{"doi":"10.1038/nmeth.3249","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.","journal":"Nature Methods","year":2015,"id":12251,"datarank":0.7401710899696038,"base_score":4.9344739331306915,"endowment":4.9344739331306915,"self_citation_contribution":0.7401710899696038,"citation_network_contribution":0.0,"self_endowment_contribution":0.7401710899696038,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":138,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.3298,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-01-12","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":27352,"name":"Aaron K. Wong","orcid":"0000-0002-7294-0646","position":1,"is_corresponding":false},{"id":34964,"name":"Krishnan, Arjun","orcid":"0000-0002-7980-4110","position":2,"is_corresponding":false},{"id":13223,"name":"Sietse Aukema","orcid":"0000-0001-5824-0320","position":3,"is_corresponding":false},{"id":96850,"name":"Alicja Tadych","orcid":"0000-0001-8645-0739","position":4,"is_corresponding":false},{"id":34966,"name":"Ran Zhang","orcid":"0000-0002-7630-1251","position":5,"is_corresponding":false},{"id":96851,"name":"David C. Corney","orcid":null,"position":6,"is_corresponding":false},{"id":308,"name":"Casey S. Greene","orcid":"0000-0001-8713-9213","position":7,"is_corresponding":false},{"id":30101,"name":"Lars A. Bongo","orcid":null,"position":8,"is_corresponding":false},{"id":57468,"name":"Vessela N Kristensen","orcid":"0000-0001-5012-7438","position":9,"is_corresponding":false},{"id":96852,"name":"Moses Charikar","orcid":"0000-0003-0807-3389","position":10,"is_corresponding":false},{"id":15526,"name":"Kai Li","orcid":"0009-0007-0432-655X","position":11,"is_corresponding":false},{"id":5951,"name":"Olga G. Troyanskaya","orcid":"0000-0002-5676-5737","position":12,"is_corresponding":false},{"id":13225,"name":"Miriam R. R. Aure","orcid":"0000-0001-7739-4982","position":13,"is_corresponding":false},{"id":30103,"name":"Lars Ailo Bongo","orcid":"0000-0002-7544-2482","position":14,"is_corresponding":false},{"id":18925,"name":"Qian Zhu","orcid":"0000-0001-7062-8221","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}