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Supervised learning approaches predicted that the Ras pathway is active in ~70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-\u03b2, TNF-\u03b1, Src, Myc, E2F3, and \u03b2-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and\/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and\/or Src, but not E2F3, \u03b2-catenin, TNF-\u03b1, or TGF-\u03b2 pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The \u201cgene expression pathway signatures\u201d we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.<\/jats:p>","DOI":"10.1016\/s1672-0229(07)60010-2","type":"journal-article","created":{"date-parts":[[2007,6,16]],"date-time":"2007-06-16T14:12:54Z","timestamp":1182003174000},"page":"15-24","source":"Crossref","is-referenced-by-count":8,"title":["Analysis of Pathway Activity in Primary Tumors and NCI60 Cell Lines Using Gene Expression Profiling Data"],"prefix":"10.1093","volume":"5","author":[{"given":"Xing-Dong","family":"Feng","sequence":"first","affiliation":[{"name":"Integrative Biology, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu-Guang","family":"Huang","sequence":"additional","affiliation":[{"name":"Global Discovery & Development Statistics, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian-Yong","family":"Shou","sequence":"additional","affiliation":[{"name":"Cancer Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bi-Rong","family":"Liao","sequence":"additional","affiliation":[{"name":"Integrative Biology, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan M.","family":"Yingling","sequence":"additional","affiliation":[{"name":"Cancer Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiang","family":"Ye","sequence":"additional","affiliation":[{"name":"Cancer Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xi","family":"Lin","sequence":"additional","affiliation":[{"name":"Cancer Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lawrence M.","family":"Gelbert","sequence":"additional","affiliation":[{"name":"Cancer Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric W.","family":"Su","sequence":"additional","affiliation":[{"name":"Integrative Biology, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jude E.","family":"Onyia","sequence":"additional","affiliation":[{"name":"Integrative Biology, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu-Yu","family":"Li","sequence":"additional","affiliation":[{"name":"Integrative Biology, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center , Indianapolis, IN, 46285 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,6,15]]},"reference":[{"key":"2024051008242986600_bib1","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nm1087","article-title":"Cancer genes and the pathways they control","volume":"10","author":"Vogelstein","year":"2004","journal-title":"Nat. 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