{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:39:15Z","timestamp":1761561555696},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-286","type":"journal-article","created":{"date-parts":[[2011,7,14]],"date-time":"2011-07-14T18:23:16Z","timestamp":1310667796000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview"],"prefix":"10.1186","volume":"12","author":[{"given":"Jeff","family":"Skinner","sequence":"first","affiliation":[]},{"given":"Yuri","family":"Kotliarov","sequence":"additional","affiliation":[]},{"given":"Sudhir","family":"Varma","sequence":"additional","affiliation":[]},{"given":"Karina L","family":"Mine","sequence":"additional","affiliation":[]},{"given":"Anatoly","family":"Yambartsev","sequence":"additional","affiliation":[]},{"given":"Richard","family":"Simon","sequence":"additional","affiliation":[]},{"given":"Yentram","family":"Huyen","sequence":"additional","affiliation":[]},{"given":"Andrey","family":"Morgun","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,7,14]]},"reference":[{"key":"4680_CR1","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"VG Tusher","year":"2001","unstructured":"Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. P Natl Acad Sci USA 2001, 98: 5116\u20135121. 10.1073\/pnas.091062498","journal-title":"P Natl Acad Sci USA"},{"key":"4680_CR2","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1198\/016214501753382129","volume":"96","author":"B Efron","year":"2001","unstructured":"Efron B, Tibshirani R, Storey JD, Tusher V: Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc 2001, 96: 1151\u20131160. 10.1198\/016214501753382129","journal-title":"J Am Stat Assoc"},{"key":"4680_CR3","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1093\/bioinformatics\/18.4.546","volume":"18","author":"W Pan","year":"2002","unstructured":"Pan W: A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18: 546\u2013554. 10.1093\/bioinformatics\/18.4.546","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"4680_CR4","doi-asserted-by":"publisher","first-page":"S7","DOI":"10.1186\/1471-2105-7-S1-S7","volume":"7","author":"AA Margolin","year":"2006","unstructured":"Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A: ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7. 10.1186\/1471-2105-7-S1-S7","journal-title":"BMC Bioinformatics"},{"key":"4680_CR5","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS: Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5: e8. 10.1371\/journal.pbio.0050008","journal-title":"PLoS Biol"},{"key":"4680_CR6","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1142\/S0219720005001004","volume":"3","author":"C Ding","year":"2005","unstructured":"Ding C, Peng H: Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol 2005, 3: 185\u2013205. 10.1142\/S0219720005001004","journal-title":"J Bioinform Comput Biol"},{"key":"4680_CR7","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1109\/TPAMI.2005.159","volume":"27","author":"H Peng","year":"2005","unstructured":"Peng H, Long F, Ding C: Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 2005, 27: 1226\u20131238.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"Suppl 1","key":"4680_CR8","doi-asserted-by":"publisher","first-page":"i194","DOI":"10.1093\/bioinformatics\/bth909","volume":"20","author":"D Kostka","year":"2004","unstructured":"Kostka D, Spang R: Finding disease specific alterations in the co-expression of genes. Bioinformatics 2004, 20(Suppl 1):i194\u2013199. 10.1093\/bioinformatics\/bth909","journal-title":"Bioinformatics"},{"key":"4680_CR9","doi-asserted-by":"crossref","unstructured":"Xiao YH, Frisina R, Gordon A, Klebanov L, Yakovlev A: Multivariate search for differentially expressed gene combinations. BMC Bioinformatics 2004., 5(20): doi:10.1186\/1471-2105-10-20","DOI":"10.1186\/1471-2105-5-164"},{"key":"4680_CR10","doi-asserted-by":"publisher","first-page":"4348","DOI":"10.1093\/bioinformatics\/bti722","volume":"21","author":"JK Choi","year":"2005","unstructured":"Choi JK, Yu US, Yoo OJ, Kim S: Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 2005, 21: 4348\u20134355. 10.1093\/bioinformatics\/bti722","journal-title":"Bioinformatics"},{"key":"4680_CR11","volume-title":"Genome Biol","author":"M Dettling","year":"2005","unstructured":"Dettling M, Gabrielson E, Giovanni P: Searching for differentially expressed gene combinations. Genome Biol 2005., 6(164):"},{"key":"4680_CR12","doi-asserted-by":"publisher","first-page":"3146","DOI":"10.1093\/bioinformatics\/bth379","volume":"20","author":"Y Lai","year":"2004","unstructured":"Lai Y, Wu B, Chen L, Zhao H: A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 2004, 20: 3146\u20133155. 