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Number of citations per year for the bioinformatics software tool RBPDB
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Protocols

RBPDB specifications

Information


Unique identifier OMICS_06123
Name RBPDB
Alternative name RNA-Binding Protein DataBase
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/RNA-binding_protein_database

Maintainer


  • person_outline Timothy Hughes

Publication for RNA-Binding Protein DataBase

RBPDB citations

 (10)
library_books

KSRP specifies monocytic and granulocytic differentiation through regulating miR 129 biogenesis and RUNX1 expression

2017
Nat Commun
PMCID: 5681548
PMID: 29127290
DOI: 10.1038/s41467-017-01425-3

[…] Fig. ).Fig. 1 To investigate the RBP expression patterns, we first performed a differential expression (DE) analysis of Ensembl-annotated human genes by EBSeq-HMM (Supplementary Data ). Combined with RBPDB- and ATrRACT-annotated, human RBP genes, the DE analysis revealed 1,100 (from batch 1) and 1,188 (from batch 2) monotonically up-regulated or downregulated genes, including 21 (from batch 1) and […]

library_books

The tyrosine kinase receptor Tyro3 enhances lifespan and neuropeptide Y (Npy) neuron survival in the mouse anorexia (anx) mutation

2017
PMCID: 5451163
PMID: 28093506
DOI: 10.1242/dmm.027433

[…] vealed that the cytosine mutated in the C19T Tyro3 mutation is invariant and located within a larger conserved 21 nucleotide sequence. Current programs designed to identify RNA binding protein sites (RBPDB: http://rbpdb.ccbr.utoronto.ca/index.php and RegRNA: http://regrna.mbc.nctu.edu.tw/html/prediction.html) did not score disruption or creation of a binding site for a known RNA binding protein (R […]

library_books

The cis acting replication element of the Hepatitis C virus genome recruits host factors that influence viral replication and translation

2016
Sci Rep
PMCID: 4863150
PMID: 27165399
DOI: 10.1038/srep25729

[…] ar ribonucleoproteins (hnRNPs), Ras-GTPase activating-binding proteins (G3BPs) and splicing factors.All the proteins belonging to the RNA-binding cluster were checked against the RNA-Binding Protein (RBPDB) database (http://rbpdb.ccbr.utoronto.ca/) to identify the type and number of RNA binding domains involved in the protein-CRE interaction. Interestingly, all showed the presence of RRMs in their […]

library_books

A unified analytic framework for prioritization of non coding variants of uncertain significance in heritable breast and ovarian cancer

2016
BMC Med Genomics
PMCID: 4828881
PMID: 27067391
DOI: 10.1186/s12920-016-0178-5

[…] iant c.-71C > G (chr16:68771248C > G; rs34033771; 7-4C) disrupts a double-stranded hairpin region to create a larger loop structure, thus increasing binding accessibility (Fig.  and ). Analysis using RBPDB and CISBP-RNA-derived IT models suggests this variant affects binding by NCL (Nucleolin, a transcription coactivator) by decreasing binding affinity 14-fold (Ri,initial = 6.6 bits, ΔRi = -3.8 bi […]

call_split

Distinct brain transcriptome profiles in C9orf72 associated and sporadic ALS

2015
Nat Neurosci
PMCID: 4830686
PMID: 26192745
DOI: 10.1038/nn.4065
call_split See protocol

[…] ing the MEME-ChIP program of the MEME suite package. The identified motifs were then cross-referenced with the known binding motifs of RNA-binding proteins (RBP) and literature, (RBP database: http://rbpdb.ccbr.utoronto.ca/), to identify RBPs that may be responsible for AS cassette exon events significantly represented in our dataset. […]

library_books

Revealing protein–lncRNA interaction

2015
Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] dentifying a large number of antisense ncRNAs regulating gene expression via binding in cis. Public data sets are also available from which RBP–lncRNA interactions detected in vitro can be retrieved. RBPDB [] is a database of binding determinants for a collection of RBPs, some of which can bind lncRNAs. Most data derive from SELEX approaches, but also a number of in vivo experiments are included. […]


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RBPDB institution(s)
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
RBPDB funding source(s)
Canadian Institutes of Health Research (MOP-93671; MOP-49451); National Institutes of Health (1R01HG00570); Natural Sciences and Engineering Research Council of Canada CGS-M

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