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.
authors.affiliation: 1] Department of Computer Science, Princeton University, Princeton, New Jersey, USA. [2] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: 1] Department of Computer Science, Princeton University, Princeton, New Jersey, USA. [2] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
authors.forename: Aaron K
authors.initials: AK
authors.lastname: Wong
authors.affiliation: Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
authors.forename: Arjun
authors.initials: A
authors.lastname: Krishnan
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.
authors.forename: Miriam R
authors.initials: MR
authors.lastname: Aure
authors.affiliation: Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
authors.forename: Alicja
authors.initials: A
authors.lastname: Tadych
authors.affiliation: 1] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA. [2] Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.
authors.forename: Ran
authors.initials: R
authors.lastname: Zhang
authors.affiliation: 1] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA. [2] Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Corney
authors.affiliation: 1] Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA. [2] Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, USA.
authors.forename: Casey S
authors.initials: CS
authors.lastname: Greene
authors.affiliation: Department of Computer Science, University of Tromsø, Tromsø, Norway.
authors.forename: Lars A
authors.initials: LA
authors.lastname: Bongo
authors.affiliation: 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway. [2] Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. [3] Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Akershus, Norway.
authors.forename: Vessela N
authors.initials: VN
authors.lastname: Kristensen
authors.affiliation: Department of Computer Science, Princeton University, Princeton, New Jersey, USA.
authors.forename: Moses
authors.initials: M
authors.lastname: Charikar
authors.affiliation: Department of Computer Science, Princeton University, Princeton, New Jersey, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Li
authors.affiliation: 1] Department of Computer Science, Princeton University, Princeton, New Jersey, USA. [2] Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, New Jersey, USA. [3] Simons Center for Data Analysis, Simons Foundation, New York, New York, USA.
authors.forename: Olga G
authors.initials: OG
authors.lastname: Troyanskaya
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D063990:Gene Ontology; D053823:Hedgehog Proteins / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012313:RNA; D057386:Search Engine; D059467:Transcriptome
chemical_list: D053823:Hedgehog Proteins; D012313:RNA