Finding function: evaluation methods for functional genomic data

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Bioinformatics. 2006\r\n \r\n \ \r\n Bioinformatics\r\n \ A Clare\r\n 19\r\n \ Suppl 2\r\n II42\r\n \ 2003\r\n 10.1093/bioinformatics/btg1058\r\n \ Clare A, King RD: Predicting gene function in Saccharomyces cerevisiae. Bioinformatics. 2003, 19 (Suppl 2): II42-II49.\r\n \r\n \r\n GR Lanckriet\r\n \ 300\r\n 2004\r\n \ Pac Symp Biocomput\r\n Lanckriet GR, Deng M, Cristianini N, Jordan MI, Noble WS: Kernel-based data fusion and its application to protein function prediction in yeast. Pac Symp Biocomput. 2004, 300-311.\r\n \r\n \ \r\n J Comput Biol\r\n P Pavlidis\r\n \ 9\r\n 2\r\n \ 401\r\n 2002\r\n \ 10.1089/10665270252935539\r\n Pavlidis P, Weston J, Cai J, Noble WS: Learning gene functional classifications from multiple data types. J Comput Biol. 2002, 9 (2): 401-411. 10.1089/10665270252935539.\r\n \ \r\n \r\n \ Bioinformatics\r\n A Ben-Hur\r\n 21\r\n Suppl 1\r\n i38\r\n 2005\r\n \ 10.1093/bioinformatics/bti1016\r\n Ben-Hur A, Noble WS: Kernel methods for predicting protein-protein interactions. Bioinformatics. 2005, 21 (Suppl 1): i38-i46. 10.1093/bioinformatics/bti1016.\r\n \ \r\n \r\n \ Science\r\n R Jansen\r\n 302\r\n 5644\r\n \ 449\r\n 2003\r\n \ 10.1126/science.1087361\r\n 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 (5644): 449-453. 10.1126/science.1087361.\r\n \ \r\n \r\n \ Science\r\n I Lee\r\n 306\r\n 5701\r\n \ 1555\r\n 2004\r\n \ 10.1126/science.1099511\r\n Lee I, Date SV, Adai AT, Marcotte EM: A probabilistic functional network of yeast genes. Science. 2004, 306 (5701): 1555-1558. 10.1126/science.1099511.\r\n \ \r\n \r\n \ BMC Bioinformatics\r\n \ N Lin\r\n 5\r\n \ 1\r\n 154\r\n \ 2004\r\n 10.1186/1471-2105-5-154\r\n \ Lin N, Wu B, Jansen R, Gerstein M, Zhao H: Information assessment on predicting protein-protein interactions. BMC Bioinformatics. 2004, 5 (1): 154-10.1186/1471-2105-5-154.\r\n \ \r\n \r\n \ Proc Natl Acad Sci USA\r\n \ OG Troyanskaya\r\n 100\r\n \ 14\r\n 8348\r\n \ 2003\r\n 10.1073/pnas.0832373100\r\n \ 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 (14): 8348-8353. 10.1073/pnas.0832373100.\r\n \ \r\n \r\n \ Trends Genet\r\n SL Wong\r\n 21\r\n 8\r\n \ 424\r\n 2005\r\n \ 10.1016/j.tig.2005.06.006\r\n Wong SL, Zhang LV, Roth FP: Discovering functional relationships: biochemistry versus genetics. Trends Genet. 2005, 21 (8): 424-427. 10.1016/j.tig.2005.06.006.\r\n \ \r\n \r\n \ Nucleic Acids Res\r\n M Kanehisa\r\n 28\r\n 1\r\n \ 27\r\n 2000\r\n \ 10.1093/nar/28.1.27\r\n Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28 (1): 27-30. 10.1093/nar/28.1.27.\r\n \r\n \ \r\n Bioinformatics\r\n \ Y Yamanishi\r\n 20\r\n \ Suppl 1\r\n I363\r\n \ 2004\r\n 10.1093/bioinformatics/bth910\r\n \ Yamanishi Y, Vert JP, Kanehisa M: Protein network inference from multiple genomic data: a supervised approach. Bioinformatics. 2004, 20 (Suppl 1): I363-I370. 10.1093/bioinformatics/bth910.\r\n \ \r\n \r\n \ GRIFn Home Page. [\r\n http://function.princeton.edu/GRIFn\r\n \ \r\n ]\r\n \r\n \ \r\n Nature\r\n \ AC Gavin\r\n 415\r\n \ 6868\r\n 141\r\n \ 2002\r\n 10.1038/415141a\r\n \ 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 (6868): 141-147. 10.1038/415141a.\r\n \ \r\n \r\n \ J Mol Biol\r\n E Sprinzak\r\n 327\r\n 5\r\n \ 919\r\n 2003\r\n \ 10.1016/S0022-2836(03)00239-0\r\n Sprinzak E, Sattath S, Margalit H: How reliable are experimental protein-protein interaction data?. J Mol Biol. 2003, 327 (5): 919-923. 10.1016/S0022-2836(03)00239-0.\r\n \ \r\n \r\n \ Nature\r\n P Uetz\r\n 403\r\n 6770\r\n \ 623\r\n 2000\r\n \ 10.1038/35001009\r\n 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 (6770): 623-627. 10.1038/35001009.\r\n \ \r\n \r\n \ Nature\r\n C von Mering\r\n 417\r\n 6887\r\n \ 399\r\n 2002\r\n \ 10.1038/nature750\r\n von Mering C, 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 (6887): 399-403. 10.1038/nature750.\r\n \ \r\n \r\n \ Bioinformatics\r\n SG Lee\r\n 20\r\n 3\r\n \ 381\r\n 2004\r\n \ 10.1093/bioinformatics/btg420\r\n Lee SG, Hur JU, Kim YS: A graph-theoretic modeling on GO space for biological interpretation of gene clusters. Bioinformatics. 2004, 20 (3): 381-388. 10.1093/bioinformatics/btg420.\r\n \ \r\n \r\n \ Nat Genet\r\n M Ashburner\r\n 25\r\n 1\r\n \ 25\r\n 2000\r\n \ 10.1038/75556\r\n Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.\r\n \ \r\n \r\n \ Nucleic Acids Res\r\n CA Ball\r\n 28\r\n 1\r\n \ 77\r\n 2000\r\n \ 10.1093/nar/28.1.77\r\n Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H: Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res. 2000, 28 (1): 77-80. 10.1093/nar/28.1.77.\r\n \r\n \ \r\n Nucleic Acids Res\r\n HW Mewes\r\n \ 30\r\n 1\r\n \ 31\r\n 2002\r\n \ 10.1093/nar/30.1.31\r\n Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2002, 30 (1): 31-34. 10.1093/nar/30.1.31.\r\n \ \r\n \r\n \ Nucleic Acids Res\r\n MC Costanzo\r\n 29\r\n 1\r\n \ 75\r\n 2001\r\n \ 10.1093/nar/29.1.75\r\n Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P: YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001, 29 (1): 75-79. 10.1093/nar/29.1.75.\r\n \ \r\n \r\n \ Curr Opin Microbiol\r\n \ R Jansen\r\n 7\r\n \ 5\r\n 535\r\n \ 2004\r\n 10.1016/j.mib.2004.08.012\r\n \ Jansen R, Gerstein M: Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol. 2004, 7 (5): 535-545. 10.1016/j.mib.2004.08.012.\r\n \r\n \ \r\n BMC Bioinformatics\r\n A Patil\r\n \ 6\r\n 1\r\n \ 100\r\n 2005\r\n \ 10.1186/1471-2105-6-100\r\n Patil A, Nakamura H: Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics. 2005, 6 (1): 100-10.1186/1471-2105-6-100.\r\n \r\n \ \r\n Nature\r\n \ WK Huh\r\n 425\r\n \ 6959\r\n 686\r\n \ 2003\r\n 10.1038/nature02026\r\n \ 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 (6959): 686-691. 10.1038/nature02026.\r\n \ \r\n \r\n \ Mol Cell Proteomics\r\n \ CM Deane\r\n 1\r\n \ 5\r\n 349\r\n \ 2002\r\n 10.1074/mcp.M100037-MCP200\r\n \ Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics. 2002, 1 (5): 349-356. 10.1074/mcp.M100037-MCP200.\r\n \r\n \ \r\n Y Qi\r\n 531\r\n 2005\r\n \ Pac Symp Biocomput\r\n Qi Y, Klein-Seetharaman J, Bar-Joseph Z: Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput. 2005, 531-542.\r\n \ \r\n \r\n \ Curr Opin Struct Biol\r\n \ P Bork\r\n 14\r\n \ 3\r\n 292\r\n \ 2004\r\n 10.1016/j.sbi.2004.05.003\r\n \ Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM: Protein interaction networks from yeast to human. Curr Opin Struct Biol. 2004, 14 (3): 292-299. 10.1016/j.sbi.2004.05.003.\r\n \ \r\n \r\n \ Nucleic Acids Res\r\n I Xenarios\r\n 28\r\n 1\r\n \ 289\r\n 2000\r\n \ 10.1093/nar/28.1.289\r\n Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D: DIP: the database of interacting proteins. Nucleic Acids Res. 2000, 28 (1): 289-291. 10.1093/nar/28.1.289.\r\n \ \r\n \r\n \ Genome Biol\r\n BJ Breitkreutz\r\n 4\r\n 3\r\n \ R23\r\n 2003\r\n \ 10.1186/gb-2003-4-3-r23\r\n Breitkreutz BJ, Stark C, Tyers M: The GRID: the General Repository for Interaction Datasets. Genome Biol. 2003, 4 (3): R23-10.1186/gb-2003-4-3-r23.\r\n \ \r\n \r\n \ 10.1093/nar/gki051\r\n \ Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E: The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2005, D418-424. 33 Database\r\n \ \r\n \r\n \ Bioinformatics\r\n PW Lord\r\n 19\r\n 10\r\n \ 1275\r\n 2003\r\n \ 10.1093/bioinformatics/btg153\r\n Lord PW, Stevens RD, Brass A, Goble CA: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003, 19 (10): 1275-1283. 10.1093/bioinformatics/btg153.\r\n \ \r\n \r\n \ BMC Bioinformatics\r\n \ A Ben-Hur\r\n 7\r\n \ Suppl61\r\n S2\r\n \ 2005\r\n Ben-Hur A, Noble WS: Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics. 2005, 7 (Suppl61): S2-\r\n \ \r\n \r\n \ Proc Natl Acad Sci U S A\r\n \ T Ito\r\n 98\r\n \ 8\r\n 4569\r\n \ 2001\r\n 10.1073/pnas.061034498\r\n \ 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 (8): 4569-4574. 10.1073/pnas.061034498.\r\n \r\n \ \r\n Science\r\n \ AH Tong\r\n 295\r\n \ 5553\r\n 321\r\n \ 2002\r\n 10.1126/science.1064987\r\n \ Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324. 10.1126/science.1064987.\r\n \r\n \ \r\n Nature\r\n \ Y Ho\r\n 415\r\n \ 6868\r\n 180\r\n \ 2002\r\n 10.1038/415180a\r\n \ Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415 (6868): 180-183. 10.1038/415180a.\r\n \ \r\n \r\n \ Mol Biol Cell\r\n AP Gasch\r\n 12\r\n 10\r\n \ 2987\r\n 2001\r\n \ 10.1091/mbc.12.10.2987\r\n 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 Mec1p. Mol Biol Cell. 2001, 12 (10): 2987-3003.\r\n \ \r\n \r\n \ Mol Biol Cell\r\n PT Spellman\r\n 9\r\n 12\r\n \ 3273\r\n 1998\r\n \ 10.1091/mbc.9.12.3273\r\n 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 (12): 3273-3297.\r\n \r\n \ \r\n \r\n \r\n \ \r\n \r\n \r\n \r\n \ \r\n" http_version: recorded_at: Wed, 09 Jun 2021 12:56:48 GMT recorded_with: VCR 3.0.3