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

Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W78-83. doi: 10.1093/nar/gkq482. Epub 2010 Jun 2.


MADNet: microarray database network web server.

Segota I, Bartonicek N, Vlahovicek K.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W332-5. doi: 10.1093/nar/gkn289. Epub 2008 May 14.


Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Haw R, Hermjakob H, D'Eustachio P, Stein L.

Proteomics. 2011 Sep;11(18):3598-613. doi: 10.1002/pmic.201100066.


Reactome: a database of reactions, pathways and biological processes.

Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L.

Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7. doi: 10.1093/nar/gkq1018. Epub 2010 Nov 9.

5. analytical web portal for high-throughput cell biology.

Antonov AV.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W323-7. doi: 10.1093/nar/gkr372. Epub 2011 May 23.


VisANT: data-integrating visual framework for biological networks and modules.

Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W352-7.


PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks.

Antonov AV, Dietmann S, Rodchenkov I, Mewes HW.

Proteomics. 2009 May;9(10):2740-9. doi: 10.1002/pmic.200800612.


KEGG Atlas mapping for global analysis of metabolic pathways.

Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W423-6. doi: 10.1093/nar/gkn282. Epub 2008 May 13.


ConsensusPathDB--a database for integrating human functional interaction networks.

Kamburov A, Wierling C, Lehrach H, Herwig R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D623-8. doi: 10.1093/nar/gkn698. Epub 2008 Oct 21.


ConsensusPathDB: toward a more complete picture of cell biology.

Kamburov A, Pentchev K, Galicka H, Wierling C, Lehrach H, Herwig R.

Nucleic Acids Res. 2011 Jan;39(Database issue):D712-7. doi: 10.1093/nar/gkq1156. Epub 2010 Nov 11.


Lists2Networks: integrated analysis of gene/protein lists.

Lachmann A, Ma'ayan A.

BMC Bioinformatics. 2010 Feb 12;11:87. doi: 10.1186/1471-2105-11-87.


Installing a local copy of the Reactome Web site and database.

Vastrik I.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 9:Unit 9.10. doi: 10.1002/0471250953.bi0910s21.


The ConsensusPathDB interaction database: 2013 update.

Kamburov A, Stelzl U, Lehrach H, Herwig R.

Nucleic Acids Res. 2013 Jan;41(Database issue):D793-800. doi: 10.1093/nar/gks1055. Epub 2012 Nov 11.


The DICS repository: module-assisted analysis of disease-related gene lists.

Dietmann S, Georgii E, Antonov A, Tsuda K, Mewes HW.

Bioinformatics. 2009 Mar 15;25(6):830-1. doi: 10.1093/bioinformatics/btp055. Epub 2009 Jan 28.


Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling.

Piro RM, Wiesberg S, Schramm G, Rebel N, Oswald M, Eils R, Reinelt G, König R.

BMC Syst Biol. 2014 May 16;8:56. doi: 10.1186/1752-0509-8-56.


ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.

Klein J, Leupold S, Münch R, Pommerenke C, Johl T, Kärst U, Jänsch L, Jahn D, Retter I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W460-4. doi: 10.1093/nar/gkn217. Epub 2008 Apr 25.


TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics.

Antonov AV, Dietmann S, Wong P, Mewes HW.

FEBS J. 2009 Apr;276(7):2084-94. doi: 10.1111/j.1742-4658.2009.06943.x.


GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists.

Antonov AV, Dietmann S, Wong P, Lutter D, Mewes HW.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W323-8. doi: 10.1093/nar/gkp313. Epub 2009 May 6.


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

Antonov AV, Dietmann S, Mewes HW.

Genome Biol. 2008;9(12):R179. doi: 10.1186/gb-2008-9-12-r179. Epub 2008 Dec 18.


A survey of metabolic databases emphasizing the MetaCyc family.

Karp PD, Caspi R.

Arch Toxicol. 2011 Sep;85(9):1015-33. doi: 10.1007/s00204-011-0705-2. Epub 2011 Apr 27. Review.

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