Literature DB >> 18798919

Access to immunology through the Gene Ontology.

Ruth C Lovering1, Evelyn B Camon, Judith A Blake, Alexander D Diehl.   

Abstract

The Gene Ontology (GO) is widely recognized as the premier tool for the organization and functional annotation of molecular aspects of cellular systems. However, for many immunologists the use of GO is a very foreign concept. Indeed, as a controlled vocabulary, GO can almost be considered a new language, and it can be difficult to appreciate the use and value of this approach for understanding the immune system. This review reflects on the application of GO to the field of immunology and explains the process of GO annotation. Finally, this review hopes to inspire immunologists to invest time and energy in improving both the content of the GO and the quality of GO annotations associated with genes of immunological interest.

Mesh:

Year:  2008        PMID: 18798919      PMCID: PMC2561138          DOI: 10.1111/j.1365-2567.2008.02940.x

Source DB:  PubMed          Journal:  Immunology        ISSN: 0019-2805            Impact factor:   7.397


  30 in total

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Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
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3.  Genome-wide prediction and analysis of function-specific transcription factor binding sites.

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Journal:  In Silico Biol       Date:  2004

4.  Vascular cell adhesion molecule-1 and the integrin VLA-4 mediate adhesion of human B cell precursors to cultured bone marrow adherent cells.

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Journal:  J Clin Invest       Date:  1991-09       Impact factor: 14.808

5.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; Vivian Lee; Emily Dimmer; John Maslen; David Binns; Nicola Harte; Rodrigo Lopez; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  CD25+CD4+ cells contribute to Th2 polarization during helminth infection by suppressing Th1 response development.

Authors:  Amy S McKee; Edward J Pearce
Journal:  J Immunol       Date:  2004-07-15       Impact factor: 5.422

8.  An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

Authors:  Evelyn B Camon; Daniel G Barrell; Emily C Dimmer; Vivian Lee; Michele Magrane; John Maslen; David Binns; Rolf Apweiler
Journal:  BMC Bioinformatics       Date:  2005-05-24       Impact factor: 3.169

9.  InterPro, progress and status in 2005.

Authors:  Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; David Binns; Paul Bradley; Peer Bork; Phillip Bucher; Lorenzo Cerutti; Richard Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Wolfgang Fleischmann; Julian Gough; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; David Lonsdale; Rodrigo Lopez; Ivica Letunic; Martin Madera; John Maslen; Jennifer McDowall; Alex Mitchell; Anastasia N Nikolskaya; Sandra Orchard; Marco Pagni; Chris P Ponting; Emmanuel Quevillon; Jeremy Selengut; Christian J A Sigrist; Ville Silventoinen; David J Studholme; Robert Vaughan; Cathy H Wu
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

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Journal:  J Cell Mol Med       Date:  2008-02-08       Impact factor: 5.310

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  14 in total

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Journal:  Genes Genomics       Date:  2017-12-01       Impact factor: 1.839

3.  An integrated analysis of the effects of microRNA and mRNA on esophageal squamous cell carcinoma.

Authors:  Yong Yang; Dianbo Li; Yang Yang; Gening Jiang
Journal:  Mol Med Rep       Date:  2015-03-27       Impact factor: 2.952

4.  Comparison of gene expression profiles and related pathways in chronic thromboembolic pulmonary hypertension.

Authors:  Song Gu; Pixiong Su; Jun Yan; Xitao Zhang; Xiangguang An; Jie Gao; Rui Xin; Yan Liu
Journal:  Int J Mol Med       Date:  2013-12-10       Impact factor: 4.101

5.  The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY.

Authors:  Simon D Harding; Joanna L Sharman; Elena Faccenda; Chris Southan; Adam J Pawson; Sam Ireland; Alasdair J G Gray; Liam Bruce; Stephen P H Alexander; Stephen Anderton; Clare Bryant; Anthony P Davenport; Christian Doerig; Doriano Fabbro; Francesca Levi-Schaffer; Michael Spedding; Jamie A Davies
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

6.  The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model.

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Journal:  BMC Cancer       Date:  2017-05-19       Impact factor: 4.430

7.  Integrated analysis of the potential roles of miRNA‑mRNA networks in triple negative breast cancer.

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8.  Expression analysis of genes and pathways associated with liver metastases of the uveal melanoma.

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Journal:  BMC Med Genet       Date:  2014-03-05       Impact factor: 2.103

9.  Integrated microRNA-mRNA analysis revealing the potential roles of microRNAs in tongue squamous cell cancer.

Authors:  Xiao-Li Zhou; Jun-Hua Wu; Xin-Juan Wang; Fu-Jun Guo
Journal:  Mol Med Rep       Date:  2015-03-11       Impact factor: 2.952

10.  Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery.

Authors:  So Young Park; Bharat Bhusan Patnaik; Se Won Kang; Hee-Ju Hwang; Jong Min Chung; Dae Kwon Song; Min Kyu Sang; Hongray Howrelia Patnaik; Jae Bong Lee; Mi Young Noh; Changmu Kim; Soonok Kim; Hong Seog Park; Jun Sang Lee; Yeon Soo Han; Yong Seok Lee
Journal:  Genes (Basel)       Date:  2016-07-22       Impact factor: 4.096

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