Complex Functionality of Gene Groups Identified from High-throughput Data

Journal of Molecular Biology

Volumn 363, Issue 1, 2006, Pages 289-296

  Antonov, Alexey V ^a   Mewes, Hans W ^a,b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

automatic functional profiling; functional annotation; gene function; high throughput data; rule mining

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STATISTICAL SIGNIFICANCE;

SACCHAROMYCES CEREVISIAE;

EID: 33748758193     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.07.062     Document Type: Article

References (34)

1. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
2. Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., et al. Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl Acad. Sci. USA 97 (2000) 1143-1147
3. Uetz P., and Hughes R.E. Systematic and large-scale two-hybrid screens. Curr. Opin. Microbiol. 3 (2000) 303-308
4. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 623-627
5. Gavin I.M., Kukhtin A., Glesne D., Schabacker D., and Chandler D.P. Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array. Biotechniques 39 (2005) 99-107
6. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (1999) 531-537
7. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9 (1998) 3273-3297
8. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
9. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl. Acids Res. 32 (2004) 5539-5545
10. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25 (2000) 25-29
11. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucl. Acids Res. 31 (2003) 365-370
12. Berriz G.F., King O.D., Bryant B., Sander C., and Roth F.P. Characterizing gene sets with FuncAssociate. Bioinformatics 19 (2003) 2502-2504
13. Khatri P., Draghici S., Ostermeier G.C., and Krawetz S.A. Profiling gene expression using onto-express. Genomics 79 (2002) 266-270
14. Khatri P., Bhavsar P., Bawa G., and Draghici S. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucl. Acids Res. 32 (2004) W449-W456
15. Khatri P., and Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21 (2005) 3587-3595
16. Khatri P., Sellamuthu S., Malhotra P., Amin K., Done A., and Draghici S. Recent additions and improvements to the Onto-Tools. Nucl. Acids Res. 33 (2005) W762-W765
17. Khatri P., Done B., Rao A., Done A., and Draghici S. A semantic analysis of the annotations of the human genome. Bioinformatics 21 (2005) 3416-3421
18. Masseroli M., Martucci D., and Pinciroli F. GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucl. Acids Res. 32 (2004) W293-W300
19. Zeeberg B.R., Feng W., Wang G., Wang M.D., Fojo A.T., Sunshine M., et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 4 (2003) R28
20. Zhang B., Kirov S., and Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucl. Acids Res. 33 (2005) W741-W748
21. Antonov A.V., and Mewes H.W. BIOREL: the benchmark resource to estimate the relevance of the gene networks. FEBS Letters 580 (2006) 844-848
22. Antonov A.V., Tetko I.V., and Mewes H.W. A systematic approach to infer biological relevance and biases of gene network structures. Nucl. Acids Res. 34 (2006) e6
23. Draghici S., Khatri P., Martins R.P., Ostermeier G.C., and Krawetz S.A. Global functional profiling of gene expression. Genomics 81 (2003) 98-104
24. Bowers P.M., O'Connor B.D., Cokus S.J., Sprinzak E., Yeates T.O., and Eisenberg D. Utilizing logical relationships in genomic data to decipher cellular processes. FEBS J. 272 (2005) 5110-5118
25. Bowers P.M., Cokus S.J., Eisenberg D., and Yeates T.O. Use of logic relationships to decipher protein network organization. Science 306 (2004) 2246-2249
26. Artamonova I.I., Frishman G., Gelfand M.S., and Frishman D. Mining sequence annotation databanks for association patterns. Bioinformatics 21 (2005) iii49-iii57
27. Black P.E. Algorithms and Theory of Computation Handbook (1999), CRC Press LLC
28. Webb G. Efficient search for association rules. Proceedings of International Conference on Knowledge Discovery and Data Mining (2000), Association for Computing Machinery, New York, USA 99-107
29. Ewens W.J., and Grant G.R. Statistical Methods in Bioinformatics (2001), Springer-Verlag, New York
30. Westfall P.N., and Young S.S. Resampling-based Multiple Testing: Examples and Methods for p-value Adjustment (1993), John Wiley and Sons, New York
31. Mager W.H., and Planta R.J. Multifunctional DNA-binding proteins mediate concerted transcription activation of yeast ribosomal protein genes. Biochim. Biophys. Acta 1050 (1990) 351-355
32. Spector M.S., Raff A., DeSilva H., Lee K., and Osley M.A. Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol. Cell Biol. 17 (1997) 545-552
33. Guo Z., Zhang T., Li X., Wang Q., Xu J., Yu H., et al. Towards precise classification of cancers based on robust gene functional expression profiles. BMC. Bioinformatics 6 (2005) 58
34. Goldberg D. Genetic Algorithms (1988), Addison Wesley