R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases

被引：49

作者：

Antonov, Alexey V. ^{[1
]}

Schmidt, Esther E. ^{[2
]}

Dietmann, Sabine ^{[1
]}

Krestyaninova, Maria ^{[2
]}

Hermjakob, Henning ^{[2
]}

机构：

[1] German Res Ctr Environm Hlth GmbH, Helmholtz Zentrum Munchen, Inst Bioinformat & Syst Biol, D-85764 Neuherberg, Germany

[2] European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

英国惠康基金; 美国国家卫生研究院;

关键词：

EXPRESSION DATA; ONTO-TOOLS;

D O I：

10.1093/nar/gkq482

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied gene list, and fully exploits the Reactome and KEGG knowledge bases. R spider provides a user-friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. R spider is freely available at http://mips.helmholtz-muenchen.de/proj/rspider.

引用

页码：W78 / W83

页数：6

共 37 条

[1] KEGGanim:: pathway animations for high-throughput data
Adler, Priit
Reimand, Jueri
Jaenes, Juergen
Kolde, Raivo
Peterson, Hedi
Vilo, Jaak
[J]. BIOINFORMATICS, 2008, 24 (04) : 588 - 590
[2] Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
Alexa, Adrian
Rahnenfuehrer, Joerg
Lengauer, Thomas
[J]. BIOINFORMATICS, 2006, 22 (13) : 1600 - 1607
[3] [Anonymous], 1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment
[4] [Anonymous], 2001, Acids Res, DOI DOI 10.1093/NAR/29.22.4633
[5] ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
Antonov, Alexey V.
Schmidt, Thorsten
Wang, Yu
Mewes, Hans W.
[J]. NUCLEIC ACIDS RESEARCH, 2008, 36 : W347 - W351
[6] PPI spider: A tool for the interpretation of proteomics data in the context of protein-protein interaction networks
Antonov, Alexey V.
Dietmann, Sabine
Rodchenkov, Igor
Mewes, Hans W.
[J]. PROTEOMICS, 2009, 9 (10) : 2740 - 2749
[7] KEGG spider: interpretation of genomics data in the context of the global gene metabolic network
Antonov, Alexey V.
Dietmann, Sabine
Mewes, Hans W.
[J]. GENOME BIOLOGY, 2008, 9 (12)
[8] GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
Antonov, Alexey V.
Dietmann, Sabine
Wong, Philip
Lutter, Dominik
Mewes, Hans W.
[J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : W323 - W328
[9] PLIPS, an Automatically Collected Database of Protein Lists Reported by Proteomics Studies
Antonov, Alexey V.
Dietmann, Sabine
Wong, Philip
Igor, Rodchenkov
Mewes, Hans W.
[J]. JOURNAL OF PROTEOME RESEARCH, 2009, 8 (03) : 1193 - 1197
[10] BIOREL: The benchmark resource to estimate the relevance of the gene networks
Antonov, AV
Mewes, HW
[J]. FEBS LETTERS, 2006, 580 (03) : 844 - 848

← 1 2 3 4 →