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dc.contributor.authorRozowsky, J
dc.contributor.authorGao, J
dc.contributor.authorBorsari, B
dc.contributor.authorYang, YT
dc.contributor.authorGaleev, T
dc.contributor.authorGürsoy, G
dc.contributor.authorEpstein, CB
dc.contributor.authorXiong, K
dc.contributor.authorXu, J
dc.contributor.authorLi, T
dc.contributor.authorLiu, J
dc.contributor.authorYu, K
dc.contributor.authorBerthel, A
dc.contributor.authorChen, Z
dc.contributor.authorNavarro, F
dc.contributor.authorSun, MS
dc.contributor.authorWright, J
dc.contributor.authorChang, J
dc.contributor.authorCameron, CJF
dc.contributor.authorShoresh, N
dc.contributor.authorGaskell, E
dc.contributor.authorDrenkow, J
dc.contributor.authorAdrian, J
dc.contributor.authorAganezov, S
dc.contributor.authorAguet, F
dc.contributor.authorBalderrama-Gutierrez, G
dc.contributor.authorBanskota, S
dc.contributor.authorCorona, GB
dc.contributor.authorChee, S
dc.contributor.authorChhetri, SB
dc.contributor.authorCortez Martins, GC
dc.contributor.authorDanyko, C
dc.contributor.authorDavis, CA
dc.contributor.authorFarid, D
dc.contributor.authorFarrell, NP
dc.contributor.authorGabdank, I
dc.contributor.authorGofin, Y
dc.contributor.authorGorkin, DU
dc.contributor.authorGu, M
dc.contributor.authorHecht, V
dc.contributor.authorHitz, BC
dc.contributor.authorIssner, R
dc.contributor.authorJiang, Y
dc.contributor.authorKirsche, M
dc.contributor.authorKong, X
dc.contributor.authorLam, BR
dc.contributor.authorLi, S
dc.contributor.authorLi, B
dc.contributor.authorLi, X
dc.contributor.authorLin, KZ
dc.contributor.authorLuo, R
dc.contributor.authorMackiewicz, M
dc.contributor.authorMeng, R
dc.contributor.authorMoore, JE
dc.contributor.authorMudge, J
dc.contributor.authorNelson, N
dc.contributor.authorNusbaum, C
dc.contributor.authorPopov, I
dc.contributor.authorPratt, HE
dc.contributor.authorQiu, Y
dc.contributor.authorRamakrishnan, S
dc.contributor.authorRaymond, J
dc.contributor.authorSalichos, L
dc.contributor.authorScavelli, A
dc.contributor.authorSchreiber, JM
dc.contributor.authorSedlazeck, FJ
dc.contributor.authorSee, LH
dc.contributor.authorSherman, RM
dc.contributor.authorShi, X
dc.contributor.authorShi, M
dc.contributor.authorSloan, CA
dc.contributor.authorStrattan, JS
dc.contributor.authorTan, Z
dc.contributor.authorTanaka, FY
dc.contributor.authorVlasova, A
dc.contributor.authorWang, J
dc.contributor.authorWerner, J
dc.contributor.authorWilliams, B
dc.contributor.authorXu, M
dc.contributor.authorYan, C
dc.contributor.authorYu, L
dc.contributor.authorZaleski, C
dc.contributor.authorZhang, J
dc.contributor.authorArdlie, K
dc.contributor.authorCherry, JM
dc.contributor.authorMendenhall, EM
dc.contributor.authorNoble, WS
dc.contributor.authorWeng, Z
dc.contributor.authorLevine, ME
dc.contributor.authorDobin, A
dc.contributor.authorWold, B
dc.contributor.authorMortazavi, A
dc.contributor.authorRen, B
dc.contributor.authorGillis, J
dc.contributor.authorMyers, RM
dc.contributor.authorSnyder, MP
dc.contributor.authorChoudhary, J
dc.contributor.authorMilosavljevic, A
dc.contributor.authorSchatz, MC
dc.contributor.authorBernstein, BE
dc.contributor.authorGuigó, R
dc.contributor.authorGingeras, TR
dc.contributor.authorGerstein, M
dc.coverage.spatialUnited States
dc.date.accessioned2023-05-23T11:58:06Z
dc.date.available2023-05-23T11:58:06Z
dc.date.issued2023-03-30
dc.identifierS0092-8674(23)00161-7
dc.identifier.citationCell, 2023, 186 (7), pp. 1493 - 1511.e40
dc.identifier.issn0092-8674
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/5796
dc.identifier.eissn1097-4172
dc.identifier.eissn1097-4172
dc.identifier.doi10.1016/j.cell.2023.02.018
dc.description.abstractUnderstanding 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.
dc.formatPrint
dc.format.extent1493 - 1511.e40
dc.languageeng
dc.language.isoeng
dc.publisherCELL PRESS
dc.relation.ispartofCell
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectENCODE
dc.subjectGTEx
dc.subjectallele-specific activity
dc.subjecteQTLs
dc.subjectfunctional epigenomes
dc.subjectfunctional genomics
dc.subjectgenome annotations
dc.subjectpersonal genome
dc.subjectpredictive models
dc.subjectstructural variants
dc.subjecttissue specificity
dc.subjecttransformer model
dc.subjectEpigenome
dc.subjectQuantitative Trait Loci
dc.subjectGenome-Wide Association Study
dc.subjectGenomics
dc.subjectPhenotype
dc.subjectPolymorphism, Single Nucleotide
dc.titleThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
dc.typeJournal Article
dcterms.dateAccepted2023-02-10
dc.date.updated2023-05-22T14:39:18Z
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1016/j.cell.2023.02.018
rioxxterms.licenseref.startdate2023-03-30
rioxxterms.typeJournal Article/Review
pubs.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/37001506
pubs.issue7
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Cancer Biology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Cancer Biology/Functional Proteomics Group
pubs.organisational-group/ICR/ImmNet
pubs.publication-statusPublished
pubs.publisher-urlhttp://dx.doi.org/10.1016/j.cell.2023.02.018
pubs.volume186
icr.researchteamFunctional Proteomics
icr.researchteamProte & Metabolomics Fac
dc.contributor.icrauthorWright, James
dc.contributor.icrauthorChoudhary, Jyoti
icr.provenanceDeposited by Dr James Wright on 2023-05-22. Deposit type is initial. No. of files: 1. Files: EnTex_2023.pdf


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