{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T19:29:55Z","timestamp":1778700595738,"version":"3.51.4"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"S12","license":[{"start":{"date-parts":[[2009,10,1]],"date-time":"2009-10-01T00:00:00Z","timestamp":1254355200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,10]]},"DOI":"10.1186\/1471-2105-10-s12-s8","type":"journal-article","created":{"date-parts":[[2009,10,15]],"date-time":"2009-10-15T18:16:02Z","timestamp":1255630562000},"source":"Crossref","is-referenced-by-count":21,"title":["Identification of functionally related genes using data mining and data integration: a breast cancer case study"],"prefix":"10.1186","volume":"10","author":[{"given":"Ettore","family":"Mosca","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gloria","family":"Bertoli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleonora","family":"Piscitelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Vilardo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rolland A","family":"Reinbold","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ileana","family":"Zucchi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luciano","family":"Milanesi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,10,15]]},"reference":[{"issue":"6912","key":"3411_CR1","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nature01254","volume":"420","author":"H Kitano","year":"2002","unstructured":"Kitano H: Computational systems biology. Nature 2002, 420(6912):206\u2013210. 10.1038\/nature01254","journal-title":"Nature"},{"key":"3411_CR2","doi-asserted-by":"crossref","unstructured":"Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R: NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, (37 Database):D885-D890. 10.1093\/nar\/gkn764","DOI":"10.1093\/nar\/gkn764"},{"key":"3411_CR3","doi-asserted-by":"crossref","unstructured":"Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A: ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007, (35 Database):D747-D750. 10.1093\/nar\/gkl995","DOI":"10.1093\/nar\/gkl995"},{"key":"3411_CR4","doi-asserted-by":"crossref","unstructured":"Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA: The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, (35 Database):D766-D770. 10.1093\/nar\/gkl1019","DOI":"10.1093\/nar\/gkl1019"},{"key":"3411_CR5","doi-asserted-by":"crossref","unstructured":"Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Kishore CJH, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A: Human Protein Reference Database-2009 update. Nucleic Acids Res 2009, (37 Database):D767-D772. 10.1093\/nar\/gkn892","DOI":"10.1093\/nar\/gkn892"},{"key":"3411_CR6","doi-asserted-by":"crossref","unstructured":"Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, B\u00e4hler J, Wood V, Dolinski K, Tyers M: The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008, (36 Database):D637-D640.","DOI":"10.1093\/nar\/gkm1001"},{"issue":"6","key":"3411_CR7","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1101\/gr.1910904","volume":"14","author":"HK Lee","year":"2004","unstructured":"Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P: Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14(6):1085\u20131094. 10.1101\/gr.1910904","journal-title":"Genome Res"},{"key":"3411_CR8","doi-asserted-by":"crossref","unstructured":"Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K: COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res 2008, (36 Database):D77-D82.","DOI":"10.1093\/nar\/gkm840"},{"key":"3411_CR9","doi-asserted-by":"crossref","unstructured":"Blake JA, Harris MA: The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr Protoc Bioinformatics 2008., Chapter 7(Unit 7.2):","DOI":"10.1002\/0471250953.bi0702s23"},{"issue":"6684","key":"3411_CR10","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 1998, 393(6684):440\u2013442. 