{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T23:21:09Z","timestamp":1725492069574},"publisher-location":"Berlin, Heidelberg","reference-count":24,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540730590"},{"type":"electronic","value":"9783540730606"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-73060-6_4","type":"book-chapter","created":{"date-parts":[[2007,9,18]],"date-time":"2007-09-18T15:35:17Z","timestamp":1190129717000},"page":"42-56","source":"Crossref","is-referenced-by-count":7,"title":["A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells"],"prefix":"10.1007","author":[{"given":"Celine","family":"Lefebvre","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei Keat","family":"Lim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katia","family":"Basso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo Dalla","family":"Favera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Califano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"16","key":"4_CR1","doi-asserted-by":"publisher","first-page":"5934","DOI":"10.1073\/pnas.0306752101","volume":"101","author":"E. Yeger-Lotem","year":"2004","unstructured":"Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U., Margalit, H.: Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl. Acad. Sci. USA\u00a0101(16), 5934\u20135939 (2004)","journal-title":"Proc Natl. Acad. Sci. USA"},{"issue":"7","key":"4_CR2","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/gb-2006-7-7-r55","volume":"7","author":"H. Yu","year":"2006","unstructured":"Yu, H., Xia, Y., Trifonov, V., Gerstein, M.: Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol.\u00a0R7(7), R55 (2006)","journal-title":"Genome Biol."},{"issue":"7062","key":"4_CR3","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1038\/nature04209","volume":"437","author":"J.F. Rual","year":"2005","unstructured":"Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P., Vidal, M.: Towards a proteome-scale map of the human protein-protein interaction network. Nature\u00a0437(7062), 1173\u20131178 (2005)","journal-title":"Nature"},{"issue":"6","key":"4_CR4","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, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., Wanker, E.E.: A human protein-protein interaction network: a resource for annotating the proteome. Cell\u00a0122(6), 957\u2013968 (2005)","journal-title":"Cell"},{"issue":"1","key":"4_CR5","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.jbi.2003.10.001","volume":"37","author":"A. Rzhetsky","year":"2004","unstructured":"Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P.A., Weng, W., Wilbur, W.J., Hatzivassiloglou, V., Friedman, C.: Geneways: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed Inform.\u00a037(1), 43\u201353 (2004)","journal-title":"J Biomed Inform."},{"issue":"Suppl 1","key":"4_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-7-S1-S7","volume":"7","author":"A.A. Margolin","year":"2006","unstructured":"Margolin, A.A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, D., Califano, A.: Aracne: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics\u00a07(Suppl 1), S1\u20137 (2006)","journal-title":"BMC Bioinformatics"},{"issue":"5644","key":"4_CR7","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1126\/science.1087361","volume":"302","author":"R. Jansen","year":"2003","unstructured":"Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F., Gerstein, M.: A bayesian networks approach for predicting protein-protein interactions from genomic data. Science\u00a0302(5644), 449\u2013453 (2003)","journal-title":"Science"},{"issue":"8","key":"4_CR8","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1038\/nbt1103","volume":"23","author":"D.R. Rhodes","year":"2005","unstructured":"Rhodes, D.R., Tomlins, S.A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A., Chinnaiyan, A.M.: Probabilistic model of the human protein-protein interaction network. Nat. Biotechnol.\u00a023(8), 951\u2013959 (2005)","journal-title":"Nat Biotechnol."},{"issue":"10","key":"4_CR9","doi-asserted-by":"publisher","first-page":"2363","DOI":"10.1101\/gr.1680803","volume":"13","author":"S. Peri","year":"2003","unstructured":"Peri, S., Navarro, J.D., Amanchy, R., Kristiansen, T.Z., Jonnalagadda, C.K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T.K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H.N., Rashmi, B.P., Ramya, M.A., Zhao, Z., Chandrika, K.N., Padma, N., Harsha, H.C., Yatish, A.J., Kavitha, M.P., Menezes, M., Choudhury, D.R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S.K., Madavan, V., Joseph, A., Wong, G.W., Schiemann, W.P., Constantinescu, S.N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G.C., Dang, C.V., Garcia, J.G., Pevsner, J., Jensen, O.N., Roepstorff, P., Deshpande, K.S., Chinnaiyan, A.M., Hamosh, A., Chakravarti, A., Pandey, A.: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res.\u00a013(10), 2363\u20132371 (2003)","journal-title":"Genome Res."},{"issue":"Database issue","key":"4_CR10","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/nar\/gkh052","volume":"32","author":"H. Hermjakob","year":"2004","unstructured":"Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., Apweiler, R.: Intact: an open source molecular interaction database. Nucleic Acids Res.\u00a032(Database issue), 452\u2013455 (2004)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"4_CR11","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1093\/nar\/gkg056","volume":"31","author":"G.D. Bader","year":"2003","unstructured":"Bader, G.D., Betel, D., Hogue, C.W.: Bind: the biomolecular interaction network database. Nucleic Acids Res.