Paper Info
Title
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.
Abstract
RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/. Database URL: http://pseudomap.mbc.nctu.edu.tw/
Year
DOI
Venue
2013
10.1093/database/bat001
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Keywords
Field
DocType
gene expression regulation,micrornas,internet,pseudogenes
Pseudogene,Trans-acting siRNA,Gene silencing,Deep sequencing,Biology,microRNA,Regulation of gene expression,Bioinformatics,Genetics,RNA interference,Small interfering RNA
Journal
Volume
ISSN
Citations 
2013
1758-0463
0
PageRank 
References 
Authors
0.34
14
4
Name
Order
Citations
PageRank
Wen-Ling Chan11136.78
Wen-Kuang Yang200.34
Hsien-Da Huang383563.83
Jan-Gowth Chang404.06