10.1038\/30918","journal-title":"Nature"},{"issue":"11","key":"3411_CR11","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498\u20132504. 10.1101\/gr.1239303","journal-title":"Genome Res"},{"issue":"3","key":"3411_CR12","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/ng0797-311","volume":"16","author":"M Bamshad","year":"1997","unstructured":"Bamshad M, Lin RC, Law DJ, Watkins WC, Krakowiak PA, Moore ME, Franceschini P, Lala R, Holmes LB, Gebuhr TC, Bruneau BG, Schinzel A, Seidman JG, Seidman CE, Jorde LB: Mutations in human TBX3 alter limb, apocrine and genital development in ulnar-mammary syndrome. Nat Genet 1997, 16(3):311\u2013315. 10.1038\/ng0797-311","journal-title":"Nat Genet"},{"issue":"15","key":"3411_CR13","doi-asserted-by":"publisher","first-page":"5132","DOI":"10.1158\/0008-5472.CAN-04-0615","volume":"64","author":"W Fan","year":"2004","unstructured":"Fan W, Huang X, Chen C, Gray J, Huang T: TBX3 and its isoform TBX3+2a are functionally distinctive in inhibition of senescence and are overexpressed in a subset of breast cancer cell lines. Cancer Res 2004, 64(15):5132\u20135139. 10.1158\/0008-5472.CAN-04-0615","journal-title":"Cancer Res"},{"issue":"3","key":"3411_CR14","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1158\/0008-5472.CAN-07-5012","volume":"68","author":"W Yarosh","year":"2008","unstructured":"Yarosh W, Barrientos T, Esmailpour T, Lin L, Carpenter PM, Osann K, Anton-Culver H, Huang T: TBX3 is overexpressed in breast cancer and represses p14 ARF by interacting with histone deacetylases. Cancer Res 2008, 68(3):693\u2013699. 10.1158\/0008-5472.CAN-07-5012","journal-title":"Cancer Res"},{"key":"3411_CR15","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1038\/msb4100129","volume":"3","author":"R Sharan","year":"2007","unstructured":"Sharan R, Ulitsky I, Shamir R: Network-based prediction of protein function. Mol Syst Biol 2007, 3: 88. 10.1038\/msb4100129","journal-title":"Mol Syst Biol"},{"issue":"6","key":"3411_CR16","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","volume":"122","author":"U Stelzl","year":"2005","unstructured":"Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toks\u00f6z E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE: A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957\u2013968. 10.1016\/j.cell.2005.08.029","journal-title":"Cell"},{"issue":"7184","key":"3411_CR17","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1038\/nature06734","volume":"452","author":"HR Christofk","year":"2008","unstructured":"Christofk HR, Heiden MGV, Harris MH, Ramanathan A, Gerszten RE, Wei R, Fleming MD, Schreiber SL, Cantley LC: The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature 2008, 452(7184):230\u2013233. 10.1038\/nature06734","journal-title":"Nature"},{"issue":"3","key":"3411_CR18","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/nrc2344","volume":"8","author":"RG Bristow","year":"2008","unstructured":"Bristow RG, Hill RP: Hypoxia and metabolism. Hypoxia, DNA repair and genetic instability. Nat Rev Cancer 2008, 8(3):180\u2013192. 10.1038\/nrc2344","journal-title":"Nat Rev Cancer"},{"issue":"7\u20138","key":"3411_CR19","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1111\/j.1600-0463.2008.01163.x","volume":"116","author":"B Quesnel","year":"2008","unstructured":"Quesnel B: Tumor dormancy and immunoescape. APMIS 2008, 116(7\u20138):685\u2013694. 10.1111\/j.1600-0463.2008.01163.x","journal-title":"APMIS"},{"key":"3411_CR20","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/1471-2148-8-111","volume":"8","author":"S Struckmann","year":"2008","unstructured":"Struckmann S, Ara\u00fazo-Bravo MJ, Sch\u00f6ler HR, Reinbold RA, Fuellen G: ReXSpecies-a tool for the analysis of the evolution of gene regulation across species. BMC Evol Biol 2008, 8: 111. 