Quantifying Protein Function Specificity in the Gene Ontology

Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) numbe...

Descripción completa

Detalles Bibliográficos
Autores principales: Louie, Brenton, Bergen, Silas, Higdon, Roger, Kolker, Eugene
Formato: Texto
Lenguaje:English
Publicado: Michigan State University 2010
Materias:
Standard Operating Procedures
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035283/
https://www.ncbi.nlm.nih.gov/pubmed/21304708
http://dx.doi.org/10.4056/sigs.561626
_version_ 1782197754191151104
author Louie, Brenton
Bergen, Silas
Higdon, Roger
Kolker, Eugene
author_facet Louie, Brenton
Bergen, Silas
Higdon, Roger
Kolker, Eugene
author_sort Louie, Brenton
collection PubMed
description Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) number of ancestor terms; 2) number of offspring terms; 3) proportion of terms; and 4) Information Content (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each.
format Text
id pubmed-3035283
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Michigan State University
record_format MEDLINE/PubMed
spelling pubmed-30352832011-02-08 Quantifying Protein Function Specificity in the Gene Ontology Louie, Brenton Bergen, Silas Higdon, Roger Kolker, Eugene Stand Genomic Sci Standard Operating Procedures Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) number of ancestor terms; 2) number of offspring terms; 3) proportion of terms; and 4) Information Content (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each. Michigan State University 2010-03-30 /pmc/articles/PMC3035283/ /pubmed/21304708 http://dx.doi.org/10.4056/sigs.561626 Text en http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Operating Procedures
Louie, Brenton
Bergen, Silas
Higdon, Roger
Kolker, Eugene
Quantifying Protein Function Specificity in the Gene Ontology
title Quantifying Protein Function Specificity in the Gene Ontology
title_full Quantifying Protein Function Specificity in the Gene Ontology
title_fullStr Quantifying Protein Function Specificity in the Gene Ontology
title_full_unstemmed Quantifying Protein Function Specificity in the Gene Ontology
title_short Quantifying Protein Function Specificity in the Gene Ontology
title_sort quantifying protein function specificity in the gene ontology
topic Standard Operating Procedures
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035283/
https://www.ncbi.nlm.nih.gov/pubmed/21304708
http://dx.doi.org/10.4056/sigs.561626
work_keys_str_mv AT louiebrenton quantifyingproteinfunctionspecificityinthegeneontology
AT bergensilas quantifyingproteinfunctionspecificityinthegeneontology
AT higdonroger quantifyingproteinfunctionspecificityinthegeneontology
AT kolkereugene quantifyingproteinfunctionspecificityinthegeneontology

Ejemplares similares