{"doi":"10.1016/j.cell.2023.02.018","title":"The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models","abstract":"Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.","journal":"Cell","year":2023,"id":317212,"datarank":1.3789939695362126,"base_score":4.418840607796598,"endowment":4.418840607796598,"self_citation_contribution":0.6628260911694899,"citation_network_contribution":0.7161678783667226,"self_endowment_contribution":0.6628260911694899,"citer_contribution":0.7161678783667226,"corpus_percentile":85.00812253423068,"corpus_rank":1939,"citation_count":82,"citer_count":62,"citers_with_citation_signal":36,"citers_with_endowment":36,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9408,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":374406,"name":"Jiahao Gao","orcid":"0000-0002-6311-3526","position":1,"is_corresponding":false},{"id":42931,"name":"Beatrice Borsari","orcid":"0000-0003-4357-3557","position":2,"is_corresponding":false},{"id":59139,"name":"Yucheng T. Yang","orcid":"0000-0002-6873-5279","position":3,"is_corresponding":false},{"id":21524,"name":"Timur R. Galeev","orcid":"0000-0002-6241-1011","position":4,"is_corresponding":false},{"id":6259,"name":"Gamze Gürsoy","orcid":"0000-0002-1352-8686","position":5,"is_corresponding":false},{"id":866,"name":"Charles B. Epstein","orcid":"0000-0001-8358-8345","position":6,"is_corresponding":false},{"id":1022361,"name":"Kun Xiong","orcid":"0000-0003-1431-6586","position":7,"is_corresponding":false},{"id":43213,"name":"Jinrui Xu","orcid":"0000-0003-1944-2821","position":8,"is_corresponding":false},{"id":434182,"name":"Tianxiao Li","orcid":"0000-0002-9147-7511","position":9,"is_corresponding":false},{"id":21432,"name":"Jason Liu","orcid":"0000-0001-7197-7319","position":10,"is_corresponding":false},{"id":1022362,"name":"Keyang Yu","orcid":"0000-0002-3880-9396","position":11,"is_corresponding":false},{"id":1022363,"name":"Ana Berthel","orcid":"0000-0001-6849-982X","position":12,"is_corresponding":false},{"id":454691,"name":"Zhanlin Chen","orcid":"0000-0002-5835-3840","position":13,"is_corresponding":false},{"id":14412,"name":"Fábio C. P. Navarro","orcid":"0000-0002-5640-9070","position":14,"is_corresponding":false},{"id":1023361,"name":"Maxwell S. Sun","orcid":null,"position":15,"is_corresponding":false},{"id":43288,"name":"James C. Wright","orcid":"0000-0001-6950-4328","position":16,"is_corresponding":false},{"id":979184,"name":"Justin Chang","orcid":"0000-0003-1486-2261","position":17,"is_corresponding":false},{"id":550029,"name":"Christopher J. F. Cameron","orcid":"0000-0003-4088-0957","position":18,"is_corresponding":false},{"id":857,"name":"Noam Shoresh","orcid":"0000-0002-5482-5046","position":19,"is_corresponding":false},{"id":721975,"name":"Elizabeth Gaskell","orcid":"0000-0001-6497-6211","position":20,"is_corresponding":false},{"id":11799,"name":"Jörg Drenkow","orcid":null,"position":21,"is_corresponding":false},{"id":4949,"name":"Jessika Adrian","orcid":"0000-0002-8078-5308","position":22,"is_corresponding":false},{"id":49013,"name":"Sergey Aganezov","orcid":"0000-0003-2458-8323","position":23,"is_corresponding":false},{"id":7740,"name":"François Aguet","orcid":"0000-0001-9414-300X","position":24,"is_corresponding":false},{"id":586763,"name":"Gabriela Balderrama-Gutierrez","orcid":"0000-0002-5794-4518","position":25,"is_corresponding":false},{"id":443572,"name":"Samridhi Banskota","orcid":"0000-0002-3934-2273","position":26,"is_corresponding":false},{"id":1023362,"name":"Guillermo Barreto Corona","orcid":null,"position":27,"is_corresponding":false},{"id":42947,"name":"Sora Chee","orcid":"0000-0003-2687-7786","position":28,"is_corresponding":false},{"id":244011,"name":"Surya B. Chhetri","orcid":null,"position":29,"is_corresponding":false},{"id":1022364,"name":"Gabriel Conte Cortez Martins","orcid":"0000-0001-5175-6076","position":30,"is_corresponding":false},{"id":42957,"name":"Cassidy Danyko","orcid":"0000-0001-7803-783X","position":31,"is_corresponding":false},{"id":244012,"name":"Carrie Davis","orcid":null,"position":32,"is_corresponding":false},{"id":1023363,"name":"Daniel Farid","orcid":null,"position":33,"is_corresponding":false},{"id":4951,"name":"Nina Farrell","orcid":"0000-0002-5452-2344","position":34,"is_corresponding":false},{"id":1023364,"name":"Idan Gabdank","orcid":null,"position":35,"is_corresponding":false},{"id":825732,"name":"Yoel Gofin","orcid":"0000-0003-3233-258X","position":36,"is_corresponding":false},{"id":42996,"name":"David U. Gorkin","orcid":"0000-0003-4944-4107","position":37,"is_corresponding":false},{"id":249233,"name":"Mengting Gu","orcid":"0000-0003-1684-0146","position":38,"is_corresponding":false},{"id":853438,"name":"Vivian Hecht","orcid":"0000-0003-4110-1388","position":39,"is_corresponding":false},{"id":43021,"name":"Benjamin C. Hitz","orcid":"0000-0003-3361-3594","position":40,"is_corresponding":false},{"id":861,"name":"Robbyn Issner","orcid":"0000-0003-4132-9219","position":41,"is_corresponding":false},{"id":19719,"name":"Yunzhe Jiang","orcid":"0000-0001-8768-0050","position":42,"is_corresponding":false},{"id":49027,"name":"Melanie Kirsche","orcid":"0000-0002-6631-4761","position":43,"is_corresponding":false},{"id":252603,"name":"Xiangmeng