10.1186\/1471-2148-8-111","journal-title":"BMC Evol Biol"},{"issue":"8","key":"3411_CR21","doi-asserted-by":"publisher","first-page":"6567","DOI":"10.1074\/jbc.M110492200","volume":"277","author":"TR Brummelkamp","year":"2002","unstructured":"Brummelkamp TR, Kortlever RM, Lingbeek M, Trettel F, MacDonald ME, van Lohuizen M, Bernards R: TBX-3, the gene mutated in Ulnar-Mammary Syndrome, is a negative regulator of p19ARF and inhibits senescence. J Biol Chem 2002, 277(8):6567\u20136572. 10.1074\/jbc.M110492200","journal-title":"J Biol Chem"},{"issue":"12","key":"3411_CR22","doi-asserted-by":"publisher","first-page":"11816","DOI":"10.1074\/jbc.M412408200","volume":"280","author":"MR Barron","year":"2005","unstructured":"Barron MR, Belaguli NS, Zhang SX, Trinh M, Iyer D, Merlo X, Lough JW, Parmacek MS, Bruneau BG, Schwartz RJ: Serum response factor, an enriched cardiac mesoderm obligatory factor, is a downstream gene target for Tbx genes. J Biol Chem 2005, 280(12):11816\u201311828. 10.1074\/jbc.M412408200","journal-title":"J Biol Chem"},{"issue":"40","key":"3411_CR23","doi-asserted-by":"publisher","first-page":"41846","DOI":"10.1074\/jbc.M405514200","volume":"279","author":"R Catena","year":"2004","unstructured":"Catena R, Tiveron C, Ronchi A, Porta S, Ferri A, Tatangelo L, Cavallaro M, Favaro R, Ottolenghi S, Reinbold R, Sch\u00f6ler H, Nicolis SK: Conserved POU binding DNA sites in the Sox2 upstream enhancer regulate gene expression in embryonic and neural stem cells. J Biol Chem 2004, 279(40):41846\u201341857. 10.1074\/jbc.M405514200","journal-title":"J Biol Chem"},{"issue":"25","key":"3411_CR24","doi-asserted-by":"publisher","first-page":"10476","DOI":"10.1073\/pnas.0703071104","volume":"104","author":"I Zucchi","year":"2007","unstructured":"Zucchi I, Sanzone S, Astigiano S, Pelucchi P, Scotti M, Valsecchi V, Barbieri O, Bertoli G, Albertini A, Reinbold RA, Dulbecco R: The properties of a mammary gland cancer stem cell. Proc Natl Acad Sci USA 2007, 104(25):10476\u201310481. 10.1073\/pnas.0703071104","journal-title":"Proc Natl Acad Sci USA"},{"issue":"44","key":"3411_CR25","doi-asserted-by":"publisher","first-page":"16940","DOI":"10.1073\/pnas.0808978105","volume":"105","author":"I Zucchi","year":"2008","unstructured":"Zucchi I, Astigiano S, Bertalot G, Sanzone S, Cocola C, Pelucchi P, Bertoli G, Stehling M, Barbieri O, Albertini A, Sch\u00f6ler HR, Neel BG, Reinbold RA, Dulbecco R: Distinct populations of tumor-initiating cells derived from a tumor generated by rat mammary cancer stem cells. Proc Natl Acad Sci USA 2008, 105(44):16940\u201316945. 10.1073\/pnas.0808978105","journal-title":"Proc Natl Acad Sci USA"},{"key":"3411_CR26","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s10616-008-9173-9","volume":"58","author":"C Cocola","year":"2008","unstructured":"Cocola C, Sanzone S, Astigiano S, Pelucchi P, Piscitelli E, Vilardo L, Barbieri O, Bertoli G, Reinbold RA, Zucchi I: A rat mammary gland cancer cell with stem cell properties of self-renewal and multi-lineage differentiation. Cytotechnology 2008, 58: 25\u201332. 10.1007\/s10616-008-9173-9","journal-title":"Cytotechnology"},{"issue":"5","key":"3411_CR27","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1016\/j.cell.2006.09.048","volume":"127","author":"H Kouros-Mehr","year":"2006","unstructured":"Kouros-Mehr H, Slorach EM, Sternlicht MD, Werb Z: GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland. Cell 2006, 127(5):1041\u20131055. 10.1016\/j.cell.2006.09.048","journal-title":"Cell"},{"issue":"2","key":"3411_CR28","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.ceb.2008.02.003","volume":"20","author":"H Kouros-Mehr","year":"2008","unstructured":"Kouros-Mehr H, whan Kim J, Bechis SK, Werb Z: GATA-3 and the regulation of the mammary luminal cell fate. Curr Opin Cell Biol 2008, 20(2):164\u2013170. 