Prediction of Mammalian MicroRNA Targets : Comparative Genomics Approach with Longer 3' UTR Databases
Genomics & Informatics
;
: 53-62, 2005.
Artículo
en Inglés
| WPRIM
| ID: wpr-57214
ABSTRACT
MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the "tight" tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.
Texto completo:
Disponible
Índice:
WPRIM (Pacífico Occidental)
Asunto principal:
Sitios de Unión
/
ADN
/
Expresión Génica
/
Genoma
/
Regiones no Traducidas 3'
/
Genómica
/
MicroARNs
/
Métodos
Tipo de estudio:
Estudio pronóstico
Idioma:
Inglés
Revista:
Genomics & Informatics
Año:
2005
Tipo del documento:
Artículo
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