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Such approaches may require arbitrary decisions about what are considered \u201cnormal\u201d phenotypes, and what each phenotype should be compared to. Instead, we adopt a holistic approach in which we characterize phenotypes in the context of a myriad of tissues and diseases. We introduce scalable methods that associate expression patterns to phenotypes in order both to assign phenotype labels to new expression samples and to select phenotypically meaningful gene signatures. By using a nonparametric statistical approach, we identify signatures that are more precise than those from existing approaches and accurately reveal biological processes that are hidden in case vs. control studies. Employing a comprehensive perspective on expression, we show how metastasized tumor samples localize in the vicinity of the primary site counterparts and are overenriched for those phenotype labels. We find that our approach provides insights into the biological processes that underlie differences between tissues and diseases beyond those identified by traditional differential expression analyses. Finally, we provide an online resource (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/concordia.csail.mit.edu\" xlink:show=\"new\">http:\/\/concordia.csail.mit.edu<\/jats:ext-link>\n                    ) for mapping users\u2019 gene expression samples onto the expression landscape of tissue and disease.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1118792109","type":"journal-article","created":{"date-parts":[[2012,3,24]],"date-time":"2012-03-24T03:51:22Z","timestamp":1332561082000},"page":"5594-5599","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":36,"title":["Making sense out of massive data by going beyond differential expression"],"prefix":"10.1073","volume":"109","author":[{"given":"Patrick R.","family":"Schmid","sequence":"first","affiliation":[{"name":"Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA 02139 and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan P.","family":"Palmer","sequence":"additional","affiliation":[{"name":"Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA 02139 and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac S.","family":"Kohane","sequence":"additional","affiliation":[{"name":"Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[{"name":"Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2012,3,23]]},"reference":[{"key":"e_1_3_3_1_2","first-page":"D1005","article-title":"NCBI GEO: Archive for functional genomics data sets\u201410\u00a0years on","author":"Barrett T","year":"2010","unstructured":"T Barrett, et al., NCBI GEO: Archive for functional genomics data sets\u201410\u00a0years on. 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