10.1093\/bioinformatics\/bth379","journal-title":"Bioinformatics"},{"key":"4680_CR13","volume-title":"BMC Bioinformatics","author":"M Watson","year":"2006","unstructured":"Watson M: CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 2006., 7(509):"},{"key":"4680_CR14","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/msb.2008.2","volume":"4","author":"KM Mani","year":"2008","unstructured":"Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A: A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 2008, 4: 169.","journal-title":"Mol Syst Biol"},{"key":"4680_CR15","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1177\/117693510700300022","volume":"3","author":"R Simon","year":"2007","unstructured":"Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y: Analysis of Gene Expression Data Using BRB-Array Tools. Cancer Inform 2007, 3: 11\u201317.","journal-title":"Cancer Inform"},{"issue":"1","key":"4680_CR16","first-page":"289","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc B Met 1995, 57(1):289\u2013300. doi:10.2307\/2346101","journal-title":"J Roy Stat Soc B Met"},{"key":"4680_CR17","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1214\/aos\/1013699998","volume":"29","author":"Y Benjamini","year":"2001","unstructured":"Benjamini Y, Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Ann Stat 2001, 29: 1165\u20131188. 10.1214\/aos\/1013699998","journal-title":"Ann Stat"},{"key":"4680_CR18","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1111\/1467-9868.00346","volume":"64","author":"JD Storey","year":"2002","unstructured":"Storey JD: A direct approach to false discovery rates. J Roy Stat Soc B 2002, 64: 479\u2013498. 10.1111\/1467-9868.00346","journal-title":"J Roy Stat Soc B"},{"key":"4680_CR19","doi-asserted-by":"publisher","first-page":"2013","DOI":"10.1214\/aos\/1074290335","volume":"31","author":"JD Storey","year":"2003","unstructured":"Storey JD: The positive false discovery rate: A Bayesian interpretation and the q-value. Ann Stat 2003, 31: 2013\u20132035. 10.1214\/aos\/1074290335","journal-title":"Ann Stat"},{"key":"4680_CR20","doi-asserted-by":"publisher","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey JD, Tibshirani R: Statistical significance for genomewide studies. P Natl Acad Sci USA 2003, 100: 9440\u20139445. 10.1073\/pnas.1530509100","journal-title":"P Natl Acad Sci USA"},{"key":"4680_CR21","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.2307\/2532694","volume":"48","author":"SP Wright","year":"1992","unstructured":"Wright SP: Adjusted P-Values for Simultaneous Inference. Biometrics 1992, 48: 1005\u20131013. 10.2307\/2532694","journal-title":"Biometrics"},{"key":"4680_CR22","doi-asserted-by":"publisher","first-page":"2366","DOI":"10.1038\/nprot.2007.324","volume":"2","author":"MS Cline","year":"2007","unstructured":"Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD: Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2: 2366\u20132382. 10.1038\/nprot.2007.324","journal-title":"Nat Protoc"},{"key":"4680_CR23","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1158\/1541-7786.MCR-08-0435","volume":"7","author":"S Madhavan","year":"2009","unstructured":"Madhavan S, Zenklusen JC, Kotliarov Y, Sahni H, Fine HA, Buetow K: Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol Cancer Res 2009, 7: 157\u2013167. 10.1158\/1541-7786.MCR-08-0435","journal-title":"Mol Cancer Res"},{"key":"4680_CR24","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/S0140-6736(03)12328-8","volume":"361","author":"A Behin","year":"2003","unstructured":"Behin A, Hoang-Xuan K, Carpentier AF, Delattre JY: Primary brain tumours in adults. Lancet 2003, 361: 323\u2013331. 10.1016\/S0140-6736(03)12328-8","journal-title":"Lancet"},{"key":"4680_CR25","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1016\/j.ccr.2006.03.003","volume":"9","author":"LX Sun","year":"2006","unstructured":"Sun LX, Hui AM, Su Q, Vortmeyer A, Kotliarov Y, Pastorino S, Passaniti A, Menon J, Walling J, Bailey R, Rosenblum M, Mikkelsen T, Fine HA: Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell 2006, 9: 287\u2013300. 10.1016\/j.ccr.2006.03.003","journal-title":"Cancer Cell"},{"key":"4680_CR26","doi-asserted-by":"publisher","first-page":"2091","DOI":"10.1158\/0008-5472.CAN-08-2100","volume":"69","author":"A Li","year":"2009","unstructured":"Li A, Walling J, Ahn S, Kotliarov Y, Su Q, Quezado M, Oberholtzer JC, Park J, Zenklusen JC, Fine HA: Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 2009, 69: 2091\u20132099.","journal-title":"Cancer Res"},{"key":"4680_CR27","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1476-4598-7-41","volume":"7","author":"F Ducray","year":"2008","unstructured":"Ducray F, Idbaih A, de Reynies A, Bieche I, Thillet J, Mokhtari K, Lair S, Marie Y, Paris S, Vidaud M, Hoang-Xuan K, Delattre O, Delattre JY, Sanson M: Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile. Mol Cancer 2008, 7: 41. 