Cluster analysis of networks generated through homology: Automatic identification of important protein communities involved in cancer metastasis

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Jonsson, Pall F ^a   Cavanna, Tamara ^a   Zicha, Daniel ^a   Bates, Paul A ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC IDENTIFICATION; COMPUTATIONAL APPROACH; CONSTRUCTED NETWORKS; EXPERIMENTAL EVIDENCE; HIGH-THROUGHPUT APPROACHES; METASTATIC POTENTIAL; MICROARRAY EXPRESSIONS; PROTEIN-PROTEIN INTERACTIONS;

AUTOMATION; CELL CULTURE; CLUSTER ANALYSIS; DISEASES; PATHOLOGY; RATS;

PROTEINS;

ENDOTHELIAL CELL GROWTH FACTOR; INSULIN RECEPTOR; JANUS KINASE; PROTEOME; STAT PROTEIN; VASCULOTROPIN; TUMOR MARKER; TUMOR PROTEIN;

ANIMAL CELL; ARTICLE; BIOINFORMATICS; CANCER CELL CULTURE; CLUSTER ANALYSIS; COMPUTER NETWORK; GENE EXPRESSION REGULATION; MATHEMATICAL COMPUTING; METASTASIS; METASTASIS POTENTIAL; MICROARRAY ANALYSIS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RAT; SCORING SYSTEM; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; VALIDATION PROCESS; ALGORITHM; ANIMAL; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CHROMOSOME MAP; COMPUTER ASSISTED DIAGNOSIS; GENE EXPRESSION PROFILING; METABOLISM; PROCEDURES; REPRODUCIBILITY; SARCOMA; SECONDARY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TUMOR CELL LINE;

ANIMALIA;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; CELL LINE, TUMOR; CHROMOSOME MAPPING; CLUSTER ANALYSIS; DIAGNOSIS, COMPUTER-ASSISTED; GENE EXPRESSION PROFILING; NEOPLASM PROTEINS; PATTERN RECOGNITION, AUTOMATED; PROTEIN INTERACTION MAPPING; RATS; REPRODUCIBILITY OF RESULTS; SARCOMA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; TUMOR MARKERS, BIOLOGICAL;

EID: 30644463216     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-2     Document Type: Article

References (61)

1. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. P Natl Acad Sci USA 1998, 95:14863-14868.
2. Niehrs C, Pollet N: Synexpression groups in eukaryotes. Nature 1999, 402:483-487.
3. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
4. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adam SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
5. Sprinzak E, Sattath S, Margalit H: How Reliable are Experimental Protein-Protein Interaction Data? J Mol Biol. 2003, 327:919-923.
6. Bader GD, Hogue CWV: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol. 2002, 20:991-997.
7. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
8. Mann M, Hendrickson RC, Pandey A: Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem. 2001, 70:437-473.
9. Park J, Lappe M, Teichmann SA: Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast. J Mol Biol. 2001, 307:329-938.
10. Valencia A, Pazos F: Computational methods for the prediction of protein interactions. Curr Opin Struc Biol. 2002, 12:368-373.
11. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol. 2004, 22:78-85.
12. Brazhnik P, de la Fuente A, Mendes P: Gene networks: how to put the function in genomics. Trends Biotechnol. 2002, 20:467-472.
13. Rogers S, Girolami M: A Bayesian regression approach to the inference of regulatory networks from gene expression data. Bioinformatics 2005, 21:3131-3137.
14. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian Networks Approach for Predicting Protein-Protein Interactions. Science 2002, 302:449-453.
15. Jansen R, Lan N, Qian J, Gerstein M: Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics 2002, 2:71-81.
16. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F: Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 2005, 436:861-865.
17. Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M: Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 2005, 15:945-953.
18. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM: Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005, 23:951-959.
19. Cabusora L, Sutton E, Fulmer A, Forst CV: Differential network expression during drug and stress response. Bioinformatics 2005, 21:2898-2905.
20. Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho,RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, Miller-Graziano C, Moldawer LL, Mindrinos MN, Davis RW, Tompkins RG, Lowry SF: A network-based analysis of systemic inflammation in humans. Nature 2005, 437(7061):1032-7.
21. Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18:S233-S240.
22. Sohler F, Hanisch D, Zimmer R: New methods for joint analysis of biological networks and expression data. Bioinformatics 2004, 20:1517-1521.
23. de Lichtenberg U, Jensen LJ, Brunak S, Bork P: Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727.
24. Goffard N, Garcia V, Iragne F, Groppi A, de Daruvar A: IPPRED:server for proteins interactions inference. Bioinformatics 2003, 19:903-904.
25. PIP: Potential Interaction's of Proteins. [http://www.bmm.icnet.uk/~pip].
26. Aloy P, Pichaud M, Russell RB: Protein complexes: structure prediction challenges for the 21st century. Curr Opin Struc Biol. 2005, 15:15-22.
27. Palla, G, Derényi I, Farkas I, Vicsek T: Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435:814-818.
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25:25-29.
29. Derenyi I, Palla G, Vicsek T: Clique percolation in random networks. Phys Rev Lett. 2005, 94:160202.
30. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001, 411:41-42.
31. Contreras-Moreira B, Bates PA: Domain fishing: a first step in protein comparative modelling. Bioinformatics 2002, 18:1141-1142.
32. Ferrara N, Gerber HP, LeCouter J: The biology of VEGF and its receptors. Nature Med. 2003, 9:669-676.
33. Hirakawa, S, Kodama S, Kunstfeld R, Kajiya K, Brown LF, Detmar M: VEGF-A induces tumor and sentinel lymph node lymphangiogenesis and promotes lymphatic metastasis. J Exp Med. 2005, 201:1089-1099.
34. Takahashi T, Ueno H, Shibuya M: EGF activates protein kinase C-dependent, but Ras-independent Raf-MEK-MAP kinase pathway for DNA synthesis in primary endothelial cells. Oncogene 1999, 18:2221-2230.
35. Bourette RP, De Sepulveda P, Arnaud S, Dubreuil P, Rottapel R, Mouchiroud G: Suppressor of cytokine signaling 1 interacts with the macrophage colony-stimulating factor receptor and negatively regulates its proliferation signal. J Biol Chem. 2001, 276:22133-22139.
36. Alexander WS, Hilton DJ: The role of suppressors of cytokine signaling (SOCS) proteins in regulation of the immune response. Annu Rev Immunol. 2004, 22:503-529.
37. Park EJ, Park SY, Joe EH, Jou I: 15d-PGJ2 and rosiglitazone suppress Janus kinase-STAT inflammatory signaling through induction of suppressor of cytokine signaling 1 (SOCS1) and SOCS3 in glia. J Biol Chem. 2003, 278:14747-14752.
38. Ali S, Nouhi Z, Chughtai N, Ali S: SHP-2 regulates SOCS-1-mediated Janus kinase-2 ubiquitination/degradation downstream of the prolactin receptor. J Biol Chem. 2003, 278:52021-52031.
39. Furukawa M, Raffeld M, Mateo C, Sakamoto A, Moody TW, Ito T, Venzon D, Serrano J, Jensen R: Increased expression of insulin-like growth factor I and/or its receptor in gastrinomas is associated with low curability, increased growth, and development of metastases. Clin Cancer Res. 2005, 11:3233-3242.
40. Hofmann F, García-Echeverríaon C: Blocking insulin-like growth factor-I receptor as a strategy for targeting cancer. Drug Discov Today 2005, 10:1041-1047.
41. All-Ericsson C, Girnita L, Seregard S, Bartolazzi A, Jager MJ, Larsson O: Insulin-like growth factor-1 receptor in uveal melanoma: a predictor for metastatic disease and a potential therapeutic target. Invest Ophthalmol Vis Sci. 2002, 43:1-8.
42. LeRoith D, Werner H, Beitner-Johnson D, Roberts CT: Molecular and cellular aspects of the insulin-like growth factor I receptor. Endocr Rev. 1995, 16:143-163.
43. Yenush L, White MF: The IRS-signalling system during insulin and cytokine action. Bioessays 1997, 19:491-500.
44. Massagué J, Czech MP: The Subunit Structures of Two Distinct Receptors for Insulin-like Growth Factors I and I1 and Their Relationship to the Insulin Receptor. J Biol Chem. 1982, 257:5038-5045.
45. Ullrich A, Gray A, Tam AW, Yang-Feng T, Tsubokawa M, Collins C, Henzel W, Le Bon T, Kathuria S, Chen E: Insulin-like growth factor I receptor primary structure: comparison with insulin receptor suggests structural determinants that define functional specificity. EMBO J. 1986, 5:2503-2512.
46. Dunn SE, Ehrlich M, Sharp NJ, Reiss K, Solomon G, Hawkins R, Baserga R, Barrett JC: A dominant negative mutant of the insulin-like growth factor-I receptor inhibits the adhesion, invasion, and metastasis of breast cancer. Cancer Res. 1998, 58:3353-3361.
47. Andre F, Janssens B, Bruyneel E, van Roy F, Gespach C, Mareel M, Bracke M: Alpha-catenin is required for IGF-I-induced cellular migration but not invasion in human colonic cancer cells. Oncogene 2004, 23:1177-1186.
48. Müller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M: identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 2005, 436:871-875.
49. Armstrong NJ, van de Wiel MA: Microarray data analysis: from hypotheses to conclusions using gene expression data. Cell Oncol. 2004, 26:279-290.
50. Segal E, Wang H, Koller D: Discovering molecular pathways from protein interaction and gene expression data. Bioiformatics 2003, 19:i264-i272.
51. Karagiannis TC, El-Osta A: RNA interference and potential theraputic applications of short interfering RNAs. Cancer Gene Ther. 2005, 12:787-795.
52. Pruitt KD, Tatusova T, Maglott DR: CBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, 33:D501-D504.
53. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, 32:D449-D451.
54. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Frishman D: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21:832-834.
55. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, E BP: The Protein Data Bank. Nucleic Acids Res. 2000, 28:235-242.
56. Ofran Y, Rost B: Analysing six types of protein-protein interfaces. J Mol Biol. 2003, 325:377-387.
57. Affymetrix genechip rat expression set 230.[http://www.affymetrix.com/ support/technical/datasheets/rat230_datasheet.pdf].
58. The Paterson Institute's target preparation for Affymetrix genechip systems protocols. [http://bioinf.picr.man.ac.uk/mbcf/downloads/ GeneChip_Target_Prep_Protocol-CR-UK-v2.pdf].
59. Affymetrix expression analysis technical manual. [http:// www.affymetrix.com/support/technical/manual/expression-manual.affx].
60. The Paterson Institute's RNA hybridisation protocols. [http://bioinf.picr.man.ac.uk/mbcf/downloads/ GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v2.pdf].
61. North S, Gansner E, Ellson J: Graphviz. 1998, [http://www.graphviz.org].