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Guidelines for the functional annotation of microRNAs using the Gene Ontology

Huntley, Rachael P. and Sitnikov, Dmitry and Orlic-Milacic, Marija and Balakrishnan, Rama and D'Eustachio, Peter and Gillespie, Marc E. and Howe, Doug and Kalea, Anastasia Z. and Maegdefessel, Lars and Osumi-Sutherland, David and Petri, Victoria and Smith, Jennifer R. and Van Auken, Kimberly and Wood, Valerie and Zampetaki, Anna and Mayr, Manuel and Lovering, Ruth C. (2016) Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA, 22 (5). pp. 667-676. ISSN 1355-8382. PMCID PMC4836642. http://resolver.caltech.edu/CaltechAUTHORS:20160307-112011723

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Abstract

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual).


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1261/rna.055301.115DOIArticle
http://rnajournal.cshlp.org/content/22/5/667PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836642/PubMed CentralArticle
ORCID:
AuthorORCID
Van Auken, Kimberly0000-0002-1706-4196
Additional Information:© 2016 Huntley et al. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. Received November 19, 2015; accepted January 19, 2016. R.P.H. and R.C.L. are supported by funding from a British Heart Foundation grant (RG/13/5/30112) and the National Institute for Health Research University College London Hospitals Biomedical Research Centre. M.M. is a Senior Research Fellow of the British Heart Foundation (FS/13/2/29892). A.Z. is an Intermediate Fellow of the British Heart Foundation (FS/13/18/30207). D.S. is supported by a grant awarded to the Mouse Genome Database from the National Human Genome Research Institute at the US National Institutes of Health (HG-00330). P.D’E., M.G., M.O.-M. are supported by grants from the US National Institutes of Health (P41 HG003751 and U54 GM114833), Ontario Research Fund, and the European Molecular Biology Laboratory. D.H. is supported by a grant awarded to the Zebrafish Information Network from the National Human Genome Research Institute at the US National Institutes of Health (HG002659). A.Z.K. is funded by an NIHR University College London Hospitals Biomedical Research Centre, Research Capability Funding award (RCF) (RCF123). L.M. is a Ragnar Söderberg fellow in Medicine (M-14/55) and received funding from Swedish Heart-Lung-Foundation (20120615, 20130664, 20140186). R.B., D.O-S., and K.V.A. are supported by a grant awarded to The Gene Ontology Consortium (Principal Investigators: J.A. Blake, J.M. Cherry, S.E. Lewis, P.W. Sternberg, and P.D. Thomas) by the National Human Genome Research Institute (NIH-NHGRI HG002273). V.P. and J. R.S. are supported by a grant from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health (HL64541). V.W. is supported by a Wellcome Trust grant (104967/Z/14/Z). We would like to thank Leonore Reiser and Tanya Berardini who provided guidance on the plant miRNA processing pathway. Also thanks to David Hill, Harold Drabkin, Judith Blake, Karen Christie, Donghui Li, and Pascale Gaudet who contributed to discussions regarding GO curation procedures and to Lisa Matthews and Bruce May who provided helpful feedback on the manuscript. We are very grateful to Tony Sawford and Maria Martin from the European Bioinformatics Institute for access to the online GO curation tool, which is an essential component of this annotation project. Many thanks to members of the GO Editorial Office for useful discussions about the placement and definition of new GO terms. We also thank Alex Bateman and Anton Petrov for being responsive to our feedback regarding RNA central functionality. Author contributions: R.C.L. initiated discussions in the GO Consortium regarding miRNA curation guidelines and supervised the project; R.P.H. researched and constructed the guidelines and wrote the manuscript; R.P.H., R.C.L., D.S., R.B., P.D’E., M.G., M. O-M., D.H., V.P., J.R.S., K.V.A., and V.W. contributed to discussions regarding GO curation procedures and provided feedback on the manuscript. D.O-S. provided the expertise on definitions and placements of miRNA-related GO terms and performed the necessary updates and additions to both the GO and to the annotation extension relations used herein. M.M., A.Z., L.M., and A.Z.K. provided guidance with the scientific aspect of the guidelines and provided feedback on the manuscript.
Funders:
Funding AgencyGrant Number
British Heart FoundationRG/13/5/30112
National Institute for Health ResearchUNSPECIFIED
British Heart FoundationFS/13/2/29892
British Heart FoundationFS/13/18/30207
NIHHG-00330
NIHP41 HG003751
NIHU54 GM114833
Ontario Research FundUNSPECIFIED
European Molecular Biology LaboratoryUNSPECIFIED
National Human Genome Research InstituteHG002659
National Institute for Health ResearchRCF123
Ragnar Söderberg FellowshipM-14/55
Swedish Heart-Lung-Foundation20120615
Swedish Heart-Lung-Foundation20130664
Swedish Heart-Lung-Foundation20140186
Gene Ontology ConsortiumUNSPECIFIED
NIHHG002273
National Heart, Lung and Blood InstituteHL64541
Wellcome Trust104967/Z/14/Z
Subject Keywords:annotation; biocuration; GO; microRNA; function; analysis
PubMed Central ID:PMC4836642
Record Number:CaltechAUTHORS:20160307-112011723
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160307-112011723
Official Citation:Guidelines for the functional annotation of microRNAs using the Gene Ontology Rachael P. Huntley, Dmitry Sitnikov, Marija Orlic-Milacic, Rama Balakrishnan, Peter D'Eustachio, Marc E. Gillespie, Doug Howe, Anastasia Z. Kalea, Lars Maegdefessel, David Osumi-Sutherland, Victoria Petri, Jennifer R. Smith, Kimberly Van Auken, Valerie Wood, Anna Zampetaki, Manuel Mayr, and Ruth C. Lovering RNA Published in Advance February 25, 2016, doi:10.1261/rna.055301.115
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:65119
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:08 Mar 2016 04:07
Last Modified:20 May 2016 17:45

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