Literature DB >> 18475267

Use and misuse of the gene ontology annotations.

Seung Yon Rhee1, Valerie Wood, Kara Dolinski, Sorin Draghici.   

Abstract

The Gene Ontology (GO) project is a collaboration among model organism databases to describe gene products from all organisms using a consistent and computable language. GO produces sets of explicitly defined, structured vocabularies that describe biological processes, molecular functions and cellular components of gene products in both a computer- and human-readable manner. Here we describe key aspects of GO, which, when overlooked, can cause erroneous results, and address how these pitfalls can be avoided.

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Year:  2008        PMID: 18475267     DOI: 10.1038/nrg2363

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


  196 in total

1.  Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.

Authors:  Daniel J Schaid; Jason P Sinnwell; Gregory D Jenkins; Shannon K McDonnell; James N Ingle; Michiaki Kubo; Paul E Goss; Joseph P Costantino; D Lawrence Wickerham; Richard M Weinshilboum
Journal:  Genet Epidemiol       Date:  2011-12-07       Impact factor: 2.135

Review 2.  Molecular diagnostics in transplantation.

Authors:  Maarten Naesens; Minnie M Sarwal
Journal:  Nat Rev Nephrol       Date:  2010-08-24       Impact factor: 28.314

3.  Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.

Authors:  KiYoung Lee; David Thorneycroft; Premanand Achuthan; Henning Hermjakob; Trey Ideker
Journal:  Plant Cell       Date:  2010-04-06       Impact factor: 11.277

4.  Gene set enrichment; a problem of pathways.

Authors:  Matthew N Davies; Emma L Meaburn; Leonard C Schalkwyk
Journal:  Brief Funct Genomics       Date:  2010-09-22       Impact factor: 4.241

Review 5.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors:  Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal:  Brief Bioinform       Date:  2015-10-22       Impact factor: 11.622

6.  Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites.

Authors:  Henri A Blomster; Ville Hietakangas; Jianmin Wu; Petri Kouvonen; Sampsa Hautaniemi; Lea Sistonen
Journal:  Mol Cell Proteomics       Date:  2009-02-24       Impact factor: 5.911

7.  GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.

Authors:  Xinan Yang; Jianrong Li; Younghee Lee; Yves A Lussier
Journal:  Bioinformatics       Date:  2011-03-17       Impact factor: 6.937

Review 8.  Principles and methods of integrative genomic analyses in cancer.

Authors:  Vessela N Kristensen; Ole Christian Lingjærde; Hege G Russnes; Hans Kristian M Vollan; Arnoldo Frigessi; Anne-Lise Børresen-Dale
Journal:  Nat Rev Cancer       Date:  2014-05       Impact factor: 60.716

9.  Large-scale reverse genetics in Arabidopsis: case studies from the Chloroplast 2010 Project.

Authors:  Imad Ajjawi; Yan Lu; Linda J Savage; Shannon M Bell; Robert L Last
Journal:  Plant Physiol       Date:  2009-11-11       Impact factor: 8.340

10.  The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Authors: 
Journal:  PLoS Comput Biol       Date:  2009-07-03       Impact factor: 4.475

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