Literature DB >> 22751426

Computational tools for prioritizing candidate genes: boosting disease gene discovery.

Yves Moreau1, Léon-Charles Tranchevent.   

Abstract

At different stages of any research project, molecular biologists need to choose - often somewhat arbitrarily, even after careful statistical data analysis - which genes or proteins to investigate further experimentally and which to leave out because of limited resources. Computational methods that integrate complex, heterogeneous data sets - such as expression data, sequence information, functional annotation and the biomedical literature - allow prioritizing genes for future study in a more informed way. Such methods can substantially increase the yield of downstream studies and are becoming invaluable to researchers.

Mesh:

Year:  2012        PMID: 22751426     DOI: 10.1038/nrg3253

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  122 in total

1.  OMIM passes the 1,000-disease-gene mark.

Authors:  S E Antonarakis; V A McKusick
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Association of genes to genetically inherited diseases using data mining.

Authors:  Carolina Perez-Iratxeta; Peer Bork; Miguel A Andrade
Journal:  Nat Genet       Date:  2002-05-13       Impact factor: 38.330

3.  A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss.

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Journal:  Hum Genet       Date:  2006-12-15       Impact factor: 4.132

Review 4.  Molecular networks as sensors and drivers of common human diseases.

Authors:  Eric E Schadt
Journal:  Nature       Date:  2009-09-10       Impact factor: 49.962

5.  Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Authors:  Insuk Lee; Young-Su Seo; Dusica Coltrane; Sohyun Hwang; Taeyun Oh; Edward M Marcotte; Pamela C Ronald
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-31       Impact factor: 11.205

6.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

7.  Crowdsourcing network inference: the DREAM predictive signaling network challenge.

Authors:  Robert J Prill; Julio Saez-Rodriguez; Leonidas G Alexopoulos; Peter K Sorger; Gustavo Stolovitzky
Journal:  Sci Signal       Date:  2011-08-30       Impact factor: 8.192

8.  BioCreative III interactive task: an overview.

Authors:  Cecilia N Arighi; Phoebe M Roberts; Shashank Agarwal; Sanmitra Bhattacharya; Gianni Cesareni; Andrew Chatr-Aryamontri; Simon Clematide; Pascale Gaudet; Michelle Gwinn Giglio; Ian Harrow; Eva Huala; Martin Krallinger; Ulf Leser; Donghui Li; Feifan Liu; Zhiyong Lu; Lois J Maltais; Naoaki Okazaki; Livia Perfetto; Fabio Rinaldi; Rune Sætre; David Salgado; Padmini Srinivasan; Philippe E Thomas; Luca Toldo; Lynette Hirschman; Cathy H Wu
Journal:  BMC Bioinformatics       Date:  2011-10-03       Impact factor: 3.169

9.  Transcriptional profiling of bovine milk using RNA sequencing.

Authors:  Saumya Wickramasinghe; Gonzalo Rincon; Alma Islas-Trejo; Juan F Medrano
Journal:  BMC Genomics       Date:  2012-01-25       Impact factor: 3.969

Review 10.  Linking genes to literature: text mining, information extraction, and retrieval applications for biology.

Authors:  Martin Krallinger; Alfonso Valencia; Lynette Hirschman
Journal:  Genome Biol       Date:  2008-09-01       Impact factor: 13.583

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  186 in total

1.  PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery.

Authors:  Rong Xu; QuanQiu Wang
Journal:  J Biomed Inform       Date:  2015-07-04       Impact factor: 6.317

2.  Integrative pathway analysis of a genome-wide association study of (V)O(2max) response to exercise training.

Authors:  Sujoy Ghosh; Juan C Vivar; Mark A Sarzynski; Yun Ju Sung; James A Timmons; Claude Bouchard; Tuomo Rankinen
Journal:  J Appl Physiol (1985)       Date:  2013-08-29

3.  Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies.

Authors:  Lin Hou; Min Chen; Clarence K Zhang; Judy Cho; Hongyu Zhao
Journal:  Hum Mol Genet       Date:  2013-12-30       Impact factor: 6.150

4.  Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks.

Authors:  Xiaotu Ma; Ting Chen; Fengzhu Sun
Journal:  Brief Bioinform       Date:  2013-06-19       Impact factor: 11.622

5.  eXtasy: variant prioritization by genomic data fusion.

Authors:  Alejandro Sifrim; Dusan Popovic; Leon-Charles Tranchevent; Amin Ardeshirdavani; Ryo Sakai; Peter Konings; Joris R Vermeesch; Jan Aerts; Bart De Moor; Yves Moreau
Journal:  Nat Methods       Date:  2013-09-29       Impact factor: 28.547

6.  Common variants in the MKL1 gene confer risk of schizophrenia.

Authors:  Xiong-Jian Luo; Liang Huang; Edwin J van den Oord; Karolina A Aberg; Lin Gan; Zhongming Zhao; Yong-Gang Yao
Journal:  Schizophr Bull       Date:  2014-11-07       Impact factor: 9.306

Review 7.  The role of replicates for error mitigation in next-generation sequencing.

Authors:  Kimberly Robasky; Nathan E Lewis; George M Church
Journal:  Nat Rev Genet       Date:  2013-12-10       Impact factor: 53.242

8.  Beegle: from literature mining to disease-gene discovery.

Authors:  Sarah ElShal; Léon-Charles Tranchevent; Alejandro Sifrim; Amin Ardeshirdavani; Jesse Davis; Yves Moreau
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

9.  Biological Interpretation of Complex Genomic Data.

Authors:  Kathleen M Fisch
Journal:  Methods Mol Biol       Date:  2019

Review 10.  Next-generation sequencing diagnostics for neurological diseases/disorders: from a clinical perspective.

Authors:  Jia Nee Foo; Jianjun Liu; Eng-King Tan
Journal:  Hum Genet       Date:  2013-03-23       Impact factor: 4.132

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