@article{6b65d43458ba4f588834e1be79fb6179,
title = "Targeted exploration and analysis of large cross-platform human transcriptomic compendia",
abstract = "We present SEEK (search-based exploration of expression compendia; http://seek.princeton.edu/), a query-based search engine for very large transcriptomic data collections, including thousands of human data sets from many different microarray and high-throughput sequencing platforms. SEEK uses a query-level cross-validation-based algorithm to automatically prioritize data sets relevant to the query and a robust search approach to identify genes, pathways and processes co-regulated with the query. SEEK provides multigene query searching with iterative metadata-based search refinement and extensive visualization-based analysis options.",
author = "Qian Zhu and Wong, {Aaron K.} and Arjun Krishnan and Aure, {Miriam R.} and Alicja Tadych and Ran Zhang and Corney, {David C.} and Greene, {Casey S.} and Bongo, {Lars A.} and Kristensen, {Vessela N.} and Moses Charikar and Kai Li and Troyanskaya, {Olga G.}",
note = "Funding Information: The work was supported in part by the US National Institutes of Health (NIH) award R01 HG005998 and partially supported by the US National Science Foundation (NSF) CAREER award (DBI-0546275) and NIH award R01 GM071966 to O.G.T. The project was also partially supported in part by the NIH awards T32 HG003284 and P50 GM071508. M.C. was supported by NSF awards CCF 1218687 and CCF 1302518. O.G.T. receives support as part of the Canadian Institute For Advanced Research in the Genetic Networks group. We thank members of the Troyanskaya lab for comments about SEEK in the regular lab meetings and Q. Zhu for critically reading the manuscript. We thank the volunteers from Princeton and other universities, including the Canadian Institute for Advanced Research Publisher Copyright: {\textcopyright} 2015 Nature America, Inc.",
year = "2015",
month = feb,
day = "26",
doi = "10.1038/nmeth.3249",
language = "English (US)",
volume = "12",
pages = "211--214",
journal = "Nature Methods",
issn = "1548-7091",
publisher = "Nature Publishing Group",
number = "3",
}