Cargando…

Gene-oriented ortholog database: a functional comparison platform for orthologous loci

The accumulation of complete genomic sequences enhances the need for functional annotation. Associating existing functional annotation of orthologs can speed up the annotation process and even examine the existing annotation. However, current protein sequence-based ortholog databases provide ambiguo...

Descripción completa

Detalles Bibliográficos
Autores principales: Ho, Meng-Ru, Chen, Chun-houh, Lin, Wen-chang
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860896/
https://www.ncbi.nlm.nih.gov/pubmed/20428317
http://dx.doi.org/10.1093/database/baq002
_version_ 1782180609113718784
author Ho, Meng-Ru
Chen, Chun-houh
Lin, Wen-chang
author_facet Ho, Meng-Ru
Chen, Chun-houh
Lin, Wen-chang
author_sort Ho, Meng-Ru
collection PubMed
description The accumulation of complete genomic sequences enhances the need for functional annotation. Associating existing functional annotation of orthologs can speed up the annotation process and even examine the existing annotation. However, current protein sequence-based ortholog databases provide ambiguous and incomplete orthology in eukaryotes. It is because that isoforms, derived by alternative splicing (AS), often share higher sequence similarity to interfere the sequence-based identification. Gene-Oriented Ortholog Database (GOOD) employs genomic locations of transcripts to cluster AS-derived isoforms prior to ortholog delineation to eliminate the interference from AS. From the gene-oriented presentation, isoforms can be clearly associated to their genes to provide comprehensive ortholog information and further be discriminated from paralogs. Aside from, displaying clusters of isoforms between orthologous genes can present the evolution variation at the transcription level. Based on orthology, GOOD additionally comprises functional annotation from the Gene Ontology (GO) database. However, there exist redundant annotations, both parent and child terms assigned to the same gene, in the GO database. It is difficult to precisely draw the numerical comparison of term counts between orthologous genes annotated with redundant terms. Instead of the description only, GOOD further provides the GO graphs to reveal hierarchical-like relationships among divergent functionalities. Therefore, the redundancy of GO terms can be examined, and the context among compared terms is more comprehensive. In sum, GOOD can improve the interpretation in the molecular function from experiments in the model organism and provide clear comparative genomic annotation across organisms. Database URL: http://goods.ibms.sinica.edu.tw/goods/
format Text
id pubmed-2860896
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-28608962010-04-28 Gene-oriented ortholog database: a functional comparison platform for orthologous loci Ho, Meng-Ru Chen, Chun-houh Lin, Wen-chang Database (Oxford) Original Article The accumulation of complete genomic sequences enhances the need for functional annotation. Associating existing functional annotation of orthologs can speed up the annotation process and even examine the existing annotation. However, current protein sequence-based ortholog databases provide ambiguous and incomplete orthology in eukaryotes. It is because that isoforms, derived by alternative splicing (AS), often share higher sequence similarity to interfere the sequence-based identification. Gene-Oriented Ortholog Database (GOOD) employs genomic locations of transcripts to cluster AS-derived isoforms prior to ortholog delineation to eliminate the interference from AS. From the gene-oriented presentation, isoforms can be clearly associated to their genes to provide comprehensive ortholog information and further be discriminated from paralogs. Aside from, displaying clusters of isoforms between orthologous genes can present the evolution variation at the transcription level. Based on orthology, GOOD additionally comprises functional annotation from the Gene Ontology (GO) database. However, there exist redundant annotations, both parent and child terms assigned to the same gene, in the GO database. It is difficult to precisely draw the numerical comparison of term counts between orthologous genes annotated with redundant terms. Instead of the description only, GOOD further provides the GO graphs to reveal hierarchical-like relationships among divergent functionalities. Therefore, the redundancy of GO terms can be examined, and the context among compared terms is more comprehensive. In sum, GOOD can improve the interpretation in the molecular function from experiments in the model organism and provide clear comparative genomic annotation across organisms. Database URL: http://goods.ibms.sinica.edu.tw/goods/ Oxford University Press 2010 2010-02-10 /pmc/articles/PMC2860896/ /pubmed/20428317 http://dx.doi.org/10.1093/database/baq002 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Ho, Meng-Ru
Chen, Chun-houh
Lin, Wen-chang
Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title_full Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title_fullStr Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title_full_unstemmed Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title_short Gene-oriented ortholog database: a functional comparison platform for orthologous loci
title_sort gene-oriented ortholog database: a functional comparison platform for orthologous loci
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860896/
https://www.ncbi.nlm.nih.gov/pubmed/20428317
http://dx.doi.org/10.1093/database/baq002
work_keys_str_mv AT homengru geneorientedorthologdatabaseafunctionalcomparisonplatformfororthologousloci
AT chenchunhouh geneorientedorthologdatabaseafunctionalcomparisonplatformfororthologousloci
AT linwenchang geneorientedorthologdatabaseafunctionalcomparisonplatformfororthologousloci