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

Nat Methods. 2015 Mar;12(3):211-4, 3 p following 214. doi: 10.1038/nmeth.3249. Epub 2015 Jan 12.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Databases, Genetic
  • Gene Ontology
  • Hedgehog Proteins / genetics
  • Hedgehog Proteins / metabolism
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • RNA
  • Search Engine*
  • Transcriptome*


  • Hedgehog Proteins
  • RNA