{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:12:41Z","timestamp":1761559961097,"version":"3.32.0"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2005,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits enormously from cross-comparing to other experiments. This process is generally performed by numerical meta-analysis of published data where the researcher chooses the datasets to be analyzed based on assumptions about the biological relations of published datasets to his own data, thus severely limiting the possibility of finding surprising connections. Here we propose using a repository of published gene lists for the identification of interesting datasets to be subjected to more detailed numerical analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have compiled lists of genes that have been reported as differentially regulated in cancer related microarray studies. We searched these gene lists for statistically significant overlaps with lists of genes regulated by the tumor suppressors p16 and pRB. We identified a highly significant overlap of p16 and pRB target genes with genes regulated by the EWS\/FLI fusion protein. Detailed numerical analysis of these data identified two sets of genes with clearly distinct roles in the G1\/S and the G2\/M phases of the cell cycle, as measured by enrichment of Gene Ontology categories.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>We show that mining of published gene lists in the absence of numerical detail about gene expression levels constitutes a fast, easy to perform, widely applicable, and unbiased route towards the identification of biologically related gene expression microarray datasets.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-6-s4-s14","type":"journal-article","created":{"date-parts":[[2005,12,3]],"date-time":"2005-12-03T19:13:49Z","timestamp":1133637229000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control"],"prefix":"10.1186","volume":"6","author":[{"given":"Giacomo","family":"Finocchiaro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Mancuso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heiko","family":"Muller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,12,1]]},"reference":[{"issue":"Suppl","key":"729_CR1","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1038\/ng1109","volume":"33","author":"M Kanehisa","year":"2003","unstructured":"Kanehisa M, Bork P: Bioinformatics in the post-sequence era. Nat Genet 2003, 33(Suppl):305\u2013310. 10.1038\/ng1109","journal-title":"Nat Genet"},{"issue":"5235","key":"729_CR2","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467\u2013470. 10.1126\/science.270.5235.467","journal-title":"Science"},{"issue":"3","key":"729_CR3","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/73439","volume":"24","author":"U Scherf","year":"2000","unstructured":"Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, et al.: A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000, 24(3):236\u2013244. 10.1038\/73439","journal-title":"Nat Genet"},{"issue":"1","key":"729_CR4","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","volume":"102","author":"TR Hughes","year":"2000","unstructured":"Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al.: Functional discovery via a compendium of expression profiles. Cell 2000, 102(1):109\u2013126. 10.1016\/S0092-8674(00)00015-5","journal-title":"Cell"},{"issue":"6896","key":"729_CR5","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature00935","volume":"418","author":"G Giaever","year":"2002","unstructured":"Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al.: Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418(6896):387\u2013391. 10.1038\/nature00935","journal-title":"Nature"},{"issue":"1","key":"729_CR6","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207\u2013210. 10.1093\/nar\/30.1.207","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"729_CR7","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1093\/nar\/gkg091","volume":"31","author":"A Brazma","year":"2003","unstructured":"Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, et al.: ArrayExpress \u2013 a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31(1):68\u201371. 10.1093\/nar\/gkg091","journal-title":"Nucleic Acids Res"},{"issue":"25","key":"729_CR8","doi-asserted-by":"publisher","first-page":"9309","DOI":"10.1073\/pnas.0401994101","volume":"101","author":"DR Rhodes","year":"2004","unstructured":"Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 2004, 101(25):9309\u20139314. 10.1073\/pnas.0401994101","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"729_CR9","doi-asserted-by":"publisher","first-page":"msb4100005-E410","DOI":"10.1038\/msb4100005","volume":"1","author":"A Tanay","year":"2005","unstructured":"Tanay A, Steinfeld I, Kupiec M, Shamir R: Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Molecular Systems Biology 2005, 1(1):msb4100005-E4100001-msb4100005-E4100010. 10.1038\/msb4100005","journal-title":"Molecular Systems Biology"},{"issue":"15","key":"729_CR10","first-page":"4427","volume":"62","author":"DR Rhodes","year":"2002","unstructured":"Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62(15):4427\u20134433.","journal-title":"Cancer Res"},{"issue":"46","key":"729_CR11","doi-asserted-by":"publisher","first-page":"46124","DOI":"10.1074\/jbc.M304930200","volume":"278","author":"R Vernell","year":"2003","unstructured":"Vernell R, Helin K, Muller H: Identification of target genes of the p16INK4A-pRB-E2F pathway. J Biol Chem 2003, 278(46):46124\u201346137. 