Literature DB >> 25400697

SuRFing the genomics wave: an R package for prioritising SNPs by functionality.

Niamh M Ryan1, Stewart W Morris1, David J Porteous2, Martin S Taylor3, Kathryn L Evans2.   

Abstract

Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biological knowledge to prioritise candidate functional variants. SuRFR is publicly available, modular, flexible, fast, and simple to use. We demonstrate that SuRFR performs with high sensitivity and specificity and provide a widely applicable and scalable benchmarking dataset for model training and validation. Website: http://www.cgem.ed.ac.uk/resources/

Entities:  

Year:  2014        PMID： 25400697      PMCID： PMC4224693          DOI： 10.1186/s13073-014-0079-1

Source DB:  PubMed          Journal:  Genome Med        ISSN： 1756-994X            Impact factor:   11.117


  44 in total

1.  Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

Authors:  Peter J Sabo; Michael S Kuehn; Robert Thurman; Brett E Johnson; Ericka M Johnson; Hua Cao; Man Yu; Elizabeth Rosenzweig; Jeff Goldy; Andrew Haydock; Molly Weaver; Anthony Shafer; Kristin Lee; Fidencio Neri; Richard Humbert; Michael A Singer; Todd A Richmond; Michael O Dorschner; Michael McArthur; Michael Hawrylycz; Roland D Green; Patrick A Navas; William S Noble; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2006-07       Impact factor: 28.547

2.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors:  Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-27       Impact factor: 11.205

3.  Regulatory polymorphisms in EGR2 are associated with susceptibility to systemic lupus erythematosus.

Authors:  Keiko Myouzen; Yuta Kochi; Kenichi Shimane; Keishi Fujio; Tomohisa Okamura; Yukinori Okada; Akari Suzuki; Tatsuya Atsumi; Satoshi Ito; Kazuki Takada; Akio Mimori; Shiro Ikegawa; Ryo Yamada; Yusuke Nakamura; Kazuhiko Yamamoto
Journal:  Hum Mol Genet       Date:  2010-03-01       Impact factor: 6.150

4.  The NIH Roadmap Epigenomics Mapping Consortium.

Authors:  Bradley E Bernstein; John A Stamatoyannopoulos; Joseph F Costello; Bing Ren; Aleksandar Milosavljevic; Alexander Meissner; Manolis Kellis; Marco A Marra; Arthur L Beaudet; Joseph R Ecker; Peggy J Farnham; Martin Hirst; Eric S Lander; Tarjei S Mikkelsen; James A Thomson
Journal:  Nat Biotechnol       Date:  2010-10       Impact factor: 54.908

5.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

6.  Discovery and characterization of chromatin states for systematic annotation of the human genome.

Authors:  Jason Ernst; Manolis Kellis
Journal:  Nat Biotechnol       Date:  2010-07-25       Impact factor: 54.908

7.  A promoter-level mammalian expression atlas.

Authors:  Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassmann; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C Clevers; Emiliano Dalla; Carrie A Davis; Michael Detmar; Alexander D Diehl; Taeko Dohi; Finn Drabløs; Albert S B Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C Farach-Carson; Geoffrey J Faulkner; Alexander V Favorov; Malcolm E Fisher; Martin C Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furino; Jun-ichi Furusawa; Teunis B Geijtenbeek; Andrew P Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J Hitchens; Shannan J Ho Sui; Oliver M Hofmann; Ilka Hoof; Furni Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; Artem S Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I Kawamura; Tsugumi Kawashima; Judith S Kempfle; Tony J Kenna; Juha Kere; Levon M Khachigian; Toshio Kitamura; S Peter Klinken; Alan J Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T Kwon; Jeroen F J Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-Sim; Ri-ichiroh Manabe; Jessica C Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Shohei Noma; Tadasuke Noazaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohimiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G D Prendergast; Owen J L Rackham; Jordan A Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A Schultes; Gundula G Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W Shin; Christophe Simon; Daisuke Sugiyama; Takaai Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K Swoboda; Peter A C 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyodo; Tetsuro Toyoda; Elvind Valen; Marc van de Wetering; Linda M van den Berg; Roberto Verado; Dipti Vijayan; Ilya E Vorontsov; Wyeth W Wasserman; Shoko Watanabe; Christine A Wells; Louise N Winteringham; Ernst Wolvetang; Emily J Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E Zabierowski; Peter G Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M Summers; Harukazu Suzuki; Carsten O Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C Freeman; Boris Lenhard; Vladimir B Bajic; Martin S Taylor; Vsevolod J Makeev; Albin Sandelin; David A Hume; Piero Carninci; Yoshihide Hayashizaki
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

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.  The Human Gene Mutation Database: 2008 update.

