RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins
| Autor: | Jin Li, Peng Yu, James D. Thomas, Jacob Vieira, Franjo Ivankovic, Alfredo Ciccodicola, Su-Ping Deng, Ching-San Tseng, Valerio Costa |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
PubMed Polyadenylation Computer science Animals Internet Mice Protein Domains Publications RNA-Binding Proteins Statistics as Topic User-Computer Interface Databases Genetic Molecular Sequence Annotation Sequence Analysis RNA RNA-Seq RNA-binding protein Computational biology Biology General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Databases Annotation 0302 clinical medicine Genetic Regulation of gene expression RNA MRNA stabilization Metadata 030104 developmental biology RNA splicing Original Article RNA-binding proteins (RBPs) General Agricultural and Biological Sciences Sequence Analysis 030217 neurology & neurosurgery Information Systems |
| Zdroj: | Database (Oxf.) 2018 (2018). doi:10.1093/database/bay054 info:cnr-pdr/source/autori:Li J.; Deng S.-P.; Vieira J.; Thomas J.; Costa V.; Tseng C.-S.; Ivankovic F.; Ciccodicola A.; Yu P./titolo:RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins/doi:10.1093%2Fdatabase%2Fbay054/rivista:Database (Oxf.)/anno:2018/pagina_da:/pagina_a:/intervallo_pagine:/volume:2018 Database: The Journal of Biological Databases and Curation |
| DOI: | 10.1101/326116 |
| Popis: | RNA-binding proteins may play a critical role in gene regulation in various diseases or biological processes by controlling post-transcriptional events such as polyadenylation, splicing, and mRNA stabilization via binding activities to RNA molecules. Due to the importance of RNA-binding proteins in gene regulation, a great number of studies have been conducted, resulting in a large amount of RNA-Seq datasets. However, these datasets usually do not have structured organization of metadata, which limits their potentially wide use. To bridge this gap, the metadata of a comprehensive set of publicly available mouse RNA-Seq datasets with perturbed RNA-binding proteins were collected and integrated into a database called RBPMetaDB. This database contains 278 mouse RNA-Seq datasets for a comprehensive list of 163 RNA-binding proteins. These RNA-binding proteins account for only ∼10% of all known RNA-binding proteins annotated in Gene Ontology, indicating that most are still unexplored using high-throughput sequencing. This negative information provides a great pool of candidate RNA-binding proteins for biologists to conduct future experimental studies. In addition, we found that DNA-binding activities are significantly enriched among RNA-binding proteins in RBPMetaDB, suggesting that prior studies of these DNA- and RNA-binding factors focus more on DNA-binding activities instead of RNA-binding activities. This result reveals the opportunity to efficiently reuse these data for investigation of the roles of their RNA-binding activities. A web application has also been implemented to enable easy access and wide use of RBPMetaDB. It is expected that RBPMetaDB will be a great resource for improving understanding of the biological roles of RNA-binding proteins.Database URL: http://rbpmetadb.yubiolab.org |
| Databáze: | OpenAIRE |
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