KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

被引：54

作者：

Antonov, Alexey V. ^{[1
]}

Dietmann, Sabine ^{[1
]}

Mewes, Hans W. ^{[1
,2
]}

机构：

[1] GSF Natl Res Ctr Environm & Hlth, Inst Bioinformat, D-85764 Neuherberg, Germany

[2] Tech Univ Munich, Wissensch Zentrum Weihenstephan, Dept Genome Oriented Bioinformat, D-85350 Freising Weihenstephan, Germany

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 12期

关键词：

D O I：

10.1186/gb-2008-9-12-r179

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

KEGG spider is a web-based tool for interpretation of experimentally derived gene lists in order to gain understanding of metabolism variations at a genomic level. KEGG spider implements a 'pathway-free' framework that overcomes a major bottleneck of enrichment analyses: it provides global models uniting genes from different metabolic pathways. Analyzing a number of experimentally derived gene lists, we demonstrate that KEGG spider provides deeper insights into metabolism variations in comparison to existing methods.

引用

页数：11

共 54 条

[1] KEGGanim:: pathway animations for high-throughput data [J].

Adler, Priit ;

Reimand, Jueri ;

Jaenes, Juergen ;

Kolde, Raivo ;

Peterson, Hedi ;

Vilo, Jaak .

BIOINFORMATICS, 2008, 24 (04) :588-590

[2]

[Anonymous], 1993, Resampling-based multiple testing: Examples and methods for P-value adjustment

[3]

[Anonymous], 2004, Statistical Applications in Genetics and Molecular Biology

[4] ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data [J].

Antonov, Alexey V. ;

Schmidt, Thorsten ;

Wang, Yu ;

Mewes, Hans W. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :W347-W351

[5] Complex functionality of gene groups identified from high-throughput data [J].

Antonov, Alexey V. ;

Mewes, Hans W. .

JOURNAL OF MOLECULAR BIOLOGY, 2006, 363 (01) :289-296

[6] Complex phylogenetic profiling reveals fundamental genotype-phenotype associations [J].

Antonov, Alexey V. ;

Mewes, Hans W. .

COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2008, 32 (06) :412-416

[7] Gene-expression profiles predict survival of patients with lung adenocarcinoma [J].

Beer, DG ;

Kardia, SLR ;

Huang, CC ;

Giordano, TJ ;

Levin, AM ;

Misek, DE ;

Lin, L ;

Chen, GA ;

Gharib, TG ;

Thomas, DG ;

Lizyness, ML ;

Kuick, R ;

Hayasaka, S ;

Taylor, JMG ;

Iannettoni, MD ;

Orringer, MB ;

Hanash, S .

NATURE MEDICINE, 2002, 8 (08) :816-824

[8] Characterizing gene sets with FuncAssociate [J].

Berriz, GF ;

King, OD ;

Bryant, B ;

Sander, C ;

Roth, FP .

BIOINFORMATICS, 2003, 19 (18) :2502-2504

[9] Protein profile changes in the human breast cancer cell line MCF-7 in response to SEL1L gene induction [J].

Bianchi, L ;

Canton, C ;

Bini, L ;

Orlandi, R ;

Ménard, S ;

Armini, A ;

Cattaneo, M ;

Pallini, V ;

Bernardi, LR ;

Biunno, I .

PROTEOMICS, 2005, 5 (09) :2433-2442

[10] Ensembl 2006 [J].

Birney, E. ;

Andrews, D. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cox, T. ;

Cunningham, F. ;

Curwen, V. ;

Cutts, T. ;

Down, T. ;

Durbin, R. ;

Fernandez-Suarez, X. M. ;

Flicek, P. ;

Graf, S. ;

Hammond, M. ;

Herrero, J. ;

Howe, K. ;

Iyer, V. ;

Jekosch, K. ;

Kahari, A. ;

Kasprzyk, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

London, D. ;

Longden, I. ;

Melsopp, C. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Proctor, G. ;

Prlic, A. ;

Rae, M. ;

Rios, D. ;

Redmond, S. ;

Schuster, M. ;

Sealy, I. ;

Searle, S. ;

Severin, J. ;

Slater, G. ;

Smedley, D. ;

Smith, J. ;

Stabenau, A. ;

Stalker, J. ;

Trevanion, S. ;

Ureta-Vidal, A. ;

Vogel, J. ;

White, S. ;

Woodwark, C. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D556-D561

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