Literature DB >> 16106031

Tools and strategies for physiological genomics: the Rat Genome Database.

Simon N Twigger1, Dean Pasko, Jeff Nie, Mary Shimoyama, Susan Bromberg, Dan Campbell, Jiali Chen, Norberto dela Cruz, Chunyu Fan, Cindy Foote, Glenn Harris, Brian Hickmann, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Nataliya Nenasheva, Rajni Nigam, Victoria Petri, Dorothy Reilly, Victor Ruotti, Eric Schauberger, Kathy Seiler, Ronit Slyper, Jennifer Smith, Weiye Wang, Wenhua Wu, Lan Zhao, Angela Zuniga-Meyer, Peter J Tonellato, Anne E Kwitek, Howard J Jacob.   

Abstract

The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.

Entities:  

Mesh：

Year:  2005        PMID： 16106031      PMCID： PMC4505745          DOI： 10.1152/physiolgenomics.00040.2005

Source DB:  PubMed          Journal:  Physiol Genomics        ISSN： 1094-8341            Impact factor:   3.107


  18 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  Physiological genomics: tools and concepts.

Authors:  Allen W Cowley
Journal:  J Physiol       Date:  2004-01-01       Impact factor: 5.182

3.  The KEGG resource for deciphering the genome.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Yasushi Okuno; Masahiro Hattori
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

5.  ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Authors:  Ivan Ovcharenko; Marcelo A Nobrega; Gabriela G Loots; Lisa Stubbs
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data.

Authors:  Simon N Twigger; Jeff Nie; Victor Ruotti; Jiaming Yu; Dan Chen; Dawei Li; Jed Mathis; Vijay Narayanasamy; Gopal R Gopinath; Dean Pasko; Mary Shimoyama; Norberto De La Cruz; Susan Bromberg; Anne E Kwitek; Howard J Jacob; Peter J Tonellato
Journal:  Genome Res       Date:  2004-04       Impact factor: 9.043

7.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:  Richard A Gibbs; George M Weinstock; Michael L Metzker; Donna M Muzny; Erica J Sodergren; Steven Scherer; Graham Scott; David Steffen; Kim C Worley; Paula E Burch; Geoffrey Okwuonu; Sandra Hines; Lora Lewis; Christine DeRamo; Oliver Delgado; Shannon Dugan-Rocha; George Miner; Margaret Morgan; Alicia Hawes; Rachel Gill; Robert A Holt; Mark D Adams; Peter G Amanatides; Holly Baden-Tillson; Mary Barnstead; Soo Chin; Cheryl A Evans; Steve Ferriera; Carl Fosler; Anna Glodek; Zhiping Gu; Don Jennings; Cheryl L Kraft; Trixie Nguyen; Cynthia M Pfannkoch; Cynthia Sitter; Granger G Sutton; J Craig Venter; Trevor Woodage; Douglas Smith; Hong-Mei Lee; Erik Gustafson; Patrick Cahill; Arnold Kana; Lynn Doucette-Stamm; Keith Weinstock; Kim Fechtel; Robert B Weiss; Diane M Dunn; Eric D Green; Robert W Blakesley; Gerard G Bouffard; Pieter J De Jong; Kazutoyo Osoegawa; Baoli Zhu; Marco Marra; Jacqueline Schein; Ian Bosdet; Chris Fjell; Steven Jones; Martin Krzywinski; Carrie Mathewson; Asim Siddiqui; Natasja Wye; John McPherson; Shaying Zhao; Claire M Fraser; Jyoti Shetty; Sofiya Shatsman; Keita Geer; Yixin Chen; Sofyia Abramzon; William C Nierman; Paul H Havlak; Rui Chen; K James Durbin; Amy Egan; Yanru Ren; Xing-Zhi Song; Bingshan Li; Yue Liu; Xiang Qin; Simon Cawley; Kim C Worley; A J Cooney; Lisa M D'Souza; Kirt Martin; Jia Qian Wu; Manuel L Gonzalez-Garay; Andrew R Jackson; Kenneth J Kalafus; Michael P McLeod; Aleksandar Milosavljevic; Davinder Virk; Andrei Volkov; David A Wheeler; Zhengdong Zhang; Jeffrey A Bailey; Evan E Eichler; Eray Tuzun; Ewan Birney; Emmanuel Mongin; Abel Ureta-Vidal; Cara Woodwark; Evgeny Zdobnov; Peer Bork; Mikita Suyama; David Torrents; Marina Alexandersson; Barbara J Trask; Janet M Young; Hui Huang; Huajun Wang; Heming Xing; Sue Daniels; Darryl Gietzen; Jeanette Schmidt; Kristian Stevens; Ursula Vitt; Jim Wingrove; Francisco Camara; M Mar Albà; Josep F Abril; Roderic Guigo; Arian Smit; Inna Dubchak; Edward M Rubin; Olivier Couronne; Alexander Poliakov; Norbert Hübner; Detlev Ganten; Claudia Goesele; Oliver Hummel; Thomas Kreitler; Young-Ae Lee; Jan Monti; Herbert Schulz; Heike Zimdahl; Heinz Himmelbauer; Hans Lehrach; Howard J Jacob; Susan Bromberg; Jo Gullings-Handley; Michael I Jensen-Seaman; Anne E Kwitek; Jozef Lazar; Dean Pasko; Peter J Tonellato; Simon Twigger; Chris P Ponting; Jose M Duarte; Stephen Rice; Leo Goodstadt; Scott A Beatson; Richard D Emes; Eitan E Winter; Caleb Webber; Petra Brandt; Gerald Nyakatura; Margaret Adetobi; Francesca Chiaromonte; Laura Elnitski; Pallavi Eswara; Ross C Hardison; Minmei Hou; Diana Kolbe; Kateryna Makova; Webb Miller; Anton Nekrutenko; Cathy Riemer; Scott Schwartz; James Taylor; Shan Yang; Yi Zhang; Klaus Lindpaintner; T Dan Andrews; Mario Caccamo; Michele Clamp; Laura Clarke; Valerie Curwen; Richard Durbin; Eduardo Eyras; Stephen M Searle; Gregory M Cooper; Serafim Batzoglou; Michael Brudno; Arend Sidow; Eric A Stone; J Craig Venter; Bret A Payseur; Guillaume Bourque; Carlos López-Otín; Xose S Puente; Kushal Chakrabarti; Sourav Chatterji; Colin Dewey; Lior Pachter; Nicolas Bray; Von Bing Yap; Anat Caspi; Glenn Tesler; Pavel A Pevzner; David Haussler; Krishna M Roskin; Robert Baertsch; Hiram Clawson; Terrence S Furey; Angie S Hinrichs; Donna Karolchik; William J Kent; Kate R Rosenbloom; Heather Trumbower; Matt Weirauch; David N Cooper; Peter D Stenson; Bin Ma; Michael Brent; Manimozhiyan Arumugam; David Shteynberg; Richard R Copley; Martin S Taylor; Harold Riethman; Uma Mudunuri; Jane Peterson; Mark Guyer; Adam Felsenfeld; Susan Old; Stephen Mockrin; Francis Collins
Journal:  Nature       Date:  2004-04-01       Impact factor: 49.962

