Discovery of biological networks from diverse functional genomic data

Genome Biology

Volumn 6, Issue 13, 2005, Pages

  Myers, Chad L ^a,b   Robson, Drew ^b   Wible, Adam ^a   Hibbs, Matthew A ^a,b   Chiriac, Camelia ^b   Theesfeld, Chandra L ^c   Dolinski, Kara ^b   Troyanskaya, Olga G ^a,b  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE PROTEIN 37; HEAT SHOCK PROTEIN 90; CDC37 PROTEIN, S CEREVISIAE; CELL CYCLE PROTEIN; CHAPERONE; SACCHAROMYCES CEREVISIAE PROTEIN;

ACCURACY; ARTICLE; CHROMOSOME SEGREGATION; COMPUTER PROGRAM; DATA ANALYSIS; FUNCTIONAL GENOMICS; GENE MAPPING; GENETIC ANALYSIS; INFORMATION SYSTEM; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN TARGETING; SACCHAROMYCES CEREVISIAE; VALIDATION PROCESS; BAYES THEOREM; BIOLOGY; COMPUTER GRAPHICS; CYTOLOGY; GENETICS; GENOMICS; METABOLISM; REPRODUCIBILITY;

SACCHAROMYCES CEREVISIAE;

BAYES THEOREM; CELL CYCLE PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; GENOMICS; HSP90 HEAT-SHOCK PROTEINS; MOLECULAR CHAPERONES; PROTEIN INTERACTION MAPPING; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33745113181     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2005-6-13-r114     Document Type: Article

References (58)

