Discovery of protein interaction networks shared by diseases

Pacific Symposium on Biocomputing 2007, PSB 2007

Volumn , Issue , 2007, Pages 76-87

  Sam, Lee ^a   Liu, Yang ^a   Li, Jianrong ^a   Friedman, Carol ^b   Lussier, Yves A ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b Teachers College   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL PATHWAY; BIOLOGICAL PROCESS; BIOMEDICAL LITERATURE; COAGULATION FACTOR; COMPLEX DISEASE; GENE ONTOLOGY; HIGH PRECISION; HIGH THROUGHPUT; KNOWLEDGE BASE; LIVER DISEASE; MOLECULAR MECHANISM; MOLECULAR NETWORKS; NATURAL LANGUAGE UNDERSTANDING; NON-TRIVIAL; PROTEIN INTERACTION; PROTEIN INTERACTION NETWORKS; PROTEIN NETWORK; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; STATISTICAL SIGNIFICANCE;

ACTIVE NETWORKS; COAGULATION; PROTEINS;

DISEASES;

ANIMAL; ARTICLE; COCKAYNE SYNDROME; DNA REPAIR; FANCONI ANEMIA; GENERAL ASPECTS OF DISEASE; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETICS; HUMAN; METABOLISM; NATURAL LANGUAGE PROCESSING; NEOPLASM; PHENOTYPE; PROTEIN ANALYSIS; PROTEOMICS; STATISTICS; SYSTEMS BIOLOGY; XERODERMA PIGMENTOSUM;

ANIMALS; COCKAYNE SYNDROME; DATABASES, GENETIC; DISEASE; DNA REPAIR; FANCONI ANEMIA; GENETIC PREDISPOSITION TO DISEASE; HUMANS; NATURAL LANGUAGE PROCESSING; NEOPLASMS; PHENOTYPE; PROTEIN INTERACTION MAPPING; PROTEOMICS; SYSTEMS BIOLOGY; XERODERMA PIGMENTOSUM;

EID: 36348967978     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (41)