8.  Entrez Gene: gene-centered information at NCBI.

Authors:  Donna Maglott; Jim Ostell; Kim D Pruitt; Tatiana Tatusova
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

9.  The Rat Genome Database (RGD): developments towards a phenome database.

Authors:  Norberto de la Cruz; Susan Bromberg; Dean Pasko; Mary Shimoyama; Simon Twigger; Jiali Chen; Chin-Fu Chen; Chunyu Fan; Cindy Foote; Gopal R Gopinath; Glenn Harris; Aubrey Hughes; Yuan Ji; Weihong Jin; Dawei Li; Jedidiah Mathis; Natalya Nenasheva; Jeff Nie; Rajni Nigam; Victoria Petri; Dorothy Reilly; Weiye Wang; Wenhua Wu; Angela Zuniga-Meyer; Lan Zhao; Anne Kwitek; Peter Tonellato; Howard Jacob
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

10.  The Universal Protein Resource (UniProt).

Authors:  Amos Bairoch; Rolf Apweiler; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971
View more
  6 in total

1.  Description of International Caenorhabditis elegans Experiment first flight (ICE-FIRST).

Authors:  N J Szewczyk; J Tillman; C A Conley; L Granger; L Segalat; A Higashitani; S Honda; Y Honda; H Kagawa; R Adachi; A Higashibata; N Fujimoto; K Kuriyama; N Ishioka; K Fukui; D Baillie; A Rose; G Gasset; B Eche; D Chaput; M Viso
Journal:  Adv Space Res       Date:  2008-09-15       Impact factor: 2.152

2.  Magnetic resonance imaging as a tool for in vivo and ex vivo anatomical phenotyping in experimental genetic models.

Authors:  Alain Pitiot; Zdenka Pausova; Malcolm Prior; Jennifer Perrin; Naomi Loyse; Tomás Paus
Journal:  Hum Brain Mapp       Date:  2007-06       Impact factor: 5.038

3.  Ventral tegmental transcriptome response to intermittent nicotine treatment and withdrawal in BALB/cJ, C57BL/6ByJ, and quasi-congenic RQI mice.

Authors:  Csaba Vadasz; Mariko Saito; Danielle O'Brien; Jiri Zavadil; Grant Morahan; Goutam Chakraborty; Ray Wang
Journal:  Neurochem Res       Date:  2007-03       Impact factor: 3.996

4.  Physiogenomic analysis of statin-treated patients: domain-specific counter effects within the ACACB gene on low-density lipoprotein cholesterol?

Authors:  Gualberto Ruaño; Paul D Thompson; John P Kane; Clive R Pullinger; Andreas Windemuth; Richard L Seip; Mohan Kocherla; Theodore R Holford; Alan H B Wu
Journal:  Pharmacogenomics       Date:  2010-07       Impact factor: 2.533

5.  Genome-wide identification of allelic expression in hypertensive rats.

Authors:  Renata I Dmitrieva; Cruz A Hinojos; Megan L Grove; Rebecca J Bell; Eric Boerwinkle; Myriam Fornage; Peter A Doris
Journal:  Circ Cardiovasc Genet       Date:  2009-02-12

6.  The Rat Genome Database, update 2007--easing the path from disease to data and back again.

Authors:  Simon N Twigger; Mary Shimoyama; Susan Bromberg; Anne E Kwitek; Howard J Jacob
Journal:  Nucleic Acids Res       Date:  2006-12-06       Impact factor: 16.971
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.