10.1074\/jbc.M304930200","journal-title":"J Biol Chem"},{"issue":"4","key":"729_CR12","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/S1535-6108(02)00056-9","volume":"1","author":"SL Lessnick","year":"2002","unstructured":"Lessnick SL, Dacwag CS, Golub TR: The Ewing's sarcoma oncoprotein EWS\/FLI induces a p53-dependent growth arrest in primary human fibroblasts. Cancer Cell 2002, 1(4):393\u2013401. 10.1016\/S1535-6108(02)00056-9","journal-title":"Cancer Cell"},{"issue":"12","key":"729_CR13","doi-asserted-by":"publisher","first-page":"899","DOI":"10.2165\/00128072-200103120-00003","volume":"3","author":"M Paulussen","year":"2001","unstructured":"Paulussen M, Frohlich B, Jurgens H: Ewing tumour: incidence, prognosis and treatment options. Paediatr Drugs 2001, 3(12):899\u2013913. 10.2165\/00128072-200103120-00003","journal-title":"Paediatr Drugs"},{"issue":"4","key":"729_CR14","first-page":"245","volume":"2","author":"A Guffanti","year":"2003","unstructured":"Guffanti A, Finocchiaro G, Reid JF, Luzi L, Alcalay M, Confalonieri S, Lassandro L, Muller H: Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases. Appl Bioinformatics 2003, 2(4):245\u2013249.","journal-title":"Appl Bioinformatics"},{"issue":"18","key":"729_CR15","doi-asserted-by":"publisher","first-page":"3670","DOI":"10.1093\/bioinformatics\/bth416","volume":"20","author":"G Finocchiaro","year":"2004","unstructured":"Finocchiaro G, Parise P, Minardi SP, Alcalay M, Muller H: GenePicker: replicate analysis of Affymetrix gene expression microarrays. Bioinformatics 2004, 20(18):3670\u20133672. 10.1093\/bioinformatics\/bth416","journal-title":"Bioinformatics"},{"issue":"57","key":"729_CR16","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"B","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society 1995, B(57):289\u2013300.","journal-title":"Journal of the Royal Statistical Society"},{"issue":"46","key":"729_CR17","doi-asserted-by":"publisher","first-page":"7209","DOI":"10.1038\/sj.onc.1206804","volume":"22","author":"AP Young","year":"2003","unstructured":"Young AP, Nagarajan R, Longmore GD: Mechanisms of transcriptional regulation by Rb-E2F segregate by biological pathway. Oncogene 2003, 22(46):7209\u20137217. 10.1038\/sj.onc.1206804","journal-title":"Oncogene"},{"issue":"12","key":"729_CR18","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1093\/bioinformatics\/18.12.1585","volume":"18","author":"E Hubbell","year":"2002","unstructured":"Hubbell E, Liu WM, Mei R: Robust estimators for expression analysis. Bioinformatics 2002, 18(12):1585\u20131592. 10.1093\/bioinformatics\/18.12.1585","journal-title":"Bioinformatics"},{"issue":"4","key":"729_CR19","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gng015","volume":"31","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15. 10.1093\/nar\/gng015","journal-title":"Nucleic Acids Res"},{"key":"729_CR20","volume-title":"Technical Report","author":"Z Wu","year":"2003","unstructured":"Wu Z, Irizarry RA, Gentleman R, Murillo F, Spencer F: A Model Based Background Adjustment for Oligonucleotide Expression Arrays. In Technical Report. John Hopkins University, Department of Biostatistics; 2003."},{"issue":"1","key":"729_CR21","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/1471-2105-5-16","volume":"5","author":"B Zhang","year":"2004","unstructured":"Zhang B, Schmoyer D, Kirov S, Snoddy J: GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 2004, 5(1):16. 10.1186\/1471-2105-5-16","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"729_CR22","doi-asserted-by":"publisher","first-page":"4684","DOI":"10.1128\/MCB.21.14.4684-4699.2001","volume":"21","author":"S Ishida","year":"2001","unstructured":"Ishida S, Huang E, Zuzan H, Spang R, Leone G, West M, Nevins JR: Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol 2001, 21(14):4684\u20134699. 10.1128\/MCB.21.14.4684-4699.2001","journal-title":"Mol Cell Biol"},{"issue":"2","key":"729_CR23","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1101\/gad.949802","volume":"16","author":"B Ren","year":"2002","unstructured":"Ren B, Cam H, Takahashi Y, Volkert T, Terragni J, Young RA, Dynlacht BD: E2F integrates cell cycle progression with DNA repair, replication, and G(2)\/M checkpoints. Genes Dev 2002, 16(2):245\u2013256. 10.1101\/gad.949802","journal-title":"Genes Dev"},{"issue":"7001","key":"729_CR24","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/nature02820","volume":"430","author":"E Hernando","year":"2004","unstructured":"Hernando E, Nahle Z, Juan G, Diaz-Rodriguez E, Alaminos M, Hemann M, Michel L, Mittal V, Gerald W, Benezra R, et al.: Rb inactivation promotes genomic instability by uncoupling cell cycle progression from mitotic control. Nature 2004, 430(7001):797\u2013802. 10.1038\/nature02820","journal-title":"Nature"},{"issue":"3","key":"729_CR25","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1200\/JCO.2005.02.081","volume":"23","author":"HY Huang","year":"2005","unstructured":"Huang HY, Illei PB, Zhao Z, Mazumdar M, Huvos AG, Healey JH, Wexler LH, Gorlick R, Meyers P, Ladanyi M: Ewing sarcomas with p53 mutation or p16\/p14ARF homozygous deletion: a highly lethal subset associated with poor chemoresponse. J Clin Oncol 2005, 23(3):548\u2013558. 10.1200\/JCO.2005.02.081","journal-title":"J Clin Oncol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-S4-S14.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T04:17:24Z","timestamp":1736137044000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-S4-S14"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,12]]},"references-count":25,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2005,12]]}},"alternative-id":["729"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-s4-s14","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,12]]},"assertion":[{"value":"1 December 2005","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S14"}}