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 journalArticlepeer-review

105 Scopus citations


We present SEEK (search-based exploration of expression compendia;, 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 languageEnglish (US)
Pages (from-to)211-214
Number of pages4
JournalNature Methods
Issue number3
StatePublished - Feb 26 2015

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry
  • Biotechnology
  • Cell Biology


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