takeshi
T
Obayashi
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Shu
S
Tadaka
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Satoshi
S
Ito
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Takafumi
T
Narise
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.
Kengo
K
Kinoshita
D000818:Animals; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000592:standards; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA