{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T15:58:07Z","timestamp":1758124687927},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It is commonly accepted that genes with similar expression profiles are functionally related. However, there are many ways one can measure the similarity of expression profiles, and it is not clear a priori what is the most effective one. Moreover, so far no clear distinction has been made as for the type of the functional link between genes as suggested by microarray data. Similarly expressed genes can be part of the same complex as interacting partners; they can participate in the same pathway without interacting directly; they can perform similar functions; or they can simply have similar regulatory sequences.<\/jats:p>\n               <jats:p>Here we conduct a study of the notion of functional link as implied from expression data. We analyze different similarity measures of gene expression profiles and assess their usefulness and robustness in detecting biological relationships by comparing the similarity scores with results obtained from databases of interacting proteins, promoter signals and cellular pathways, as well as through sequence comparisons. We also introduce variations on similarity measures that are based on statistical analysis and better discriminate genes which are functionally nearby and faraway.<\/jats:p>\n               <jats:p>Our tools can be used to assess other similarity measures for expression profiles, and are accessible at<\/jats:p>\n               <jats:p>Contact: \u00a0golan@cs.technion.ac.il<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl127","type":"journal-article","created":{"date-parts":[[2006,4,5]],"date-time":"2006-04-05T00:24:30Z","timestamp":1144196670000},"page":"1616-1622","source":"Crossref","is-referenced-by-count":37,"title":["Effective similarity measures for expression profiles"],"prefix":"10.1093","volume":"22","author":[{"given":"Golan","family":"Yona","sequence":"first","affiliation":[{"name":"Department of Computer Science, Cornell University 1 \u00a0 1 \u00a0 \u00a0 NY, USA"},{"name":"Center of Applied Mathematics, Cornell University 2 \u00a0 2 \u00a0 \u00a0 NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William","family":"Dirks","sequence":"additional","affiliation":[{"name":"Center of Applied Mathematics, Cornell University 2 \u00a0 2 \u00a0 \u00a0 NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shafquat","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Cornell University 1 \u00a0 1 \u00a0 \u00a0 NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Cornell University 3 \u00a0 3 \u00a0 \u00a0 NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,4,4]]},"reference":[{"key":"2023012408322859900_b1","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1128\/AAC.44.5.1255-1265.2000","article-title":"Genome-wide expression patterns in Saccharomyces cerevisiae: comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol","volume":"44","author":"Bammer","year":"2000","journal-title":"Antimicrob. Agents Chemother."},{"key":"2023012408322859900_b2","doi-asserted-by":"crossref","first-page":"D235","DOI":"10.1093\/nar\/gkj153","article-title":"The BIOZON Database: a hub of heterogeneous biological data","volume":"34","author":"Birkland","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012408322859900_b3","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/S1097-2765(00)80114-8","article-title":"A genome-wide transcriptional analysis of the mitotic cell cycle","volume":"2","author":"Cho","year":"1998","journal-title":"Mol. Cell"},{"key":"2023012408322859900_b4","doi-asserted-by":"crossref","first-page":"H830","DOI":"10.1152\/ajpheart.00761.2002","article-title":"Microarray expression analysis of effects of exercise training: increase in atrial MLC-1 in rat ventricles","volume":"284","author":"Diffee","year":"2003","journal-title":"Am. J. Physiol. Heart Circ. Physiol."},{"key":"2023012408322859900_b5","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","article-title":"Genomic expression programs in the response of yeast cells to environmental changes","volume":"11","author":"Gasch","year":"2000","journal-title":"Mol. Biol. Cell"},{"key":"2023012408322859900_b6","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1128\/MCB.19.3.1720","article-title":"Correlation between protein and mRNA abundance in yeast","volume":"19","author":"Gygi","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"2023012408322859900_b7","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1148\/radiology.143.1.7063747","article-title":"The meaning and use of the area under the Receiver Operating Characteristic (ROC) curve","volume":"143","author":"Hanley","year":"1982","journal-title":"Radiology"},{"key":"2023012408322859900_b8","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","article-title":"Functional discovery via a compendium of expression profiles","volume":"102","author":"Hughes","year":"2000","journal-title":"Cell"},{"key":"2023012408322859900_b9","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S0959-437X(03)00008-X","article-title":"Classification of cancers by expression profiling","volume":"13","author":"Liu","year":"2003","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2023012408322859900_b10","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/oby.2003.30","article-title":"DNA microarray analysis of genes differentially expressed in diet-induced (cafeteria) obese rats","volume":"11","author":"Lopez","year":"2003","journal-title":"Obes. Res."},{"key":"2023012408322859900_b11","first-page":"5","article-title":"Microarray analysis of shear stressed endothelial cells","volume":"40","author":"McCormick","year":"2003","journal-title":"Biorheology"},{"key":"2023012408322859900_b12","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/S0092-8674(00)80126-9","article-title":"The role of the genome project in determining gene function: insights from model organisms","volume":"86","author":"Miklos","year":"1996","journal-title":"Cell"},{"key":"2023012408322859900_b13","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/1471-2105-6-217","article-title":"Automation of gene assignments to metabolic pathways using high-throughput expression data","volume":"6","author":"Popescu","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012408322859900_b14","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1006\/jmbi.2000.5219","article-title":"Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions","volume":"312","author":"Qian","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012408322859900_b15","doi-asserted-by":"crossref","first-page":"5659","DOI":"10.1091\/mbc.e04-04-0340","article-title":"Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress","volume":"15","author":"Shapira","year":"2004","journal-title":"Mol. Biol. Cell"},{"key":"2023012408322859900_b16","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"key":"2023012408322859900_b17","doi-asserted-by":"crossref","first-page":"377","DOI":"10.2307\/2347111","article-title":"Tail probabilities for Spearman's rho","volume":"24","author":"Algorithm AS 89.","year":"1975","journal-title":"Applied Statistics algorithms"},{"key":"2023012408322859900_b18","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1177\/000313480306900109","article-title":"The future of clinical cancer management: one tumor, one chip","volume":"69","author":"Yeatman","year":"2003","journal-title":"Am. Surg."},{"key":"2023012408322859900_b19","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/S0169-328X(02)00586-7","article-title":"Oxidative stress regulated genes in nigral dopaminergic neurnol cell: correlation with the known pathology in Parkinson\u2019s disease","volume":"110","author":"Yoo","year":"2003","journal-title":"Brain Res. Mol. Brain Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1616\/48837918\/bioinformatics_22_13_1616.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1616\/48837918\/bioinformatics_22_13_1616.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T08:47:39Z","timestamp":1674550059000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/13\/1616\/193334"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,4,4]]},"references-count":19,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2006,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl127","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,7,1]]},"published":{"date-parts":[[2006,4,4]]}}}