Authors:  Peter D Stenson; Matthew Mort; Edward V Ball; Katy Howells; Andrew D Phillips; Nick St Thomas; David N Cooper
Journal:  Genome Med       Date:  2009-01-22       Impact factor: 11.117

10.  ClinVar: public archive of relationships among sequence variation and human phenotype.

Authors:  Melissa J Landrum; Jennifer M Lee; George R Riley; Wonhee Jang; Wendy S Rubinstein; Deanna M Church; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2013-11-14       Impact factor: 16.971
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  11 in total

1.  Predicting regulatory variants with composite statistic.

Authors:  Mulin Jun Li; Zhicheng Pan; Zipeng Liu; Jiexing Wu; Panwen Wang; Yun Zhu; Feng Xu; Zhengyuan Xia; Pak Chung Sham; Jean-Pierre A Kocher; Miaoxin Li; Jun S Liu; Junwen Wang
Journal:  Bioinformatics       Date:  2016-06-06       Impact factor: 6.937

Review 2.  Principles and methods of in-silico prioritization of non-coding regulatory variants.

Authors:  Phil H Lee; Christian Lee; Xihao Li; Brian Wee; Tushar Dwivedi; Mark Daly
Journal:  Hum Genet       Date:  2017-12-29       Impact factor: 4.132

3.  VIPdb, a genetic Variant Impact Predictor Database.

Authors:  Zhiqiang Hu; Changhua Yu; Mabel Furutsuki; Gaia Andreoletti; Melissa Ly; Roger Hoskins; Aashish N Adhikari; Steven E Brenner
Journal:  Hum Mutat       Date:  2019-08-17       Impact factor: 4.878

Review 4.  New statistical approaches exploit the polygenic architecture of schizophrenia--implications for the underlying neurobiology.

Authors:  Andrew J Schork; Yunpeng Wang; Wesley K Thompson; Anders M Dale; Ole A Andreassen
Journal:  Curr Opin Neurobiol       Date:  2015-11-08       Impact factor: 6.627

5.  Identification of a novel locus on chromosome 2q13, which predisposes to clinical vertebral fractures independently of bone density.

Authors:  Nerea Alonso; Karol Estrada; Omar M E Albagha; Lizbeth Herrera; Sjur Reppe; Ole K Olstad; Kaare M Gautvik; Niamh M Ryan; Kathryn L Evans; Carrie M Nielson; Yi-Hsiang Hsu; Douglas P Kiel; George Markozannes; Evangelia E Ntzani; Evangelos Evangelou; Bjarke Feenstra; Xueping Liu; Mads Melbye; Laura Masi; Maria Luisa Brandi; Philip Riches; Anna Daroszewska; José Manuel Olmos; Carmen Valero; Jesús Castillo; José A Riancho; Lise B Husted; Bente L Langdahl; Matthew A Brown; Emma L Duncan; Stephen Kaptoge; Kay-Tee Khaw; Ricardo Usategui-Martín; Javier Del Pino-Montes; Rogelio González-Sarmiento; Joshua R Lewis; Richard L Prince; Patrizia D'Amelio; Natalia García-Giralt; Xavier Nogués; Simona Mencej-Bedrac; Janja Marc; Orit Wolstein; John A Eisman; Ling Oei; Carolina Medina-Gómez; Katharina E Schraut; Pau Navarro; James F Wilson; Gail Davies; John Starr; Ian Deary; Toshiko Tanaka; Luigi Ferrucci; Fernando Gianfrancesco; Luigi Gennari; Gavin Lucas; Roberto Elosua; André G Uitterlinden; Fernando Rivadeneira; Stuart H Ralston
Journal:  Ann Rheum Dis       Date:  2017-11-23       Impact factor: 19.103

6.  CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.

Authors:  Yao Yao; Zheng Liu; Qi Wei; Stephen A Ramsey
Journal:  BMC Bioinformatics       Date:  2019-02-06       Impact factor: 3.169

7.  regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants.

Authors:  Shijie Zhang; Yukun He; Huanhuan Liu; Haoyu Zhai; Dandan Huang; Xianfu Yi; Xiaobao Dong; Zhao Wang; Ke Zhao; Yao Zhou; Jianhua Wang; Hongcheng Yao; Hang Xu; Zhenglu Yang; Pak Chung Sham; Kexin Chen; Mulin Jun Li
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

8.  Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population.

Authors:  Prashantha Hebbar; Jehad Ahmed Abubaker; Mohamed Abu-Farha; Osama Alsmadi; Naser Elkum; Fadi Alkayal; Sumi Elsa John; Arshad Channanath; Rasheeba Iqbal; Janne Pitkaniemi; Jaakko Tuomilehto; Robert Sladek; Fahd Al-Mulla; Thangavel Alphonse Thanaraj
Journal:  Hum Genet       Date:  2020-09-09       Impact factor: 4.132

9.  Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma.

Authors:  Deke Jiang; Jiaen Deng; Changzheng Dong; Xiaopin Ma; Qianyi Xiao; Bin Zhou; Chou Yang; Lin Wei; Carly Conran; S Lilly Zheng; Irene Oi-Lin Ng; Long Yu; Jianfeng Xu; Pak C Sham; Xiaolong Qi; Jinlin Hou; Yuan Ji; Guangwen Cao; Miaoxin Li
Journal:  BMC Cancer       Date:  2020-05-11       Impact factor: 4.430

10.  CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.

Authors:  Yao Yao; Stephen A Ramsey
Journal:  Pac Symp Biocomput       Date:  2020
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