Literature DB >> 14527297

Gene annotation: prediction and testing.

Jennifer L Ashurst1, John E Collins.   

Abstract

Fifty years after the publication of DNA structure, the whole human genome sequence will be officially finished. This achievement marks the beginning of the task to catalogue every human gene and identify each of their function expression patterns. Currently, researchers estimate that there are about 30,000 human genes and approximately 70% of these can be automatically predicted using a combination of ab initio and similarity-based programs. However, to experimentally investigate every gene's function, the research community requires a high-quality annotation of alternative splicing, pseudogenes, and promoter regions that can only be provided by manual intervention. Manual curation of the human genome will be a long-term project as experimental data are continually produced to confirm or refine the predictions, and new features such as noncoding RNAs and enhancers have not been fully identified. Such a highly curated human gene-set made publicly available will be a great asset for the experimental community and for future comparative genome projects.

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Mesh:

Year:  2003        PMID: 14527297     DOI: 10.1146/annurev.genom.4.070802.110300

Source DB:  PubMed          Journal:  Annu Rev Genomics Hum Genet        ISSN: 1527-8204            Impact factor:   8.929


  22 in total

1.  EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.

Authors:  Biju Issac; Gajendra Pal Singh Raghava
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

2.  An intermediate grade of finished genomic sequence suitable for comparative analyses.

Authors:  Robert W Blakesley; Nancy F Hansen; James C Mullikin; Pamela J Thomas; Jennifer C McDowell; Baishali Maskeri; Alice C Young; Beatrice Benjamin; Shelise Y Brooks; Bradley I Coleman; Jyoti Gupta; Shi-Ling Ho; Eric M Karlins; Quino L Maduro; Sirintorn Stantripop; Cyrus Tsurgeon; Jennifer L Vogt; Michelle A Walker; Catherine A Masiello; Xiaobin Guan; Gerard G Bouffard; Eric D Green
Journal:  Genome Res       Date:  2004-10-12       Impact factor: 9.043

3.  A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.

Authors:  Ligeng Ma; Chen Chen; Xigang Liu; Yuling Jiao; Ning Su; Lin Li; Xiangfeng Wang; Mengliang Cao; Ning Sun; Xiuqing Zhang; Jingyue Bao; Jian Li; Soren Pedersen; Lars Bolund; Hongyu Zhao; Longping Yuan; Gane Ka-Shu Wong; Jun Wang; Xing Wang Deng; Jian Wang
Journal:  Genome Res       Date:  2005-09       Impact factor: 9.043

4.  Direct isolation and identification of promoters in the human genome.

Authors:  Tae Hoon Kim; Leah O Barrera; Chunxu Qu; Sara Van Calcar; Nathan D Trinklein; Sara J Cooper; Rosa M Luna; Christopher K Glass; Michael G Rosenfeld; Richard M Myers; Bing Ren
Journal:  Genome Res       Date:  2005-05-17       Impact factor: 9.043

5.  Methodology for the inference of gene function from phenotype data.

Authors:  Joao A Ascensao; Mary E Dolan; David P Hill; Judith A Blake
Journal:  BMC Bioinformatics       Date:  2014-12-12       Impact factor: 3.169

6.  A novel ARMS2 splice variant is identified in human retina.

Authors:  Gaofeng Wang; William K Scott; Patrice Whitehead; Brenda L Court; Jaclyn L Kovach; Stephen G Schwartz; Anita Agarwal; Sander Dubovy; Jonathan L Haines; Margaret A Pericak-Vance
Journal:  Exp Eye Res       Date:  2011-11-22       Impact factor: 3.467

7.  yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.

Authors:  Matthew D Wilkerson; Shannon D Schlueter; Volker Brendel
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

8.  Complete MHC haplotype sequencing for common disease gene mapping.

Authors:  C Andrew Stewart; Roger Horton; Richard J N Allcock; Jennifer L Ashurst; Alexey M Atrazhev; Penny Coggill; Ian Dunham; Simon Forbes; Karen Halls; Joanna M M Howson; Sean J Humphray; Sarah Hunt; Andrew J Mungall; Kazutoyo Osoegawa; Sophie Palmer; Anne N Roberts; Jane Rogers; Sarah Sims; Yu Wang; Laurens G Wilming; John F Elliott; Pieter J de Jong; Stephen Sawcer; John A Todd; John Trowsdale; Stephan Beck
Journal:  Genome Res       Date:  2004-05-12       Impact factor: 9.043

9.  Prediction of beta-barrel membrane proteins by searching for restricted domains.

Authors:  Oliver Mirus; Enrico Schleiff
Journal:  BMC Bioinformatics       Date:  2005-10-14       Impact factor: 3.169

10.  Ensembl 2006.

Authors:  E Birney; D Andrews; M Caccamo; Y Chen; L Clarke; G Coates; T Cox; F Cunningham; V Curwen; T Cutts; T Down; R Durbin; X M Fernandez-Suarez; P Flicek; S Gräf; M Hammond; J Herrero; K Howe; V Iyer; K Jekosch; A Kähäri; A Kasprzyk; D Keefe; F Kokocinski; E Kulesha; D London; I Longden; C Melsopp; P Meidl; B Overduin; A Parker; G Proctor; A Prlic; M Rae; D Rios; S Redmond; M Schuster; I Sealy; S Searle; J Severin; G Slater; D Smedley; J Smith; A Stabenau; J Stalker; S Trevanion; A Ureta-Vidal; J Vogel; S White; C Woodwark; T J P Hubbard
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

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