\u00a031(1), 248\u2013250 (2003)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"4_CR12","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1093\/nar\/30.1.303","volume":"30","author":"I. Xenarios","year":"2002","unstructured":"Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., Eisenberg, D.: Dip, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res.\u00a030(1), 303\u2013305 (2002)","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"4_CR13","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1101\/gad.970902","volume":"16","author":"A. Kumar","year":"2002","unstructured":"Kumar, A., Agarwal, S., Heyman, J.A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., Cheung, K.H., Miller, P., Gerstein, M., Roeder, G.S., Snyder, M.: Subcellular localization of the yeast proteome. Genes Dev.\u00a016(6), 707\u2013719 (2002)","journal-title":"Genes Dev"},{"issue":"10","key":"4_CR14","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/gb-2003-4-10-r69","volume":"4","author":"K.I. Zeller","year":"2003","unstructured":"Zeller, K.I., Jegga, A.G., Aronow, B.J., O\u2019Donnell, K.A., Dang, C.V.: An integrated database of genes responsive to the myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol.\u00a04(10), R69 (2003)","journal-title":"Genome Biol."},{"issue":"4","key":"4_CR15","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/ng1532","volume":"37","author":"K. Basso","year":"2005","unstructured":"Basso, K., Margolin, A.A., Stolovitzky, G., Klein, U., Dalla-Favera, R., Califano, A.: Reverse engineering of regulatory networks in human b cells. Nat. Genet.\u00a037(4), 382\u2013390 (2005)","journal-title":"Nat. Genet."},{"key":"4_CR16","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1007\/11732990_30","volume-title":"Research in Computational Molecular Biology","author":"K. Wang","year":"2006","unstructured":"Wang, K., Banerjee, N., Margolin, A., Nemenman, I., Califano, A.: Genome-wide discovery of modulators of transcriptional interactions in human b lymphocytes. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol.\u00a03909, pp. 348\u2013362. Springer, Heidelberg (2006)"},{"key":"4_CR17","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1093\/nar\/gkl799","volume":"35","author":"G. Alterovitz","year":"2006","unstructured":"Alterovitz, G., Xiang, M., Mohan, M., Ramoni, M.F.: Go pad: the gene ontology partition database. Nucleic Acids Res.\u00a035, D322\u2013D327 (2006)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"4_CR18","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M. Ashburner","year":"2000","unstructured":"Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet.\u00a025(1), 25\u201329 (2000)","journal-title":"Nat Genet."},{"issue":"1","key":"4_CR19","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/gkg108","volume":"31","author":"V. Matys","year":"2003","unstructured":"Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., Kloos, D.U., Land, S., Lewicki-Potapov, B., Michael, H., Munch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S., Wingender, E.: Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res.\u00a031(1), 374\u2013378 (2003)","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"4_CR20","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1093\/nar\/gkj148","volume":"34","author":"H.W. Mewes","year":"2006","unstructured":"Mewes, H.W., Frishman, D., Mayer, K.F., Munsterkotter, M., Noubibou, O., Pagel, P., Rattei, T., Oesterheld, M., Ruepp, A., Stumpflen, V.: Mips: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res.\u00a034(Database issue), D169\u2013D172 (2006)","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"4_CR21","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1093\/nar\/gki107","volume":"33","author":"K.P. O\u2019Brien","year":"2005","unstructured":"O\u2019Brien, K.P., Remm, M., Sonnhammer, E.L.: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res.\u00a033(Database issue), D476\u2013D480 (2005)","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"4_CR22","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1038\/nbt825","volume":"21","author":"A. Vazquez","year":"2003","unstructured":"Vazquez, A., Flammini, A., Maritan, A., Vespignani, A.: Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol.\u00a021(6), 697\u2013700 (2003)","journal-title":"Nat Biotechnol."},{"issue":"4","key":"4_CR23","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1038\/ng776","volume":"29","author":"H. Ge","year":"2001","unstructured":"Ge, H., Liu, Z., Church, G.M., Vidal, M.: Correlation between transcriptome and interactome mapping data from saccharomyces cerevisiae. Nat Genet.\u00a029(4), 482\u2013486 (2001)","journal-title":"Nat Genet."},{"issue":"23","key":"4_CR24","doi-asserted-by":"publisher","first-page":"13130","DOI":"10.1073\/pnas.96.23.13130","volume":"96","author":"X. Hua","year":"1999","unstructured":"Hua, X., Miller, Z.A., Wu, G., Shi, Y., Lodish, H.F.: Specificity in transforming growth factor beta-induced transcription of the plasminogen activator inhibitor-1 gene: interactions of promoter dna, transcription factor mue3, and smad proteins. Proc Natl Acad Sci. USA\u00a096(23), 13130\u201313135 (1999)","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Lecture Notes in Computer Science","Systems Biology and Computational Proteomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-73060-6_4.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T09:58:47Z","timestamp":1619517527000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-73060-6_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540730590","9783540730606"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-73060-6_4","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[]}}