dc.contributor.author | Rozowsky, J | |
dc.contributor.author | Gao, J | |
dc.contributor.author | Borsari, B | |
dc.contributor.author | Yang, YT | |
dc.contributor.author | Galeev, T | |
dc.contributor.author | Gürsoy, G | |
dc.contributor.author | Epstein, CB | |
dc.contributor.author | Xiong, K | |
dc.contributor.author | Xu, J | |
dc.contributor.author | Li, T | |
dc.contributor.author | Liu, J | |
dc.contributor.author | Yu, K | |
dc.contributor.author | Berthel, A | |
dc.contributor.author | Chen, Z | |
dc.contributor.author | Navarro, F | |
dc.contributor.author | Sun, MS | |
dc.contributor.author | Wright, J | |
dc.contributor.author | Chang, J | |
dc.contributor.author | Cameron, CJF | |
dc.contributor.author | Shoresh, N | |
dc.contributor.author | Gaskell, E | |
dc.contributor.author | Drenkow, J | |
dc.contributor.author | Adrian, J | |
dc.contributor.author | Aganezov, S | |
dc.contributor.author | Aguet, F | |
dc.contributor.author | Balderrama-Gutierrez, G | |
dc.contributor.author | Banskota, S | |
dc.contributor.author | Corona, GB | |
dc.contributor.author | Chee, S | |
dc.contributor.author | Chhetri, SB | |
dc.contributor.author | Cortez Martins, GC | |
dc.contributor.author | Danyko, C | |
dc.contributor.author | Davis, CA | |
dc.contributor.author | Farid, D | |
dc.contributor.author | Farrell, NP | |
dc.contributor.author | Gabdank, I | |
dc.contributor.author | Gofin, Y | |
dc.contributor.author | Gorkin, DU | |
dc.contributor.author | Gu, M | |
dc.contributor.author | Hecht, V | |
dc.contributor.author | Hitz, BC | |
dc.contributor.author | Issner, R | |
dc.contributor.author | Jiang, Y | |
dc.contributor.author | Kirsche, M | |
dc.contributor.author | Kong, X | |
dc.contributor.author | Lam, BR | |
dc.contributor.author | Li, S | |
dc.contributor.author | Li, B | |
dc.contributor.author | Li, X | |
dc.contributor.author | Lin, KZ | |
dc.contributor.author | Luo, R | |
dc.contributor.author | Mackiewicz, M | |
dc.contributor.author | Meng, R | |
dc.contributor.author | Moore, JE | |
dc.contributor.author | Mudge, J | |
dc.contributor.author | Nelson, N | |
dc.contributor.author | Nusbaum, C | |
dc.contributor.author | Popov, I | |
dc.contributor.author | Pratt, HE | |
dc.contributor.author | Qiu, Y | |
dc.contributor.author | Ramakrishnan, S | |
dc.contributor.author | Raymond, J | |
dc.contributor.author | Salichos, L | |
dc.contributor.author | Scavelli, A | |
dc.contributor.author | Schreiber, JM | |
dc.contributor.author | Sedlazeck, FJ | |
dc.contributor.author | See, LH | |
dc.contributor.author | Sherman, RM | |
dc.contributor.author | Shi, X | |
dc.contributor.author | Shi, M | |
dc.contributor.author | Sloan, CA | |
dc.contributor.author | Strattan, JS | |
dc.contributor.author | Tan, Z | |
dc.contributor.author | Tanaka, FY | |
dc.contributor.author | Vlasova, A | |
dc.contributor.author | Wang, J | |
dc.contributor.author | Werner, J | |
dc.contributor.author | Williams, B | |
dc.contributor.author | Xu, M | |
dc.contributor.author | Yan, C | |
dc.contributor.author | Yu, L | |
dc.contributor.author | Zaleski, C | |
dc.contributor.author | Zhang, J | |
dc.contributor.author | Ardlie, K | |
dc.contributor.author | Cherry, JM | |
dc.contributor.author | Mendenhall, EM | |
dc.contributor.author | Noble, WS | |
dc.contributor.author | Weng, Z | |
dc.contributor.author | Levine, ME | |
dc.contributor.author | Dobin, A | |
dc.contributor.author | Wold, B | |
dc.contributor.author | Mortazavi, A | |
dc.contributor.author | Ren, B | |
dc.contributor.author | Gillis, J | |
dc.contributor.author | Myers, RM | |
dc.contributor.author | Snyder, MP | |
dc.contributor.author | Choudhary, J | |
dc.contributor.author | Milosavljevic, A | |
dc.contributor.author | Schatz, MC | |
dc.contributor.author | Bernstein, BE | |
dc.contributor.author | Guigó, R | |
dc.contributor.author | Gingeras, TR | |
dc.contributor.author | Gerstein, M | |
dc.coverage.spatial | United States | |
dc.date.accessioned | 2023-05-23T11:58:06Z | |
dc.date.available | 2023-05-23T11:58:06Z | |
dc.date.issued | 2023-03-30 | |
dc.identifier | S0092-8674(23)00161-7 | |
dc.identifier.citation | Cell, 2023, 186 (7), pp. 1493 - 1511.e40 | |
dc.identifier.issn | 0092-8674 | |
dc.identifier.uri | https://repository.icr.ac.uk/handle/internal/5796 | |
dc.identifier.eissn | 1097-4172 | |
dc.identifier.eissn | 1097-4172 | |
dc.identifier.doi | 10.1016/j.cell.2023.02.018 | |
dc.description.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. | |
dc.format | Print | |
dc.format.extent | 1493 - 1511.e40 | |
dc.language | eng | |
dc.language.iso | eng | |
dc.publisher | CELL PRESS | |
dc.relation.ispartof | Cell | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.subject | ENCODE | |
dc.subject | GTEx | |
dc.subject | allele-specific activity | |
dc.subject | eQTLs | |
dc.subject | functional epigenomes | |
dc.subject | functional genomics | |
dc.subject | genome annotations | |
dc.subject | personal genome | |
dc.subject | predictive models | |
dc.subject | structural variants | |
dc.subject | tissue specificity | |
dc.subject | transformer model | |
dc.subject | Epigenome | |
dc.subject | Quantitative Trait Loci | |
dc.subject | Genome-Wide Association Study | |
dc.subject | Genomics | |
dc.subject | Phenotype | |
dc.subject | Polymorphism, Single Nucleotide | |
dc.title | The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. | |
dc.type | Journal Article | |
dcterms.dateAccepted | 2023-02-10 | |
dc.date.updated | 2023-05-22T14:39:18Z | |
rioxxterms.version | VoR | |
rioxxterms.versionofrecord | 10.1016/j.cell.2023.02.018 | |
rioxxterms.licenseref.startdate | 2023-03-30 | |
rioxxterms.type | Journal Article/Review | |
pubs.author-url | https://www.ncbi.nlm.nih.gov/pubmed/37001506 | |
pubs.issue | 7 | |
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-status | Published | |
pubs.publisher-url | http://dx.doi.org/10.1016/j.cell.2023.02.018 | |
pubs.volume | 186 | |
icr.researchteam | Functional Proteomics | |
icr.researchteam | Prote & Metabolomics Fac | |
dc.contributor.icrauthor | Wright, James | |
dc.contributor.icrauthor | Choudhary, Jyoti | |
icr.provenance | Deposited by Dr James Wright on 2023-05-22. Deposit type is initial. No. of files: 1. Files: EnTex_2023.pdf | |