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Unique identifier OMICS_06132
Name CISBP-RNA
Alternative name Catalog of Inferred Sequence Binding Preferences of RNA binding proteins
Restrictions to use None
Maintained Yes

Publication for Catalog of Inferred Sequence Binding Preferences of RNA binding proteins

CISBP-RNA citations

 (12)
library_books

Full length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

2018
Genome Biol
PMCID: 5877393
PMID: 29598823
DOI: 10.1186/s13059-018-1418-0

[…] ase, a maximum of ten motifs with E-values < 0.05 was reported. The remaining parameters were kept as default. We then compared each motif found by DREME against the human RNA-binding motifs database CISBP-RNA using TOMTOM Motif Comparison tool []. We ran the analysis by setting the Pearson correlation coefficient as comparison function and considered only matches with a minimum FDR (q-values) < 0 […]

library_books

Inferring RNA sequence preferences for poorly studied RNA binding proteins based on co evolution

2018
BMC Bioinformatics
PMCID: 5848454
PMID: 29529991
DOI: 10.1186/s12859-018-2091-8

[…] necessity of our KNN method for the poorly studied proteins. Fig. 3Finally, after demonstrating the capability of our KNN method, we made inference of PWMs for 1000 poorly studied RBPs selected from cisBP-RNA database []. These RBPs contain either KH or RRM RNA-binding domain, from a diverse range of eukaryotes. They were categorized as “inferred” in the “motif evidence” menu in the cisBP-RNA dat […]

library_books

Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow

2018
eLife
PMCID: 5771670
PMID: 29293084
DOI: 10.7554/eLife.29494.044

[…] y flanking motifs, we developed an analysis pipeline using the ranking algorithm in GSEA and taking advantage of the recent development of a comprehensive database of RNA-protein binding preferences (CisBP-RNA) to provide the RNA-binding protein ‘finger-prints’ to be ranked (). We confirmed that this pipeline was able to correctly identify known regulatory splicing factors from raw RNA-seq data fr […]

library_books

In situ functional dissection of RNA cis regulatory elements by multiplex CRISPR Cas9 genome engineering

2017
Nat Commun
PMCID: 5727397
PMID: 29235467
DOI: 10.1038/s41467-017-00686-2

[…] ed target sites of most abundant S2 miRNAs (miRanda-mirSVR and TargetScanFly 6.2); AU-rich elements (AREScore; http://arescore.dkfz.de/arescore.pl); polyA signals (AATAAA/ATTAAA); HuR binding motifs (CISBP-RNA; http://cisbp-rna.ccbr.utoronto.ca/TFTools.php) and Pumilio response elements (TGTANA(TA)). Comparative analysis of UNS distributions (Wilcoxon rank-sum test) between UDPs +/− additional put […]

library_books

RNA protein binding motifs mining with a new hybrid deep learning based cross domain knowledge integration approach

2017
BMC Bioinformatics
PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] eotide within window, resulting in 101 dimensional features. Motif. Motif scores are used for numerical representation of the RNA sequences []. We firstly downloaded 102 human RBP binding motifs from CISBP-RNA [], then Cluster-Buster [] was employed to score RNA sequences for binding sites clusters. For individual sequence, we can get a score per motif, resulting in a 102 dimensional features. CNN […]

library_books

CLK dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor

2017
Nat Commun
PMCID: 5431906
PMID: 28232751
DOI: 10.1038/s41467-016-0008-7

[…] sis. We searched seven regions on each transcript comprising constitutive and alternative exons, along with regions of the intermediate introns and calculated the density of 128 human RBP motifs from cisBP-RNA. We observed distinct and mirror image patterns of RBP motif enrichment (two-sided unequal-variance t-test on ranked data, p < 0.05) in the SE of the AS event and surrounding introns and ups […]

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CISBP-RNA institution(s)
Donnelly Centre, University of Toronto, Toronto, Canada

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