Literature DB >> 29019975

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease.

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Abstract

Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.

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Year:  2017        PMID: 29019975      PMCID: PMC6636856          DOI: 10.1038/ng.3969

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  61 in total

1.  Colocalization of GWAS and eQTL Signals Detects Target Genes.

Authors:  Farhad Hormozdiari; Martijn van de Bunt; Ayellet V Segrè; Xiao Li; Jong Wha J Joo; Michael Bilow; Jae Hoon Sul; Sriram Sankararaman; Bogdan Pasaniuc; Eleazar Eskin
Journal:  Am J Hum Genet       Date:  2016-11-17       Impact factor: 11.025

2.  Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

Authors:  Kate D Meyer; Yogesh Saletore; Paul Zumbo; Olivier Elemento; Christopher E Mason; Samie R Jaffrey
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

3.  Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.

Authors:  J Raphael Gibbs; Marcel P van der Brug; Dena G Hernandez; Bryan J Traynor; Michael A Nalls; Shiao-Lin Lai; Sampath Arepalli; Allissa Dillman; Ian P Rafferty; Juan Troncoso; Robert Johnson; H Ronald Zielke; Luigi Ferrucci; Dan L Longo; Mark R Cookson; Andrew B Singleton
Journal:  PLoS Genet       Date:  2010-05-13       Impact factor: 5.917

4.  Extensive variation in chromatin states across humans.

Authors:  Maya Kasowski; Sofia Kyriazopoulou-Panagiotopoulou; Fabian Grubert; Judith B Zaugg; Anshul Kundaje; Yuling Liu; Alan P Boyle; Qiangfeng Cliff Zhang; Fouad Zakharia; Damek V Spacek; Jingjing Li; Dan Xie; Anthony Olarerin-George; Lars M Steinmetz; John B Hogenesch; Manolis Kellis; Serafim Batzoglou; Michael Snyder
Journal:  Science       Date:  2013-10-17       Impact factor: 47.728

5.  Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Authors:  Manuel A Rivas; Matti Pirinen; Donald F Conrad; Monkol Lek; Emily K Tsang; Konrad J Karczewski; Julian B Maller; Kimberly R Kukurba; David S DeLuca; Menachem Fromer; Pedro G Ferreira; Kevin S Smith; Rui Zhang; Fengmei Zhao; Eric Banks; Ryan Poplin; Douglas M Ruderfer; Shaun M Purcell; Taru Tukiainen; Eric V Minikel; Peter D Stenson; David N Cooper; Katharine H Huang; Timothy J Sullivan; Jared Nedzel; Carlos D Bustamante; Jin Billy Li; Mark J Daly; Roderic Guigo; Peter Donnelly; Kristin Ardlie; Michael Sammeth; Emmanouil T Dermitzakis; Mark I McCarthy; Stephen B Montgomery; Tuuli Lappalainen; Daniel G MacArthur
Journal:  Science       Date:  2015-05-08       Impact factor: 47.728

6.  Genomic variation. Impact of regulatory variation from RNA to protein.

Authors:  Alexis Battle; Zia Khan; Sidney H Wang; Amy Mitrano; Michael J Ford; Jonathan K Pritchard; Yoav Gilad
Journal:  Science       Date:  2014-12-18       Impact factor: 47.728

7.  Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing.

Authors:  Maria Gutierrez-Arcelus; Halit Ongen; Tuuli Lappalainen; Stephen B Montgomery; Alfonso Buil; Alisa Yurovsky; Julien Bryois; Ismael Padioleau; Luciana Romano; Alexandra Planchon; Emilie Falconnet; Deborah Bielser; Maryline Gagnebin; Thomas Giger; Christelle Borel; Audrey Letourneau; Periklis Makrythanasis; Michel Guipponi; Corinne Gehrig; Stylianos E Antonarakis; Emmanouil T Dermitzakis
Journal:  PLoS Genet       Date:  2015-01-29       Impact factor: 5.917

