{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T14:58:51Z","timestamp":1787497131206,"version":"build-2736575974"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a \"treated\" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method \u2013 based on the PageRank algorithm employed by the popular search engine Google \u2013 that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2105-6-233","type":"journal-article","created":{"date-parts":[[2005,9,22]],"date-time":"2005-09-22T14:18:10Z","timestamp":1127398690000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":205,"title":["GeneRank: Using search engine technology for the analysis of microarray experiments"],"prefix":"10.1186","volume":"6","author":[{"given":"Julie L","family":"Morrison","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rainer","family":"Breitling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Desmond J","family":"Higham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R","family":"Gilbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2005,9,21]]},"reference":[{"key":"558_CR1","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1080\/15427951.2004.10129091","volume":"1","author":"AN Langville","year":"2005","unstructured":"Langville AN, Meyer CD: Deeper inside PageRank. Internet Mathematics 2005, 1: 335\u2013380.","journal-title":"Internet Mathematics"},{"key":"558_CR2","volume-title":"Tech rep Stanford Digital Library Technologies Project","author":"L Page","year":"1998","unstructured":"Page L, Brin S, Motwani R, Winograd T: The PageRank citation ranking: bringing order to the web. Tech rep Stanford Digital Library Technologies Project 1998. [http:\/\/citeseer.ist.psu.edu\/page98pagerank.html]"},{"key":"558_CR3","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/424610a","volume":"424","author":"C Tilstone","year":"2003","unstructured":"Tilstone C: Vital statistics. Nature 2003, 424: 610\u2013612. 10.1038\/424610a","journal-title":"Nature"},{"key":"558_CR4","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1038\/sj.tpj.6500209","volume":"3","author":"S Hanash","year":"2003","unstructured":"Hanash S, Creighton C: Making sense of microarray data to classify cancer. The Pharmacogenomics Journal 2003, 3: 308\u2013311. 10.1038\/sj.tpj.6500209","journal-title":"The Pharmacogenomics Journal"},{"key":"558_CR5","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/1471-2105-5-100","volume":"5","author":"R Breitling","year":"2004","unstructured":"Breitling R, Amtmann A, Herzyk P: Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics 2004, 5: 100. 10.1186\/1471-2105-5-100","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 1","key":"558_CR6","doi-asserted-by":"publisher","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl. 1):S233-S240.","journal-title":"Bioinformatics"},{"issue":"21","key":"558_CR7","doi-asserted-by":"publisher","first-page":"6283","DOI":"10.1093\/nar\/gkg838","volume":"31","author":"S Tornow","year":"2003","unstructured":"Tornow S, Mewes H: Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Research 2003, 31(21):6283\u20136289. 10.1093\/nar\/gkg838","journal-title":"Nucleic Acids Research"},{"key":"558_CR8","doi-asserted-by":"publisher","first-page":"i363","DOI":"10.1093\/bioinformatics\/bth910","volume":"20","author":"Y Yamanishi","year":"2004","unstructured":"Yamanishi Y, Vert JP, Kanehisa M: Protein network inference from multiple genomic data: a supervised approach. Bioinformatics 2004, 20: i363-i370. 10.1093\/bioinformatics\/bth910","journal-title":"Bioinformatics"},{"key":"558_CR9","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1016\/S1097-2765(02)00531-2","volume":"9","author":"P Kemmeren","year":"2002","unstructured":"Kemmeren P, van Berkurn NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC: Protein Interaction Verification and Functional Annotation by Integrating Analysis of Genome-Scale Data. Molecular Cell 2002, 9: 1133\u20131143. 10.1016\/S1097-2765(02)00531-2","journal-title":"Molecular Cell"},{"key":"558_CR10","unstructured":"Google[http:\/\/www.google.com]"},{"key":"558_CR11","unstructured":"Gene Ontology[http:\/\/geneontology.org]"},{"key":"558_CR12","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1126\/science.278.5338.680","volume":"278","author":"JL DeRisi","year":"1997","unstructured":"DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278: 680\u2013686. 