1. 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 from genomic data. Science 2003, 302:449-453.
2. Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D: A Bayesian framework for combining heterogeneous data sources for gene function prediction in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100:8348-8353.
3. Lee I, Date SV, Adai AT, Marcotte EM: A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558.
4. Jaimovich A, Elidan G, Margalit H, Friedman N: Towards an integrated protein-protein interaction network. In Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB, Proceedings: May 14-18 2005, Cambridge, MA Edited by: Miyano S, Mesirov J, Kasif S, Istrail S, Pevzner P, Waterman M. Springer Verlag-GmbH; 2005:14-30.
5. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31:258-261.
6. Deng M, Tu Z, Sun F, Chen T: Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics 2004, 20:895-902.
7. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S: Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci USA 2004, 101:2888-2893.
8. Letovsky S, Kasif S: Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 2003, 19(Suppl 1):i 197-204.
9. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2.
10. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003, 100:12123-12128.
11. Gagneur J, Krause R, Bouwmeester T, Casari G: Modular decomposition of protein-protein interaction networks. Genome Biol 2004. 5:R57.
12. Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of functional modules from protein interaction networks. Proteins 2004, 54:49-57.
13. Asthana S, King OD, Gibbons FD, Roth FP: Predicting protein complex membership using probabilistic network reliability. Genome Res 2004, 14:1170-1175.
14. Bader JS: Greedily building protein networks with confidence. Bioinformatics 2003, 19:1869-1874.
15. bioPIXIE Online Supplement [http://pixie.princeton.edu/supplement]
16. Prakash S, Prakash L: Nucleotide excision repair in yeast. Mutat Res 2000, 451:13-24.
17. van Laar T, van der Eb AJ, Terleth C: A role for Rad23 proteins in 26S proteasome-dependent protein degradation?. Mutat Res 2002, 499:53-61.
18. Schauber C, Chen L, Tongaonkar P, Vega I, Lambertson D, Potts W, Madura K: Rad23 links DNA repair to the ubiquitin/proteasome pathway. Nature 1998, 391:715-718.
19. Miles J, Formosa T: Evidence that POBI, a Saccharomyces cerevisiae protein that binds to DNA polymerase alpha, acts in DNA metabolism in vivo. Mol Cell Biol 1992, 12:5724-5735.
20. Bagatell R, Whitesell L: Altered Hsp90 function in cancer: a unique therapeutic opportunity. Mol Cancer Ther 2004, 3:1021-1030.
21. Gerber MR, Farrell A, Deshaies RJ, Herskowitz I, Morgan DO: Cdc37 is required for association of the protein kinase Cdc28 with GI and mitotic cyclins. Proc Natl Acad Sci USA 1995, 92:4651-4655.
22. Beliakoff J, Whitesell L: Hsp90: an emerging target for breast cancer therapy. Anticancer Drugs 2004, 15:651-662.
23. Hunter T, Poon RYC: Cdc37: a protein kinase chaperone?. Trends in Cell Biology 1997, 7:157-161.
24. Mort-Bontemps-Soret M, Facca C, Faye G: Physical interaction of Cdc28 with Cdc37 in Saccharomyces cerevisiae. Mol Genet Genomics 2002, 267:447-458.
25. Farrell A, Morgan DO: Cdc37 promotes the stability of protein kinases Cdc28 and Cak1.. Mol Cell Biol 2000, 20:749-754.
26. Schutz AR, Giddings TH Jr, Steiner E, Winey M: The yeast CDC37 gene interacts with MPS1 and is required for proper execution of spindle pole body duplication. J Cell Biol 1997, 136:969-982.
27. Lee P, Shabbir A, Cardozo C, Caplan AJ: Sti1 and Cdc37 can stabilize Hsp90 in chaperone complexes with a protein kinase. Mol Biol Cell 2004, 15:1785-1792.
28. Abbas-Terki T, Donze O, Picard D: The molecular chaperone Cdc37 is required for Ste11 function and pheromone-induced cell cycle arrest. FEBS Lett 2000, 467:111-116.
29. Johnston LH, Masai H, Sugino A: First the CDKs, now the DDKs. Trends Cell Biol 1999, 9:249-252.
30. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, et al.: Global mapping of the yeast genetic interaction network. Science 2004, 303:808-813.
31. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257.
32. Kent NA, Eibert SM, Mellor J: Cbflp is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast. J Biol Chem 2004, 279:27116-27123.
33. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
34. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I: The transcriptional program of sporulation in budding yeast. Science 1998, 282:699-705.
35. Saccharomyces Genome Database [ftp://ftp.yeastgenome.org/yeast/]
36. Du YC, Stillman B: Yphlp, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis. Cell 2002, 109:835-848.
37. Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M, Meagher D, Imai B, Guo Y, Brame CJ, et al.: Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell 2001, 8:505-515.
38. Oeffinger M, Leung A, Lamond A, Tollervey D: Yeast Pescadillo is required for multiple activities during 60S ribosomal subunit synthesis. RNA 2002, 8:626-636.
39. Adams CC, Jakovljevic J, Roman J, Harnpicharnchai P, Woolford JL Jr: Saccharomyces cerevisiae nucleolar protein Nop7p is necessary for biogenesis of 60S ribosomal subunits. RNA 2002, 8:150-165.
40. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, et al.: The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005:D418-424.
41. Breitkreutz BJ, Stark C, Tyers M: The GRID: the General Repository for Interaction Datasets. Genome Biol 2003, 4:R23.
42. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK: Global analysis of protein localization in budding yeast. Nature 2003, 425:686-691.
43. Zhu J, Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15:607-611.
44. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
45. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Meclp. Mol Biol Cell 2001, 12:2987-3003.
46. Ogawa N, DeRisi J, Brown PO: New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 2000, 11:4309-4321.
47. Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC: Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Mol Biol Cell 2004, 15:1233-1243.
48. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B: Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 2000, 406:90-94.
49. Sudarsanam P, Iyer VR, Brown PO, Winston F: Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2000, 97:3364-3369.
50. Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS: Genome-wide analysis of gene expression regulated by the calcineurin/Crzlp signaling pathway in Saccharomyces cerevisiae. J Biol Chem 2002, 277:31079-31088.
51. bioPIXIE Genomic data source list [http://pixie.princeton.edu/pixie/ supplement/sources.html]
52. Eddy SR: What is Bayesian statistics? Nat Biotechnol 2004, 22:1177-1178.
53. Dempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via Em algorithm. J Roy Statistical Soc Methodological 1977, 39:1-38.
54. bioPIXIE [http://pixie.princeton.edu]
55. Decision Systems Laboratory [http://dsl.sis.pitt.edu/]
56. Graphviz [http://genie.sis.pitt.edu/downloads.html]
57. GeNIe [http://www.genie.sis.pitt.edu]
58. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al.: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.