ArticleNature communications2020
An integrative ENCODE resource for cancer genomics.
Open access · goldAbstract read
In one paragraph
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
126citing papers in PubMed, 1 pooled it
9.5field-weighted citation impact, top 1% of its field
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Who cites it
126 citing papers in PubMed, 1 synthesis or guideline pooled it, 179 citations in OpenAlex.
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- Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs.bioRxiv : the preprint server for biology · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
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- Defective plasticity in dermatomyositis patients muscle stem cells is associated with sustained intrinsic inflammatory signaling and disruption of the histone H3.3 chromatin loading pathway.NAR molecular medicine · 2026Article
66 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
58 authors at 16 institutions in 3 countries.
Jing Zhang *Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Donghoon Lee *Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Vineet Dhiman *Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Peng Jiang *Department of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
Jie Xu *Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
Patrick McGillivray *Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Hongbo Yang *Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
Jason LiuProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
William MeyersonProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Declan ClarkeProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Mengting GuProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0003-1684-0146
Shantao LiProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0002-5440-2780
Shaoke LouProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Jinrui XuProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Lucas LochovskyProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Matthew UngDepartment of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03765, USA.
Lijia MaDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Shan YuDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Qin CaoDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
Arif HarmanciCenter for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.ORCID http://orcid.org/0000-0002-9696-1118
Koon-Kiu YanProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Anurag SethiProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Gamze GürsoyProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Michael Rutenberg SchoenbergProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Joel RozowskyProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0002-3565-0762
Jonathan WarrellProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Prashant EmaniProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Yucheng T YangProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0002-6873-5279
Timur GaleevProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Xiangmeng KongProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Shuang LiuProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Xiaotong LiProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0003-1644-6835
Jayanth KrishnanProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Yanlin FengProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
Juan Carlos Rivera-MuliaDepartment of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.ORCID http://orcid.org/0000-0002-7566-3875
Jessica AdrianDepartment of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA.ORCID http://orcid.org/0000-0002-8078-5308
James R BroachDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA.
Michael BoltDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Jennifer MoranDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Dominic FitzgeraldDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
Vishnu DileepDepartment of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
Tingting LiuDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
Shenglin MeiDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
Takayo SasakiDepartment of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
Claudia Trevilla-GarciaDepartment of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
Su WangDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
Yanli WangDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA.
Chongzhi ZangCenter for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.ORCID http://orcid.org/0000-0003-4812-3627
Daifeng WangDepartment of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53726, USA.ORCID http://orcid.org/0000-0001-9190-3704
Robert J KleinDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.ORCID http://orcid.org/0000-0003-3539-5391
Michael SnyderDepartment of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA.ORCID http://orcid.org/0000-0003-0784-7987
David M GilbertDepartment of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.ORCID http://orcid.org/0000-0001-8087-9737
Kevin YipDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.ORCID http://orcid.org/0000-0001-5516-9944
Chao ChengDepartment of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03765, USA.
Feng YueDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. yue@northwestern.edu.ORCID http://orcid.org/0000-0002-7954-5462
X Shirley LiuDepartment of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. xsliu@ds.dfci.harvard.edu.ORCID http://orcid.org/0000-0003-4736-7339
Kevin P WhiteDepartment of Human Genetics, University of Chicago, Chicago, IL, 60637, USA. kevin@tempus.com.
Mark GersteinProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA. mark@gersteinlab.org.ORCID http://orcid.org/0000-0002-9746-3719
Yale University · USFlorida State University · USNorthwestern University · USUniversity of Chicago · USChinese University of Hong Kong · HKDana-Farber Cancer Institute · USDartmouth College · USHarvard University · USPennsylvania State University · USStanford University · USIcahn School of Medicine at Mount Sinai · USOffice of Public Health Genomics · USThe University of Texas Health Science Center at Houston · USUniversity of Illinois Chicago · USUniversity of Wisconsin–Madison · USWestlake University · CN
Funding
MEDICAL SCIENTIST TRAINING PROGRAMT32GM007205 · NIGMS · YALE UNIVERSITY · PI KAZMIERCZAK, BARBARA I · 1985 to 2019
$42.9MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MVISION: ValIdated Systematic IntegratiON of epigenomic dataR24DK106766 · NIDDK · PENNSYLVANIA STATE UNIVERSITY, THE · PI BLOBEL, GERD A, BODINE, DAVID M. · 2016 to 2020
$6.2MGenome Plasticity during ES Cell Differentiation to Neural LineagesR01GM083337 · NIGMS · SAN DIEGO BIOMEDICAL RESEARCH INSTITUTE · PI David M Gilbert · 2007 to 2026
$6.1MImpact of genetic variants on gene regulation and 3D genome organization in human diseasesR35GM124820 · NIGMS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI Feng Yue · 2017 to 2026
$4.0MVisualization, modeling and validation of chromatin interaction dataR01HG009906 · NHGRI · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI YUE, FENG · 2018 to 2022
$2.0MThe WashU 4DN Network Data Coordination and Integration CenterU01CA200060 · NCI · WASHINGTON UNIVERSITY · PI WANG, TING · 2015 to 2019
$1.9MLinking disease-associated variants to transcriptional regulation using ENCODEU01HG007033 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI KLEIN, ROBERT J. · 2012 to 2015
$1.9MData-driven approaches to identify biomarkers and regulators of cancer drug resistanceK99CA218900 · NCI · DANA-FARBER CANCER INST · PI JIANG, PENG · 2018 to 2018
$100kNCI NIH HHS K99 CA218900NCI NIH HHS U01 CA200060NHGRI NIH HHS R01 HG009906NHGRI NIH HHS U01 HG007033NHGRI NIH HHS U24 HG009446NIDDK NIH HHS R24 DK106766NIGMS NIH HHS R01 GM083337NIGMS NIH HHS R35 GM124820NIGMS NIH HHS T32 GM007205
Abstract
ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.
Indexed as
Databases, GeneticGenomicsCell Line, TumorCell Transformation, NeoplasticGene Regulatory NetworksHumansMutationNeoplasmsReproducibility of ResultsTranscription FactorsTranscription Factors
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.