COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia

被引：28

作者：

Meysman, Pieter ^{[1
,2
]}

Sonego, Paolo ^{[3
]}

Bianco, Luca ^{[3
]}

Fu, Qiang ^{[4
]}

Ledezma-Tejeida, Daniela ^{[5
]}

Gama-Castro, Socorro ^{[5
]}

Liebens, Veerle ^{[4
]}

Michiels, Jan ^{[4
]}

Laukens, Kris ^{[1
,2
]}

Marchal, Kathleen ^{[4
,6
,7
]}

Collado-Vides, Julio ^{[5
]}

Engelen, Kristof ^{[3
,4
]}

机构：

[1] Univ Antwerp, Dept Math & Comp Sci, B-2020 Antwerp, Belgium

[2] Univ Antwerp, Univ Antwerp Hosp, Biomed Informat Res Ctr Antwerp Biomina, B-2650 Edegem, Belgium

[3] Fdn Edmund Mach, Res & Innovat Ctr, Dept Computat Biol, I-38010 Trento, TN, Italy

[4] Katholieke Univ Leuven, Dept Microbial & Mol Sci, B-3001 Louvain, Belgium

[5] Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Cuernavaca 62210, Morelos, Mexico

[6] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

[7] Univ Ghent, IMinds, Dept Informat Technol, B-9052 Ghent, Belgium

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

基金：

比利时弗兰德研究基金会;

关键词：

GENE-EXPRESSION; RNA-SEQ; ESCHERICHIA-COLI; DATA SETS; MICROARRAYS; NETWORK; RESOLUTION; ALIGNMENT; GENOMICS; DATABASE;

D O I：

10.1093/nar/gkt1086

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMBOS was originally published in PLoS One, and COLOMBOS v2.0 includes both an update of the expression data, by expanding the previously available compendia and by adding compendia for several new species, and an update of the surrounding functionality, with improved search and visualization options and novel tools for programmatic access to the database. The scope of the database has also been extended to incorporate RNA-seq data in our compendia by a dedicated analysis pipeline. We demonstrate the validity and robustness of this approach by comparing the same RNA samples measured in parallel using both microarrays and RNA-seq. As far as we know, COLOMBOS currently hosts the largest homogenized gene expression compendia available for seven bacterial model organisms.

引用

页码：D649 / D653

页数：5

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