10.1126\/science.278.5338.680","journal-title":"Science"},{"key":"558_CR13","doi-asserted-by":"publisher","first-page":"016125","DOI":"10.1103\/PhysRevE.66.016125","volume":"66","author":"H Zhou","year":"2002","unstructured":"Zhou H: Scaling exponents and clustering coefficients of a growing random network. Phy Rev E Stat Nonlin Sofa Matler Phys 2002, 66: 016125.","journal-title":"Phy Rev E Stat Nonlin Sofa Matler Phys"},{"key":"558_CR14","doi-asserted-by":"publisher","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","volume":"11","author":"AP Gasch","year":"2000","unstructured":"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. Molecular Biology of the Cell 2000, 11: 4241\u20134257.","journal-title":"Molecular Biology of the Cell"},{"key":"558_CR15","unstructured":"Weisstein EW: Correlation Coefficient.[http:\/\/mathworld.wolfram.com\/CorrelationCoefficient.html]"},{"key":"558_CR16","unstructured":"Stanford Microarray Database[http:\/\/genome-www5.stanford.edu\/]"},{"key":"558_CR17","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/0022-2496(75)90001-2","volume":"12","author":"D Bamber","year":"1975","unstructured":"Bamber D: The area above the ordinal dominance graph and the area below the receiver operating characteristic graph. Journal of Mathematical Psychology 1975, 12: 387\u2013415. 10.1016\/0022-2496(75)90001-2","journal-title":"Journal of Mathematical Psychology"},{"key":"558_CR18","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0097-8485(96)80004-0","volume":"20","author":"M Gribskov","year":"1996","unstructured":"Gribskov M, Robinson NL: Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Computer and Chemistry 1996, 20: 25\u201333. 10.1016\/S0097-8485(96)80004-0","journal-title":"Computer and Chemistry"},{"issue":"5500","key":"558_CR19","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1126\/science.290.5500.2306","volume":"290","author":"B Ren","year":"2000","unstructured":"Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA: Genome-wide location and function of DNA binding proteins. Science 2000, 290(5500):2306\u20132309. 10.1126\/science.290.5500.2306","journal-title":"Science"},{"issue":"6819","key":"558_CR20","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/35054095","volume":"409","author":"VR Iyer","year":"2001","unstructured":"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409(6819):533\u2013538. 10.1038\/35054095","journal-title":"Nature"},{"issue":"23","key":"558_CR21","doi-asserted-by":"publisher","first-page":"3017","DOI":"10.1101\/gad.1039602","volume":"16","author":"CE Horak","year":"2002","unstructured":"Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M: Complex transcriptional circuitry at the G1\/S transition in Saccharomyces cerevisiae. Genes & Development 2002, 16(23):3017\u20133033. 10.1101\/gad.1039602","journal-title":"Genes & Development"},{"key":"558_CR22","first-page":"192","volume":"39","author":"DJ Higham","year":"2003","unstructured":"Higham DJ, Taylor A: The sleekest link algorithm. Inst of Math and Its Appl. (IMA) Mathematics Today 2003, 39: 192\u2013197.","journal-title":"Inst of Math and Its Appl. (IMA) Mathematics Today"},{"key":"558_CR23","volume-title":"Matrix computations","author":"GH Golub","year":"1996","unstructured":"Golub GH, Van Loan CF: Matrix computations. third edition. The John Hopkins University Press; 1996.","edition":"third"},{"key":"558_CR24","unstructured":"Higham DJ: Google PageRank as mean playing time for pinball on the reverse web. Applied Mathematics Letters, in press."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-233.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T12:47:04Z","timestamp":1706791624000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-233"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,9,21]]},"references-count":24,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["558"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-233","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,9,21]]},"assertion":[{"value":"19 April 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"233"}}