10.1186\/1476-4598-7-41","journal-title":"Mol Cancer"},{"key":"4680_CR28","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1111\/j.1750-3639.2004.tb00495.x","volume":"14","author":"A Mukasa","year":"2004","unstructured":"Mukasa A, Ueki K, Ge X, Ishikawa S, Ide T, Fujimaki T, Nishikawa R, Asai A, Kirino T, Aburatani H: Selective expression of a subset of neuronal genes in oligodendroglioma with chromosome 1p loss. Brain Pathol 2004, 14: 34\u201342.","journal-title":"Brain Pathol"},{"key":"4680_CR29","doi-asserted-by":"publisher","first-page":"6899","DOI":"10.1073\/pnas.84.19.6899","volume":"84","author":"AJ Wong","year":"1987","unstructured":"Wong AJ, Bigner SH, Bigner DD, Kinzler KW, Hamilton SR, Vogelstein B: Increased Expression of the Epidermal Growth-Factor Receptor Gene in Malignant Gliomas Is Invariably Associated with Gene Amplification. P Natl Acad Sci USA 1987, 84: 6899\u20136903. 10.1073\/pnas.84.19.6899","journal-title":"P Natl Acad Sci USA"},{"key":"4680_CR30","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1038\/nature08797","volume":"463","author":"T Vierbuchen","year":"2010","unstructured":"Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Sudhof TC, Wernig M: Direct conversion of fibroblasts to functional neurons by defined factors. Nature 2010, 463: 1035-U1050. 10.1038\/nature08797","journal-title":"Nature"},{"key":"4680_CR31","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/nature09347","volume":"467","author":"A Aguirre","year":"2010","unstructured":"Aguirre A, Rubio ME, Gallo V: Notch and EGFR pathway interaction regulates neural stem cell number and self-renewal. Nature 2010, 467: 323\u2013327. 10.1038\/nature09347","journal-title":"Nature"},{"key":"4680_CR32","doi-asserted-by":"publisher","first-page":"re6","DOI":"10.1126\/scisignal.287re6","volume":"2","author":"PH Huang","year":"2009","unstructured":"Huang PH, Xu AM, White FM: Oncogenic EGFR signaling networks in glioma. Sci Signal 2009, 2: re6. 10.1126\/scisignal.287re6","journal-title":"Sci Signal"},{"key":"4680_CR33","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/313144a0","volume":"313","author":"TA Libermann","year":"1985","unstructured":"Libermann TA, Nusbaum HR, Razon N, Kris R, Lax I, Soreq H, Whittle N, Waterfield MD, Ullrich A, Schlessinger J: Amplification, enhanced expression and possible rearrangement of EGF receptor gene in primary human brain tumours of glial origin. Nature 1985, 313: 144\u2013147. 10.1038\/313144a0","journal-title":"Nature"},{"key":"4680_CR34","first-page":"1398","volume":"1","author":"JR Sainsbury","year":"1987","unstructured":"Sainsbury JR, Farndon JR, Needham GK, Malcolm AJ, Harris AL: Epidermal-growth-factor receptor status as predictor of early recurrence of and death from breast cancer. Lancet 1987, 1: 1398\u20131402.","journal-title":"Lancet"},{"key":"4680_CR35","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/bjc.1987.104","volume":"55","author":"D Veale","year":"1987","unstructured":"Veale D, Ashcroft T, Marsh C, Gibson GJ, Harris AL: Epidermal growth factor receptors in non-small cell lung cancer. Br J Cancer 1987, 55: 513\u2013516. 10.1038\/bjc.1987.104","journal-title":"Br J Cancer"},{"key":"4680_CR36","first-page":"3639","volume":"23","author":"S Yano","year":"2003","unstructured":"Yano S, Kondo K, Yamaguchi M, Richmond G, Hutchison M, Wakeling A, Averbuch S, Wadsworth P: Distribution and function of EGFR in human tissue and the effect of EGFR tyrosine kinase inhibition. Anticancer Res 2003, 23: 3639\u20133650.","journal-title":"Anticancer Res"},{"key":"4680_CR37","doi-asserted-by":"publisher","first-page":"387","DOI":"10.2353\/ajpath.2010.090748","volume":"177","author":"J Soikkeli","year":"2010","unstructured":"Soikkeli J, Podlasz P, Yin M, Nummela P, Jahkola T, Virolainen S, Krogerus L, Heikkila P, von Smitten K, Saksela O, Holtta E: Metastatic outgrowth encompasses COL-I, FN1, and POSTN up-regulation and assembly to fibrillar networks regulating cell adhesion, migration, and growth. Am J Pathol 2010, 177: 387\u2013403. 10.2353\/ajpath.2010.090748","journal-title":"Am J Pathol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-286.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T14:59:56Z","timestamp":1630508396000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-286"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,7,14]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4680"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-286","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,14]]},"assertion":[{"value":"7 March 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 July 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 July 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"286"}}