463
Views
85
CrossRef citations to date
0
Altmetric
Research Article

The analysis of the drug–targets based on the topological properties in the human protein–protein interaction network

, , , , , , , , , & show all
Pages 524-532 | Received 28 Nov 2008, Accepted 17 May 2009, Published online: 16 Jun 2009

References

  • Barabasi AL, Oltvai ZN. (2004). Network biology: understanding the cell’s functional organization. Nat Rev Genet, 5, 101–113.
  • Blake JA, Bult CJ. (2006). Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform, 39, 314–320.
  • Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M. (2008). The BioGRID Interaction Database: 2008 update. Nucleic Acids Res, 36, D637–D640.
  • Butte AJ, Kohane IS. (2006). Creation and implications of a phenome-genome network. Nat Biotechnol, 24, 55–62.
  • Goldberg DS, Roth FP. (2003). Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA, 100, 4372–4376.
  • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res, 33, D514–D517.
  • Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. (2004). Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88–93.
  • Hermeking H. (2003). The MYC oncogene as a cancer drug target. Curr Cancer Drug Targets, 3, 163–175.
  • Hopkins AL, Groom CR. (2002). The druggable genome. Nat Rev Drug Discov, 1, 727–730.
  • James CR, Quinn JE, Mullan PB, Johnston PG, Harkin DP. (2007). BRCA1, a potential predictive biomarker in the treatment of breast cancer. Oncologist, 12, 142–150.
  • Jiang T, Keating AE. (2005). AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics, 6, 136.
  • Jonsson PF, Bates PA. (2006). Global topological features of cancer proteins in the human interactome. Bioinformatics, 22, 2291–2297.
  • Loging W, Harland L, Williams-Jones B. (2007). High-throughput electronic biology: mining information for drug discovery. Nat Rev Drug Discov, 6, 220–230.
  • Ma X, Tarone AM, Li W. (2008). Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS ONE, 3, e1922.
  • Maloney A, Workman P. (2002). HSP90 as a new therapeutic target for cancer therapy: the story unfolds. Expert Opin Biol Ther, 2, 3–24.
  • Mete M, Tang F, Xu X, Yuruk N. (2008). A structural approach for finding functional modules from large biological networks. BMC Bioinformatics, 9(Suppl. 9), S19.
  • Nahi H, Selivanova G, Lehmann S, Möllgård L, Bengtzen S, Concha H, Svensson A, Wiman KG, Merup M, Paul C. (2008). Mutated and non-mutated TP53 as targets in the treatment of leukaemia. Br J Haematol, 141, 445–453.
  • Plewczynski D, Rychlewski L. (2009). Meta-basic estimates the size of druggable human genome. J Mol Model, 15, 695–699.
  • Potts SJ, Edwards DJ, Hoffman R. (2005). Challenges of target/compound data integration from disease to chemistry: a case study of dihydrofolate reductase inhibitors. Curr Drug Discov Technol, 2, 75–87.
  • Rakotomamonjy A. (2004). Optimizing area under ROC curve with SVMs. In Proceedings of the Workshop on ROC Analysis in Artificial Intelligence, pp. 71–80.
  • Schwikowski B, Uetz P, Fields S. (2000). A network of protein-protein interactions in yeast. Nat Biotechnol, 18, 1257–1261.
  • Tu Z, Wang L, Xu M, Zhou X, Chen T, Sun F. (2006). Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics, 7, 31.
  • Turkson J. (2004). STAT proteins as novel targets for cancer drug discovery. Expert Opin Ther Targets, 8, 409–422.
  • Ulitsky I, Shamir R. (2007). Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol, 3, 104.
  • Vazquez A, Flammini A, Maritan A, Vespignani A. (2003). Global protein function prediction from protein-protein interaction networks. Nat Biotechnol, 21, 697–700.
  • Wachi S, Yoneda K, Wu R. (2005). Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics, 21, 4205–4208.
  • Wang J, Yang Y, Xia HH, Gu Q, Lin MC, Jiang B, Peng Y, Li G, An X, Zhang Y, Zhuang Z, Zhang Z, Kung HF, Wong BC. (2007). Suppression of FHL2 expression induces cell differentiation and inhibits gastric and colon carcinogenesis. Gastroenterology, 132, 1066–1076.
  • Watts DJ, Strogatz SH. (1998). Collective dynamics of “small-world” networks. Nature, 393, 440–442.
  • Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. (2008). DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res, 36, D901–906.
  • Wuchty S, Almaas E. (2005a). Peeling the yeast protein network. Proteomics, 5, 444–449.
  • Wuchty S, Almaas E. (2005b). Evolutionary cores of domain co- occurrence networks. BMC Evol Biol, 5, 24.
  • Yang L, Vondriska TM, Han Z, Maclellan WR, Weiss JN, Qu Z. (2008). Deducing topology of protein-protein interaction networks from experimentally measured sub-networks. BMC Bioinformatics, 9, 301.
  • Yildirim MA, Goh KI, Cusick ME, Barabási AL, Vidal M. (2007). Drug-target network. Nat Biotechnol, 25, 1119–1126.
  • Zhu M, Gao L, Guo Z, Li Y, Wang D, Wang J, Wang C. (2007). Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. Gene, 391, 113–119.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.