1. Pinsky, L., The polythetic (phenotypic community) system of classifying human malformation syndromes. Birth Defects Orig Artie Ser, 1977. 13(3A): p. 13-30.
2. Bertola, D.R., C.A. Kim, L.M. Albano, H. Scheffer, R. Meijer H. van Bokhoven, Molecular evidence that AEC syndrome and Rapp-Hodgkin syndrome are variable expression of a single genetic disorder. Clin Genet, 2004. 66(1): p. 79-80.
3. Sorasio, L.G.B. Ferrero E. Garelli G. Brunello C. Martano A. Carando, et al.,. Eur J Med Genet, 2006.
4. Zenteno, J.C., C. Venegas S. Kofman-Alfaro, Evidence that AEC syndrome and Bowen-Armstrong syndrome are variable expressions of the same disease. Pediatr Dermatol, 1999. 16(2): p. 103-7.
5. Morton, N.E., Am J Hum Genet, 1956. 8(2): p. 80-96.
6. Brunner, H.G.M.A. van Driel, Nat Rev Genet, 2004. 5(7): p. 545-51.
7. Xenarios, I., D.W. Rice, L. Salwinski, M.K. Baron, E.M. Marcotte D. Eisenberg, Nucleic Acids Res, 2000. 28(1): p. 289-91.
8. Joshi-Tope, G.M. Gillespie I. Vastrik P. D'Eustachio E. Schmidt B. de Bono, et al., Reactome: a knowledgebase of biological pathways. Nucleic Acids Res, 2005. 33(Database issue): p. D428-32.
9. Kutler, D.I.B. Singh J. Satagopan S.D. Batish M. Berwick P.F. Giampietro, et al, A 20-year perspective on the International Fanconi Anemia Registry (WAR). Blood 2003 101 4 1249-56.
10. Ogata, H., S. Goto, W. Fujibuchi M. Kanehisa, Computation with the KEGG pathway database. Biosystems, 1998. 47(1-2): p. 119-28.
11. Ogata, H., S. Goto, K. Sato, W. Fujibuchi, H. Bono M. Kanehisa, KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res, 1999. 27(1): p. 29-34.
12. Bader, G.D., I. Donaldson, C. Wolting, B.F. Ouellette, T. PawsonC.W. Hogue, Nucleic Acids Res, 2001. 29(1): p. 242-5.
13. Zanzoni, A., L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-CitterichG. Cesareni, FEBS Lett, 2002. 513(1): p. 135-40.
14. Breitkreutz, B.J., C. StarkM. Tyers, Genome Biol, 2002. 3(12): p. PREPRINT0013.
15. Sharan, R.T. Ideker, Modeling cellular machinery through biological network comparison. Nat Biotechnol, 2006. 24(4): p. 427-33.
16. Nabieva, E., K. Jim, A. Agarwal, B. ChazelleM. Singh, Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 2005. 21 Suppll:p. i302-10.
17. Lubovac, Z., J. GamalielssonB. Olsson, Combining functional and topological properties to identify core modules in protein interaction networks. Proteins, 2006.
18. Rhodes, D.R.S.A. TomlinsS. VaramballyV. MahavisnoT. BarretteS. Kalyana-Sundaram, et al, Nat Biotechnol, 2005. 23(8): p. 951-9.
19. Jansen, R.H. YuD. GreenbaumY. KlugerN.J. KroganS. Chung, et al, A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 2003. 302(5644): p. 449-53.
20. Lee, I., S.V. Date, A.T. AdaiE.M. Marcotte, A probabilistic functional network of yeast genes. Science, 2004. 306(5701): p. 1555-8.
21. Wong, S.L.L.V. ZhangA.H. TongZ. LiD.S. GoldbergO.D. King, et al, Proc Natl Acad Sci USA, 2004. 101(44): p. 15682-7.
22. Berg, J., M. LassigA. Wagner, Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol, 2004. 4(1): p. 51.
23. Rzhetsky, A.S.M. Gomez, Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics, 2001. 17(10): p. 988-96.
24. Barabasi, A.L.R. Albert, Emergence of scaling in random networks. Science, 1999. 286(5439): p. 509-12.
25. Wagner, A.D.A. Fell, The small world inside large metabolic networks. Proc Biol Sci, 2001. 268(1478): p. 1803-10.
26. Eisenberg, E.E.Y. Levanon, Preferential attachment in the protein network evolution. Phys Rev Lett, 2003. 91(13): p. 138701.
27. Ashburner, M.C.A. BallJ.A. BlakeD. BotsteinH. ButlerJ.M. Cherry, et al, The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25-9.
28. National Library of Medicine. Medical Subject Headings (MeSH®) Fact Sheet. 27 May 2005 http://www.nlm.nih.gov/pubs/factsheets/mesh.html.
29. Lussier, Y., D. Rappaport, T. BorlawskyC. Friedman. PhenoGO: a Multistrategy Language Processing System Assigning Phenotypic Context to Gene Ontology Annotations, in Pacific Symposium on Biocomputing. 2006. Maui, HI, USA.
30. Bairoch, A.R. ApweilerC.H. WuW.C. BarkerB. BoeckmannS. Ferro, et al, Nucleic Acids Res, 2005. 33(Database issue): p. D154-9.
31. Online Mendelian Inheritance in Man, MIM Number: Excision-Repair, Complementing Defective, In Chinese Hamster, 5; ERCC5 (#133530); last edited 11/29/2005: http://www.ncbi.nlm.nih.gov/omim/
32. Hoogervorst, E.M.C.T. van OostromR.B. BeemsJ. van BenthemS. GielisJ.P. Vermeulen, et al, Cancer Res, 2004. 64(15): p. 5118-26.
33. Online Mendelian Inheritance in Man, MIM Number: Colorectal Cancer (#114500); last edited 5/17/2006: http://www.ncbi.nlm.nih.gov/omim/
34. Worth, A., A.J. Thrasher H.B. Gaspar, Br J Haematol, 2006. 133(2): p. 124-40.
35. Blanco, R., B. McLaren, B. Davis, P. SteeleR. Smith, Systemic lupus erythematosus-associated lymphoproliferative disorder: report of a case and discussion in light of the literature. Hum Pathol, 1997. 28(8): p. 980-5.
36. Spivak, G., The many faces of Cockayne syndrome. Proc Natl Acad Sci USA 2004 101 43 15273-4.
37. Hanawalt, P.C., Subpathways of nucleotide excision repair and their regulation. Oncogene, 2002. 21(58): p. 8949-56.
38. Cotran, R.S., V. KumarT. Collins, Robbins Pathologic Basis of Diseases. 1999: p. 169,296.
39. Online Mendelian Inheritance in Man, MIM Number: Fanconi Anemia (#227650); last edited 3/15/2006: http://www.ncbi.nlm.nih.sov/omim/
40. Joenje, H.K.J. Patel, The emerging genetic and molecular basis of Fanconi anaemia. Nat Rev Genet, 2001. 2(6): p. 446-57.
41. Martin, D., C. Brun, E. Remy, P. Mouren, D. ThieffryB. Jacq, GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol, 2004. 5(12): p. R101.