ConsensusPathDB: Toward a more complete picture of cell biology

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Kamburov, Atanas ^a   Pentchev, Konstantin ^a   Galicka, Hanna ^a   Wierling, Christoph ^a   Lehrach, Hans ^a   Herwig, Ralf ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLIENT SERVER APPLICATION; COMPLEX FORMATION; COMPUTER INTERFACE; CONSENSUSPATHDB; CYTOLOGY; DATA ANALYSIS; FACTUAL DATABASE; GENE EXPRESSION; GENE FUNCTION; GENETIC REGULATION; INFORMATION PROCESSING; INTERNET; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TAXONOMY;

ANIMALS; DATABASES, FACTUAL; DATABASES, GENETIC; GENE EXPRESSION; GENE REGULATORY NETWORKS; HUMANS; INTERNET; METABOLIC NETWORKS AND PATHWAYS; MICE; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; USER-COMPUTER INTERFACE;

EID: 78651335912     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1156     Document Type: Article

References (30)

1. Ideker, T. and Sharan, R. (2008) Protein networks in disease. Genome Res., 18, 644-652.
2. Bader, G.D., Cary, M.P. and Sander, C. (2006) Pathguide: A pathway resource list. Nucleic Acids Res., 34, D504-D506.
3. Kamburov, A., Wierling, C., Lehrach, H. and Herwig, R. (2009) ConsensusPathDB - a database for integrating human functional interaction networks. Nucleic Acids Res., 37, D623-D628.
4. Ruepp, A., Waegele, B., Lechner, M., Brauner, B., Dunger- Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C. and Mewes, H. (2010) CORUM: The comprehensive resource of mammalian protein complexes - 2009. Nucleic Acids Res., 38, D497-D501.
5. Aranda, B., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S.N., Orchard, S., Perreau, V. et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res., 38, D525-D531.
6. Mewes, H., Ruepp, A., Frishman, D., Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
7. Driscoll, T., Dyer, M.D., Murali, T.M. and Sobral, B.W. (2009) PIG - the pathogen interaction gateway. Nucleic Acids Res., 37, D647-D650.
8. Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O. and Goryanin, I. (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol., 3, 135.
9. Ravasi, T., Bertin, N., Carninci, P., Daub, C.O., Forrest, A.R.R., Gough, J., Grimmond, S., Han, J., Hashimoto, T., Hide, W. et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140, 744-752.
10. Thorn, C.F., Klein, T.E. and Altman, R.B. (2010) Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics, 11, 501-505.
11. Matthews, L., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
12. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
13. López-Bigas, N., Karp, P.D., Ouzounis, C.A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N. and Kunin, V. (2005) Expansion of the BioCyc collection of pathway/ genome databases to 160 genomes. Nucleic Acids Res., 33, 6083-6089.
14. Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
15. Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L. and Cesareni, G. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532-D539.
16. Wood, V., Dolinski, K., Tyers, M., Breitkreutz, B., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R. et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Res., 36, D637-D640.
17. Güldener, U., Münsterkötter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H. and Stümpflen, V. (2006) MPact: The MIPS protein interaction resource on yeast. Nucleic Acids Res., 34, D436-D441.
18. The Gene Ontology Consortium. (2010) The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Res., 38, D331-D335.
19. Makrantonaki, E., Adjaye, J., Herwig, R., Brink, T.C., Groth, D., Hultschig, C., Lehrach, H. and Zouboulis, C.C. (2006) Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro. Aging Cell, 5, 331-344.
20. Yu, Y.P., Landsittel, D., Jing, L., Nelson, J., Ren, B., Liu, L., McDonald, C., Thomas, R., Dhir, R., Finkelstein, S. et al. (2004) Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J. Clin. Oncol., 22, 2790-2799.
21. Rhodes, D.R., Kalyana-Sundaram, S., Mahavisno, V., Varambally, R., Yu, J., Briggs, B.B., Barrette, T.R., Anstet, M.J., Kincead-Beal, C., Kulkarni, P. et al. (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles. Neoplasia, 9, 166-180.
22. Hanahan, D. and Weinberg, R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70.
23. Vaarala, M.H., Porvari, K.S., Kyllönen, A.P., Mustonen, M.V., Lukkarinen, O. and Vihko, P.T. (1998) Several genes encoding ribosomal proteins are over-expressed in prostate-cancer cell lines: Confirmation of L7a and L37 over-expression in prostate-cancer tissue samples. Int. J. Cancer, 78, 27-32.
24. UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
25. Yoon, K.A., Hwangbo, B., Kim, I.J., Park, S., Kim, H.S., Kee, H.J., Lee, J.E., Jang, Y.K., Park, J.G. and Lee, J.S. (2006) Novel polymorphisms in the SUV39H2 histone methyltransferase and the risk of lung cancer. Carcinogenesis, 27, 2217-2222. (Pubitemid 44644810)
26. Peters, A.H., O'Carroll, D., Scherthan, H., Mechtler, K., Sauer, S., Schöfer, C., Weipoltshammer, K., Pagani, M., Lachner, M., Kohlmaier, A. et al. (2001) Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell, 107, 323-337.
27. Chuang, H.Y., Lee, E., Liu, Y.T., Lee, D. and Ideker, T. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140.
28. Sherman, D., Tyers, M., Salama, J.J., Moore, S., Ceol, A., Chatr-Aryamontri, A., Oesterheld, M., Stümpflen, V., Salwinski, L., Nerothin, J. et al. (2007) Broadening the horizon - level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol., 5, 44.
29. Pentchev, K., Ono, K., Herwig, R., Ideker, T. and Kamburov, A. (2010) Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics, 26, 2796-2797.
30. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.