Kong","orcid":null,"position":44,"is_corresponding":false},{"id":1022365,"name":"Bonita R. Lam","orcid":"0000-0001-9897-3238","position":45,"is_corresponding":false},{"id":13126,"name":"Shantao Li","orcid":"0000-0002-5440-2780","position":46,"is_corresponding":false},{"id":258337,"name":"Bian Li","orcid":"0000-0002-8280-5018","position":47,"is_corresponding":false},{"id":419471,"name":"Xiqi Li","orcid":"0000-0003-0875-8337","position":48,"is_corresponding":false},{"id":1022366,"name":"Khine Lin","orcid":"0000-0002-5222-2428","position":49,"is_corresponding":false},{"id":35110,"name":" Ruibang Luo","orcid":"0000-0001-9711-6533","position":50,"is_corresponding":false},{"id":43071,"name":"Mark Mackiewicz","orcid":"0000-0002-7088-1902","position":51,"is_corresponding":false},{"id":1022367,"name":"Ran Meng","orcid":"0000-0003-1190-4710","position":52,"is_corresponding":false},{"id":21450,"name":"Jill E. Moore","orcid":"0000-0002-3023-0806","position":53,"is_corresponding":false},{"id":105367,"name":"Jonathan M. 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Mendenhall","orcid":"0000-0002-7395-6295","position":85,"is_corresponding":false},{"id":4958,"name":"William Stafford Noble","orcid":"0000-0001-7283-4715","position":86,"is_corresponding":false},{"id":368,"name":"Zhiping Weng","orcid":"0000-0002-3032-7966","position":87,"is_corresponding":false},{"id":218505,"name":"Morgan E. 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Schatz","orcid":"0000-0002-4118-4446","position":98,"is_corresponding":false},{"id":235415,"name":"B Bernstein","orcid":"0000-0002-5726-6278","position":99,"is_corresponding":false},{"id":11731,"name":"Joel Rozowsky","orcid":"0000-0002-3565-0762","position":0,"is_corresponding":true}],"reference_count":188,"raw_metadata":null,"created_at":"2026-07-19T01:06:50.336418Z","pmid":"37001506","pmcid":"PMC10074325","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":61.1111,"fair_a":81.25,"fair_i":40.0,"fair_r":41.6667,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The data, analysis and software tools from the project are all open access, with everything being directly available from the EN-TEx portal (entex.encodeproject.org)","grounded":false,"rationale":"The paper provides a URL to the EN-TEx portal but no persistent identifier string from a standard scheme. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper references external resources but does not provide any persistent identifier for them. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name a standard reuse licence for the data; the CC-BY licence is for the article.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Libraries were sequenced on an Illumina NovaSeq 6000 sequencer using 2 × 150 bp cycles to a minimum depth of 30X.","grounded":true,"rationale":"The paper names specific instruments and software used to produce the data, such as the Illumina NovaSeq 6000.","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not mention a README or data dictionary accompanying the data. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"The EN-TEx assays and analyses were funded by the National Human Genome Research Institute (NHGRI) using ENCODE funds.","grounded":true,"rationale":"The paper names NHGRI as a funder but does not give an award number.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The data, analysis and software tools from the project are all open access, with everything being directly available from the EN-TEx portal (entex.encodeproject.org)","why":"The paper provides a URL to the EN-TEx portal but no persistent identifier string from a standard scheme. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name a standard reuse licence for the data; the CC-BY licence is for the article.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"the EN-TEx portal (entex.encodeproject.org, Details in STAR methods “Portal” Section)","why":"The dataset identifier (URL) appears only in the body text, not as a reference list entry. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"as of the date of publication","why":"The paper gives a date (as of the date of publication) but no version token. [majority verdict 'partial' (4/5 passes agreed)]","gain":2.08,"priority":"useful","scored":true},{"key":"x_funding_attribution","dimension":"R","label":"Funder and award number","action":"State the funder AND the award number in the paper, and put them in the dataset's FundingReference metadata. A funder name alone cannot be linked back to the award, so the funding provenance of the data is lost the moment the paper is indexed.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The EN-TEx assays and analyses were funded by the National Human Genome Research Institute (NHGRI) using ENCODE funds.","why":"The paper names NHGRI as a funder but does not give an award number.","gain":2.08,"priority":"useful","scored":true},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. 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[majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","State the funder AND the award number in the paper, and put them in the dataset's FundingReference metadata. 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