Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Xiong, Jianghui ^a   Rayner, Simon ^b   Luo, Kunyi ^a   Li, Yinghui ^a   Chen, Shanguang ^a  

^a China Astronaut Research and Training Center   (China)

^b WUHAN INSTITUTE OF VIROLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CELLULAR COMPONENTS; INTERACTION NETWORKS; MOLECULAR FUNCTION; OPEN READING FRAME; PREDICTION OF PROTEIN FUNCTION; PROTEIN METABOLISM; RIBONUCLEOPROTEIN COMPLEX;

ABSTRACTING; GENES; MOLECULAR BIOLOGY; PROTEINS; YEAST;

FORECASTING;

RIBONUCLEOPROTEIN; PROTEIN;

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; FUNGAL GENETICS; INFORMATION PROCESSING; NONHUMAN; OPEN READING FRAME; PREDICTION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN METABOLISM; PROTEIN TRANSPORT; RELIABILITY; SACCHAROMYCES CEREVISIAE; ALGORITHM; ARTIFICIAL INTELLIGENCE; CHROMOSOME MAP; CLASSIFICATION; EVIDENCE BASED MEDICINE; INFORMATION RETRIEVAL; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PROCEDURES; PROTEIN DATABASE; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS;

SACCHAROMYCES CEREVISIAE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CHROMOSOME MAPPING; DATABASES, PROTEIN; EVIDENCE-BASED MEDICINE; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PROTEINS; SIGNAL TRANSDUCTION; SYSTEMS INTEGRATION;

EID: 33745317477     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-268     Document Type: Article

References (47)

1. 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.
2. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH: Functional discovery via a compendium of expression profiles. Cell 2000, 102:109-126.
3. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dal H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH: Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 2000, 287:873-880.
4. Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-171.
5. Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18:1257-1261.
6. Bader GD, Hogue CW: 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, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
8. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
9. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85:2444-2448.
10. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucliec Acids Res 1997, 25:3389-3402.
11. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285:751-753.
12. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein Interaction maps for complete genomes based on gene fusion events. Nature 1999, 402:86-90.
13. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 1999, 96:4285-4288.
14. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 1999, 96:2896-2901.
15. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D: A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402:83-86.
16. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95:14863-14868.
17. Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares MJ, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 2000, 97:262-267.
18. Zhou X, Kao MC, Wong WH: Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci U S A 2002, 99:12783-12788.
19. Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ: Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet 2002, 31:255-265.
20. Lagreid A, Hvidsten TP, Midelfart H, Komorowski J, Sandvik AK: Predicting gene ontology biological process from temporal gene expression patterns. Genome Res 2003, 13:965-979.
21. 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 U S A 2003, 100:8348-8353.
22. Chen Y, Xu D: Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res 2004, 32:6414-6424.
23. Tanay A. Sharan R, Kupiec M, Shamir R: Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A 2004, 101:2981-2986.
24. 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 U S A 2004, 101:2888-2893.
25. Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JRIII, Davis TN: Assigning function to yeast proteins by integration of technologies. Mol Cell 2003, 12:1353-1365.
26. 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 [http://www.geneontology.org].
27. Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 2004, 32:D41-D44.
28. Drawid A, Jansen R, Gerstein M: Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet 2000, 16:426-430.
29. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N: Revealing modular organization in the yeast transcriptional network. Nat Genet 2002, 31:370-377.
30. 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.
31. Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M: A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 2004, 18:2491-2505.
32. Cherel I, Thuriaux P: The IFHI gene product interacts with a fork head protein In Saccharomyces cerevisiae. Yeast 1995, 11:261-270.
33. Deng M, Chen T, Sun F: An integrated probabilistic model for functional prediction of proteins. J Comput Biol 2004, 11:463-475.
34. Yeast Proteome Database. :[http://www.incyte.com].
35. ExpressDB RNA Expression Database. :[http://salt2.med.harvard.edu/cgi-bin/ExpressDByeast/(EXDStart].
36. Protein interaction data in MIPS database. :[ftp://ftp-mips.gsf.de/yeast/ PPI/].
37. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98:4569-4574.
38. Uetz P, Giot L. Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
39. Database of Interacting Proteins. :[http://dip.doe-mbi.ucla.edu/].
40. BIND: the Biomolecular Interaction Network Database. :[http://bind.ca/].
41. Complex data in MIPS. :[ftp://ftpmips.gsf.de/yeast/catalogues/ complexes/].
42. Predictome. :[http://predictome.bu.edu/].
43. von MC, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
44. Deng M, Sun F, Chen T. Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput 2003:140-151 [http://www.cmb.usc.edu/msms/AssessInteraction/].
45. SGD Gene Nomenclature Conventions. :[http://www.yeastgenome.org/help/yeastGeneNomenclature.shtml].
46. Kohavi R, Provost F: Glossary of Terms. Machine Learning 1998, 30:271-274.
47. Training feedforward networks with the Marquardt algorithm. IEEE Transactions on Neural Networks 1994, 5:989-993.