{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T16:39:25Z","timestamp":1743093565928,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":42,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642163449"},{"type":"electronic","value":"9783642163456"}],"license":[{"start":{"date-parts":[[2011,1,1]],"date-time":"2011-01-01T00:00:00Z","timestamp":1293840000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2011,1,1]],"date-time":"2011-01-01T00:00:00Z","timestamp":1293840000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011]]},"DOI":"10.1007\/978-3-642-16345-6_23","type":"book-chapter","created":{"date-parts":[[2011,5,16]],"date-time":"2011-05-16T16:31:03Z","timestamp":1305563463000},"page":"479-500","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information"],"prefix":"10.1007","author":[{"given":"Zhidong","family":"Tu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,4,9]]},"reference":[{"issue":"6","key":"23_CR1_23","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1016\/j.cell.2007.11.025","volume":"131","author":"K Rikova","year":"2007","unstructured":"Rikova, K., Guo, A., Zeng, Q., et al. (2007). Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell, 131(6), 1190\u20131203.","journal-title":"Cell"},{"issue":"3","key":"23_CR2_23","doi-asserted-by":"publisher","first-page":"e1816","DOI":"10.1371\/journal.pone.0001816","volume":"3","author":"CJ Creighton","year":"2008","unstructured":"Creighton, C. J. (2008). Multiple oncogenic pathway signatures show coordinated exression atterns in human prostate tumors. PLos ONE, 3(3), e1816.","journal-title":"PLos ONE"},{"issue":"1","key":"23_CR3_23","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1146\/annurev.genet.41.110306.130206","volume":"42","author":"S Zaman","year":"2008","unstructured":"Zaman, S., Lippman, S. I., Zhao, X., et al. (2008). How saccharomyces responds to nutrients. Annual Review of Genetics, 42(1), 27\u201381.","journal-title":"Annual Review of Genetics"},{"issue":"5","key":"23_CR4_23","doi-asserted-by":"publisher","first-page":"e128","DOI":"10.1371\/journal.pbio.0020128","volume":"2","author":"Y Wang","year":"2004","unstructured":"Wang, Y., Pierce, M., Schneper, L., et al. (2004). Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLos Biology, 2(5), e128.","journal-title":"PLos Biology"},{"key":"23_CR5_23","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/msb.2009.2","volume":"5","author":"S Zaman","year":"2009","unstructured":"Zaman, S., Lippman, S. I., Schneper, L., et al. (2009). Glucose regulates transcription in yeast through a network of signaling pathways. Molecular Systems Biology, 5, 245.","journal-title":"Molecular Systems Biology"},{"issue":"7068","key":"23_CR6_23","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/nature04187","volume":"438","author":"J Ptacek","year":"2005","unstructured":"Ptacek, J., Devgan, G., Michaud, G., et al. (2005). Global analysis of protein phosphorylation in yeast. Nature, 438(7068), 679\u2013684.","journal-title":"Nature"},{"issue":"7001","key":"23_CR7_23","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1038\/nature02797","volume":"430","author":"M Morley","year":"2004","unstructured":"Morley, M., Molony, C. M., Weber, T. M., et al. (2004). Genetic analysis of genome-wide variation in human gene expression. Nature, 430(7001), 743\u2013747.","journal-title":"Nature"},{"issue":"5568","key":"23_CR8_23","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1126\/science.1069516","volume":"296","author":"RB Brem","year":"2002","unstructured":"Brem, R. B., Yvert, G., Clinton, R., et al. (2002). Genetic dissection of transcriptional regulation in budding yeast. Science, 296(5568), 752\u2013755.","journal-title":"Science"},{"key":"23_CR9_23","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1038\/nature01434","volume":"422","author":"EE Schadt","year":"2003","unstructured":"Schadt, E. E., et al. (2003). Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297\u2013302.","journal-title":"Nature"},{"issue":"7186","key":"23_CR10_23","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1038\/nature06757","volume":"452","author":"Y Chen","year":"2008","unstructured":"Chen, Y., Zhu, J., Lum, P. Y., et al. (2008). Variation in DNA elucidate molecular networks that cause disease. Nature, 452(7186), 429\u2013435.","journal-title":"Nature"},{"key":"23_CR11_23","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1038\/ng1589","volume":"37","author":"EE Schadt","year":"2005","unstructured":"Schadt, E. E., et al. (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics, 37, 710\u2013717.","journal-title":"Nature Genetics"},{"issue":"5","key":"23_CR12_23","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1073\/pnas.0408709102","volume":"102","author":"RB Brem","year":"2005","unstructured":"Brem, R. B., & Kruglyak, L. (2005). The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proceedings of the National Academy of Sciences of the United States of America, 102(5), 1572\u20131577.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7051","key":"23_CR13_23","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1038\/nature03865","volume":"436","author":"RB Brem","year":"2005","unstructured":"Brem, R. B., Storey, J. D., Whittle, J., et al. (2005). Genetic interactions between polymorphisms that affect gene expression in yeast. Nature, 436(7051), 701\u2013703.","journal-title":"Nature"},{"issue":"11","key":"23_CR14_23","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nrg1964","volume":"7","author":"MV Rockman","year":"2006","unstructured":"Rockman, M. V., & Kruglyak, L. (2006). Genetics of global gene expression. Nature Reviews Genetics, 7(11), 862\u2013872.","journal-title":"Nature Reviews Genetics"},{"issue":"14","key":"23_CR15_23","doi-asserted-by":"publisher","first-page":"e489","DOI":"10.1093\/bioinformatics\/btl234","volume":"22","author":"Z Tu","year":"2006","unstructured":"Tu, Z., Wang, L., Arbeitman, M. N., et al. (2006). An integrative approach for causal gene identification and gene regulatory pathway inferece. Bioinformatics, 22(14), e489\u2013e496.","journal-title":"Bioinformatics"},{"issue":"6959","key":"23_CR16_23","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/nature02046","volume":"425","author":"S Ghaemmaghami","year":"2003","unstructured":"Ghaemmaghami, S., Huh, W.-K., Bower, K., et al. (2003). Global analysis of protein expression in yeast. Nature, 425(6959), 737\u2013741.","journal-title":"Nature"},{"key":"23_CR17_23","first-page":"407","volume":"8","author":"A Zien","year":"2000","unstructured":"Zien, A., Kuffner, R., Zimmer, R., et al. (2000). Analysis of gene expression data with pathway scores. Proceedings of the International Conference on Intelligent Systems and Molecular Biology, 8, 407\u2013417.","journal-title":"Proceedings of the International Conference on Intelligent Systems and Molecular Biology"},{"issue":"1","key":"23_CR18_23","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","volume":"102","author":"TR Hughes","year":"2000","unstructured":"Hughes, T. R., Marton, M. J., Jones, A. R., et al. (2000). Functional discovery via a compendium of expression profiles. Cell, 102(1), 109\u2013126.","journal-title":"Cell"},{"issue":"5701","key":"23_CR19_23","doi-asserted-by":"publisher","first-page":"1508","DOI":"10.1126\/science.1104568","volume":"306","author":"Y Wang","year":"2004","unstructured":"Wang, Y., & Dohlman, H. G. (2004). Pheromone signaling mechanisms in yeast. Science, 306(5701), 1508\u20131509.","journal-title":"Science"},{"issue":"1","key":"23_CR20_23","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/ng1222","volume":"35","author":"G Yvert","year":"2003","unstructured":"Yvert, G., Brem, R. B., Whittle, J., et al. (2003). Trans-acting regulatory variation in Saccaromyces cerevisiae and the role of transcription factors. Nature Genetics, 35(1), 57\u201364.","journal-title":"Nature Genetics"},{"issue":"7","key":"23_CR21_23","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1038\/ng.167","volume":"40","author":"J Zhu","year":"2008","unstructured":"Zhu, J., Zhang, B., Smith, E. N., et al. (2008). Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nature Genetics, 40(7), 854\u2013861.","journal-title":"Nature Genetics"},{"issue":"13","key":"23_CR22_23","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1093\/bioinformatics\/btm151","volume":"23","author":"A Fujita","year":"2007","unstructured":"Fujita, A., Sato, J. R., Garay-Malpartida, H. M., et al. (2007). Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics, 23(13), 1623\u20131630.","journal-title":"Bioinformatics"},{"issue":"18","key":"23_CR23_23","doi-asserted-by":"publisher","first-page":"3594","DOI":"10.1093\/bioinformatics\/bth448","volume":"20","author":"J Yu","year":"2004","unstructured":"Yu, J., Smith, V. A., Wang, P. P., et al. (2004). Advances to bayesian network inference for generating causal networks from observational biological data. Bioinformatics, 20(18), 3594\u20133603.","journal-title":"Bioinformatics"},{"key":"23_CR24_23","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1038\/msb.2008.27","volume":"4","author":"X Wu","year":"2008","unstructured":"Wu, X., Jiang, R., Zhang, M. Q., et al. (2008). Network-based global inference of human disease genes. Molecular Systems Biology, 4, 189.","journal-title":"Molecular Systems Biology"},{"issue":"5643","key":"23_CR25_23","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1126\/science.1087447","volume":"302","author":"JM Stuart","year":"2003","unstructured":"Stuart, J. M., Segal, E., Koller, D., et al. (2003). A gene-coexpression network for global discovery of conserved genetic modules. Science, 302(5643), 249\u2013255.","journal-title":"Science"},{"key":"23_CR26_23","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/1471-2164-7-125","volume":"7","author":"JM Start","year":"2006","unstructured":"Start, J. M., Jagalur, M., et al. (2006). Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC Genomics, 7, 125.","journal-title":"BMC Genomics"},{"issue":"2\u20134","key":"23_CR27_23","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1159\/000078209","volume":"105","author":"J Zhu","year":"2004","unstructured":"Zhu, J., Lum, P. Y., Lamb, J., et al. (2004). An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenetics and Genome Research, 105(2\u20134), 363\u2013374.","journal-title":"Cytogenetics and Genome Research"},{"issue":"4","key":"23_CR28_23","doi-asserted-by":"publisher","first-page":"e69","DOI":"10.1371\/journal.pcbi.0030069","volume":"3","author":"J Zhu","year":"2007","unstructured":"Zhu, J., Wiener, M. C., Zhang, C., et al. (2007). Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. Plos Computational Biology, 3(4), e69.","journal-title":"Plos Computational Biology"},{"key":"23_CR29_23","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-7-113","volume":"7","author":"KD MacIsaac","year":"2006","unstructured":"MacIsaac, K. D., Wang, T., Gordon, D. B., et al. (2006). An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.","journal-title":"BMC Bioinformatics"},{"key":"23_CR30_23","doi-asserted-by":"publisher","first-page":"D436","DOI":"10.1093\/nar\/gkj003","volume":"34","author":"U Guldener","year":"2006","unstructured":"Guldener, U., Munsterkotter, M., Oesterheld, M., et al. (2006). MPact: The MIPS protein interaction resource on yeast. Nucleic Acids Research, 34, D436\u2013441.","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"23_CR31_23","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1038\/ng.167","volume":"40","author":"J Zhu","year":"2008","unstructured":"Zhu, J., Zhang, B., Smith, E. N., et al. (2008). Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nature Genetics, 40(7), 854\u2013861.","journal-title":"Nature Genetics"},{"issue":"6794","key":"23_CR32_23","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1038\/35019019","volume":"406","author":"R Albert","year":"2000","unstructured":"Albert, R., Jeong, H., Barabasi, A. L., et al. (2000). Error and attack tolerance of complex networks. Nature, 406(6794), 378\u2013382.","journal-title":"Nature"},{"issue":"5085","key":"23_CR33_23","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1126\/science.1439822","volume":"258","author":"JY Sze","year":"1992","unstructured":"Sze, J. Y., Woontner, M., Jaehning, J. A., et al. (1992). In vitro transcriptional activation by a metabolic intermediate: Activation by Leu3 depends on alpha-isopropylmalate. Science, 258(5085), 1143\u20131145.","journal-title":"Science"},{"key":"23_CR34_23","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/msb.2008.4","volume":"4","author":"S Suthram","year":"2008","unstructured":"Suthram, S., Beyer, A., Karp, R. M., et al. (2008). eQED: An efficient method for interpreting eQTL associations using protein networks. Molecular Systems Biology, 4, 162.","journal-title":"Molecular Systems Biology"},{"issue":"4","key":"23_CR35_23","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., et al. (2005). Reverse engineering of regulatory networks in human B cells. Nature Genetics, 37,(4), 382\u2013390.","journal-title":"Nature Genetics"},{"issue":"38","key":"23_CR36_23","doi-asserted-by":"publisher","first-page":"14062","DOI":"10.1073\/pnas.0601852103","volume":"103","author":"SI Lee","year":"2006","unstructured":"Lee, S. I., Pe\u2019er, D., Dudley, A. M., et al. (2006). Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proceedings of the National Academy of Sciences of the United States of America, 103(38), 14062\u201314067.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1","key":"23_CR37_23","doi-asserted-by":"publisher","first-page":"e1000358","DOI":"10.1371\/journal.pgen.1000358","volume":"5","author":"SI Lee","year":"2009","unstructured":"Lee, S. I., Dudley, A. M., Drubin, D., et al. (2009). Learning a prior on regulatory potential from eQTL data. PLoS Genetics, 5(1), e1000358.","journal-title":"PLoS Genetics"},{"issue":"4","key":"23_CR38_23","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/ng.325","volume":"41","author":"X Yang","year":"2009","unstructured":"Yang, X., Deignan, J. L., Qi, H., et al. (2009). Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature Genetics, 41(4), 415\u2013423.","journal-title":"Nature Genetics"},{"issue":"2","key":"23_CR39_23","doi-asserted-by":"publisher","first-page":"1089","DOI":"10.1534\/genetics.107.085167","volume":"179","author":"E Chaibub Neto","year":"2008","unstructured":"Chaibub Neto, E., Ferrara, C. T., Attie, A. D., et al. (2008). Inferring causal phenotype networks from segregating populations. Genetics, 179(2), 1089\u20131100.","journal-title":"Genetics"},{"issue":"10","key":"23_CR40_23","doi-asserted-by":"publisher","first-page":"R219","DOI":"10.1186\/gb-2007-8-10-r219","volume":"8","author":"LS Chen","year":"2007","unstructured":"Chen, L. S., Emmert-Streib, F., & Storey, J. D. (2007). Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8(10), R219.","journal-title":"Genome Biology"},{"key":"23_CR41_23","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/msb4100200","volume":"3","author":"Q Cui","year":"2007","unstructured":"Cui, Q., Ma, Y., Jaramillo, M., et al. (2007). A map of human cancer signaling. Molecular Systems Biology, 3, 152.","journal-title":"Molecular Systems Biology"},{"key":"23_CR42_23","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1038\/msb4100180","volume":"3","author":"H-Y Chuang","year":"2007","unstructured":"Chuang, H.-Y., Lee, E., Liu, Y.-T., et al. (2007). Network-based classification of breast cancer metastasis. Molecular Systems Biology, 3, 140.","journal-title":"Molecular Systems Biology"}],"container-title":["Handbook of Statistical Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-16345-6_23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T14:04:35Z","timestamp":1674482675000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-642-16345-6_23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011]]},"ISBN":["9783642163449","9783642163456"],"references-count":42,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-16345-6_23","relation":{},"subject":[],"published":{"date-parts":[[2011]]},"assertion":[{"value":"9 April 2011","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}