10.1016\/j.ceb.2008.02.003","journal-title":"Curr Opin Cell Biol"},{"issue":"2","key":"3411_CR29","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1002\/(SICI)1097-0215(19990420)84:2<122::AID-IJC5>3.0.CO;2-S","volume":"84","author":"RV Hoch","year":"1999","unstructured":"Hoch RV, Thompson DA, Baker RJ, Weigel RJ: GATA-3 is expressed in association with estrogen receptor in breast cancer. Int J Cancer 1999, 84(2):122\u2013128. 10.1002\/(SICI)1097-0215(19990420)84:2<122::AID-IJC5>3.0.CO;2-S","journal-title":"Int J Cancer"},{"issue":"24","key":"3411_CR30","doi-asserted-by":"publisher","first-page":"11259","DOI":"10.1158\/0008-5472.CAN-05-2495","volume":"65","author":"R Mehra","year":"2005","unstructured":"Mehra R, Varambally S, Ding L, Shen R, Sabel MS, Ghosh D, Chinnaiyan AM, Kleer CG: Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Res 2005, 65(24):11259\u201311264. 10.1158\/0008-5472.CAN-05-2495","journal-title":"Cancer Res"},{"key":"3411_CR31","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1023\/A:1009516515338","volume":"6","author":"MT Lewis","year":"2001","unstructured":"Lewis MT: Hedgehog signaling in mouse mammary gland development and neoplasia. J Mammary Gland Biol Neoplasia 2001, 6: 53\u201366. 10.1023\/A:1009516515338","journal-title":"J Mammary Gland Biol Neoplasia"},{"issue":"15","key":"3411_CR32","doi-asserted-by":"publisher","first-page":"7548","DOI":"10.1158\/0008-5472.CAN-06-0452","volume":"66","author":"JA Sterling","year":"2006","unstructured":"Sterling JA, Oyajobi BO, Grubbs B, Padalecki SS, Munoz SA, Gupta A, Story B, Zhao M, Mundy GR: The hedgehog signaling molecule Gli2 induces parathyroid hormone-related peptide expression and osteolysis in metastatic human breast cancer cells. Cancer Res 2006, 66(15):7548\u20137553. 10.1158\/0008-5472.CAN-06-0452","journal-title":"Cancer Res"},{"key":"3411_CR33","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/1471-2105-6-79","volume":"6","author":"VD Marinescu","year":"2005","unstructured":"Marinescu VD, Kohane IS, Riva A: MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 2005, 6: 79. 10.1186\/1471-2105-6-79","journal-title":"BMC Bioinformatics"},{"issue":"13","key":"3411_CR34","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/bti473","volume":"21","author":"K Cartharius","year":"2005","unstructured":"Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T: MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21(13):2933\u20132942. 10.1093\/bioinformatics\/bti473","journal-title":"Bioinformatics"},{"key":"3411_CR35","doi-asserted-by":"crossref","unstructured":"Sandelin A, Alkema W, Engstr\u00f6m P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, (32 Database):D91-D94. 10.1093\/nar\/gkh012","DOI":"10.1093\/nar\/gkh012"},{"issue":"4","key":"3411_CR36","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1093\/bib\/bbn016","volume":"9","author":"E Wingender","year":"2008","unstructured":"Wingender E: The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 2008, 9(4):326\u2013332. 10.1093\/bib\/bbn016","journal-title":"Brief Bioinform"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S12-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-S12-S8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S12-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T05:32:06Z","timestamp":1558589526000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S12-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10]]},"references-count":36,"journal-issue":{"issue":"S12","published-print":{"date-parts":[[2009,10]]}},"alternative-id":["3411"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s12-s8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10]]},"article-number":"S8"}}