GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Simon Fishilevich,Ron Nudel,Noa Rappaport,Rotem Hadar,Inbar Plaschkes,Tsippi Iny Stein,Naomi Rosen,Asher Kohn,Michal Twik,Marilyn Safran,Doron Lancet,Dana Cohen +11 more
TLDR
GeneHancer is presented, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards, which assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant–phenotype interpretation of whole-genome sequences in health and disease.Abstract:
A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser. Employing an integration algorithm that aims to remove redundancy, GeneHancer portrays 285 000 integrated candidate enhancers (covering 12.4% of the genome), 94 000 of which are derived from more than one source, and each assigned an annotation-derived confidence score. GeneHancer subsequently links enhancers to genes, using: tissue co-expression correlation between genes and enhancer RNAs, as well as enhancer-targeted transcription factor genes; expression quantitative trait loci for variants within enhancers; and capture Hi-C, a promoter-specific genome conformation assay. The individual scores based on each of these four methods, along with gene–enhancer genomic distances, form the basis for GeneHancer’s combinatorial likelihood-based scores for enhancer–gene pairing. Finally, we define ‘elite’ enhancer–gene relations reflecting both a high-likelihood enhancer definition and a strong enhancer–gene association.
GeneHancer predictions are fully integrated in the widely used GeneCards Suite, whereby candidate enhancers and their annotations are displayed on every relevant GeneCard. This assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant–phenotype interpretation of whole-genome sequences in health and disease.
Database URL: http://www.genecards.org/read more
Citations
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
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Nicholas Ekow Thomford,Dimakatso Alice Senthebane,Arielle Rowe,Daniella Munro,Palesa Seele,Alfred Maroyi,Kevin Dzobo,Kevin Dzobo +7 more
TL;DR: This review discusses plant-based natural product drug discovery and how innovative technologies play a role in next-generation drug discovery.
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Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
David A. Quigley,Ha X. Dang,Shuang G. Zhao,Paul Lloyd,Rahul Aggarwal,Joshi J. Alumkal,Adam Foye,Vishal Kothari,Marc D. Perry,Adina M. Bailey,Denise Playdle,Travis J. Barnard,Li Zhang,Jin Zhang,Jack F. Youngren,Marcin Cieslik,Abhijit Parolia,Tomasz M. Beer,George Thomas,Kim N. Chi,Martin E. Gleave,Nathan A. Lack,Amina Zoubeidi,Robert E. Reiter,Robert E. Reiter,Matthew Rettig,Owen N. Witte,Charles J. Ryan,Lawrence Fong,Won Kim,Terence W. Friedlander,Jonathan Chou,Haolong Li,Rajdeep Das,Hui Li,Ruhollah Moussavi-Baygi,Hani Goodarzi,Luke A. Gilbert,Primo N. Lara,Christopher P. Evans,Theodore C. Goldstein,Theodore C. Goldstein,Joshua M. Stuart,Scott A. Tomlins,Daniel E. Spratt,R. Keira Cheetham,Donavan T. Cheng,Kyle Kai-How Farh,Julian S. Gehring,Jörg Hakenberg,Arnold Liao,P. G. Febbo,John Shon,Brad Sickler,Serafim Batzoglou,Karen E. Knudsen,Housheng Hansen He,Jiaoti Huang,Alexander W. Wyatt,Scott M. Dehm,Alan Ashworth,Arul M. Chinnaiyan,Christopher G. Maher,Eric J. Small,Felix Y. Feng +64 more
TL;DR: Integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches, providing a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.
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Genomic basis for RNA alterations in cancer
Claudia Calabrese,Natalie R. Davidson,Deniz Demircioğlu,Deniz Demircioğlu,Nuno A. Fonseca,Yao He,André Kahles,Kjong-Van Lehmann,Fenglin Liu,Yuichi Shiraishi,Cameron M. Soulette,Lara Urban,Liliana Greger,Siliang Li,Dongbing Liu,Marc D. Perry,Marc D. Perry,Qian Xiang,Fan Zhang,Junjun Zhang,Peter Bailey,Serap Erkek,Katherine A. Hoadley,Yong Hou,Matthew R. Huska,Helena Kilpinen,Jan O. Korbel,Maximillian G. Marin,Julia Markowski,Tannistha Nandi,Qiang Pan-Hammarström,Chandra Sekhar Pedamallu,Chandra Sekhar Pedamallu,Reiner Siebert,Stefan G. Stark,Hong Su,Patrick Tan,Patrick Tan,Sebastian M. Waszak,Christina K. Yung,Shida Zhu,Philip Awadalla,Philip Awadalla,Chad J. Creighton,Matthew Meyerson,Matthew Meyerson,B. F. Francis Ouellette,Kui Wu,Huanming Yang,Alvis Brazma,Angela N. Brooks,Angela N. Brooks,Angela N. Brooks,Jonathan Göke,Gunnar Rätsch,Roland F. Schwarz,Oliver Stegle,Oliver Stegle,Zemin Zhang +58 more
TL;DR: The most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Gome Atlas (TCGA) was presented in this article.
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An atlas of dynamic chromatin landscapes in mouse fetal development
David U. Gorkin,David U. Gorkin,Iros Barozzi,Iros Barozzi,Yuan Zhao,Yuan Zhao,Yanxiao Zhang,Hui Huang,Hui Huang,Ah Young Lee,Bin Li,Joshua Chiou,Andre Wildberg,Bo Ding,Bo Zhang,Mengchi Wang,J. Seth Strattan,Jean M. Davidson,Yunjiang Qiu,Yunjiang Qiu,Veena Afzal,Jennifer A. Akiyama,Ingrid Plajzer-Frick,Catherine S. Novak,Momoe Kato,Tyler H. Garvin,Quan T. Pham,Anne N. Harrington,Brandon J. Mannion,Elizabeth Lee,Yoko Fukuda-Yuzawa,Yupeng He,Yupeng He,Sebastian Preissl,Sebastian Preissl,Sora Chee,Jee Yun Han,Brian A. Williams,Diane Trout,Henry Amrhein,Hongbo Yang,J. Michael Cherry,Wei Wang,Kyle J. Gaulton,Joseph R. Ecker,Yin Shen,Diane E. Dickel,Axel Visel,Axel Visel,Axel Visel,Len A. Pennacchio,Len A. Pennacchio,Len A. Pennacchio,Bing Ren +53 more
TL;DR: Analysis of chromatin state and accessibility in mouse tissues from twelve sites and eight developmental stages provides the most comprehensive view of Chromatin dynamics to date.
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