Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Qian Zhu; Aaron K. Wong; Arjun Krishnan; Miriam R. Aure; Alicja Tadych; Ran Zhang; David C. Corney; Casey S. Greene; Lars A. Bongo; Vessela N. Kristensen; Moses Charikar; Kai Li; Olga G. Troyanskaya

doi:10.1038/nmeth.3249

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Qian Zhu, Aaron K. Wong, Arjun Krishnan, Miriam R. Aure, Alicja Tadych, Ran Zhang, David C. Corney, Casey S. Greene, Lars A. Bongo, Vessela N. Kristensen, Moses Charikar, Kai Li, Olga G. Troyanskaya

Research output: Contribution to journal › Article › peer-review

113 Scopus citations

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.

Original language	English (US)
Pages (from-to)	211-214
Number of pages	4
Journal	Nature Methods
Volume	12
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.3249
State	Published - Feb 26 2015

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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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.}",

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AU - Zhu, Qian

AU - Wong, Aaron K.

AU - Krishnan, Arjun

AU - Aure, Miriam R.

AU - Tadych, Alicja

AU - Zhang, Ran

AU - Corney, David C.

AU - Greene, Casey S.

AU - Bongo, Lars A.

AU - Kristensen, Vessela N.

AU - Charikar, Moses

AU - Li, Kai

AU - Troyanskaya, Olga G.

PY - 2015/2/26

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Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Abstract

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