8.  An expansive human regulatory lexicon encoded in transcription factor footprints.

Authors:  Shane Neph; Jeff Vierstra; Andrew B Stergachis; Alex P Reynolds; Eric Haugen; Benjamin Vernot; Robert E Thurman; Sam John; Richard Sandstrom; Audra K Johnson; Matthew T Maurano; Richard Humbert; Eric Rynes; Hao Wang; Shinny Vong; Kristen Lee; Daniel Bates; Morgan Diegel; Vaughn Roach; Douglas Dunn; Jun Neri; Anthony Schafer; R Scott Hansen; Tanya Kutyavin; Erika Giste; Molly Weaver; Theresa Canfield; Peter Sabo; Miaohua Zhang; Gayathri Balasundaram; Rachel Byron; Michael J MacCoss; Joshua M Akey; M A Bender; Mark Groudine; Rajinder Kaul; John A Stamatoyannopoulos
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

9.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

10.  Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.

Authors:  Natsuhiko Kumasaka; Andrew J Knights; Daniel J Gaffney
Journal:  Nat Genet       Date:  2015-12-14       Impact factor: 38.330

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  60 in total

1.  An integrative systems-based analysis of substance use: eQTL-informed gene-based tests, gene networks, and biological mechanisms.

Authors:  Zachary F Gerring; Angela Mina Vargas; Eric R Gamazon; Eske M Derks
Journal:  Am J Med Genet B Neuropsychiatr Genet       Date:  2020-12-23       Impact factor: 3.568

2.  Single nucleotide variant counts computed from RNA sequencing and cellular traffic into human kidney allografts.

Authors:  Gaurav Thareja; Hua Yang; Shahina Hayat; Franco B Mueller; John R Lee; Michelle Lubetzky; Darshana M Dadhania; Aziz Belkadi; Surya V Seshan; Karsten Suhre; Manikkam Suthanthiran; Thangamani Muthukumar
Journal:  Am J Transplant       Date:  2018-05-15       Impact factor: 8.086

3.  Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs.

Authors:  Annie Robic; Thomas Faraut; Sarah Djebali; Rosemarie Weikard; Katia Feve; Sarah Maman; Christa Kuehn
Journal:  RNA Biol       Date:  2019-06-03       Impact factor: 4.652

4.  GWAS-linked hot loci predict short-term functional outcome and recurrence of ischemic stroke in Chinese population.

Authors:  Ruixia Zhu; Yating Zhao; Dandan Tian; Na Guo; Chenguang Zhang; Xu Liu
Journal:  Am J Transl Res       Date:  2021-05-15       Impact factor: 4.060

5.  Gene expression: Principles of gene regulation across tissues.

Authors:  Darren J Burgess
Journal:  Nat Rev Genet       Date:  2017-11-07       Impact factor: 53.242

Review 6.  Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions.

Authors:  Jamison McCorrison; Thomas Girke; Laura H Goetz; Richard A Miller; Nicholas J Schork
Journal:  J Gerontol A Biol Sci Med Sci       Date:  2019-11-13       Impact factor: 6.053

7.  A Quantitative Proteome Map of the Human Body.

Authors:  Lihua Jiang; Meng Wang; Shin Lin; Ruiqi Jian; Xiao Li; Joanne Chan; Guanlan Dong; Huaying Fang; Aaron E Robinson; Michael P Snyder
Journal:  Cell       Date:  2020-09-10       Impact factor: 41.582

Review 8.  Genome-Wide Association Studies in Glioma.

Authors:  Ben Kinnersley; Richard S Houlston; Melissa L Bondy
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2018-01-30       Impact factor: 4.254

9.  The complex genetics of human insulin-like growth factor 2 are not reflected in public databases.

Authors:  Peter Rotwein
Journal:  J Biol Chem       Date:  2018-02-02       Impact factor: 5.157

Review 10.  The Musculoskeletal Knowledge Portal: Making Omics Data Useful to the Broader Scientific Community.

Authors:  Douglas P Kiel; John P Kemp; Fernando Rivadeneira; Jennifer J Westendorf; David Karasik; Emma L Duncan; Yuuki Imai; Ralph Müller; Jason Flannick; Lynda Bonewald; Noël Burtt
Journal:  J Bone Miner Res       Date:  2020-09       Impact factor: 6.741

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