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cisRED specifications


Unique identifier OMICS_01857
Name cisRED
Restrictions to use None
Maintained Yes

Publication for cisRED

cisRED citations


Characterization of Human Chromosomal Material Exchange with Regard to the Chromosome Translocations Using Next Generation Sequencing Data

Genome Biol Evol
PMCID: 4255766
PMID: 25349267
DOI: 10.1093/gbe/evu234

[…] were investigated for their evolutionary conservation. For translocation hot regions, we used phastCons and phyloP scores in UCSC Genome Browser (; ). For the motifs, their sequences were searched in cisRED, a database holding “conserved sequence motifs identified by genome-scale motif discovery, similarity, clustering, cooccurrence, and coexpression calculations” (). […]


TdIF1 Recognizes a Specific DNA Sequence through Its Helix Turn Helix and AT Hook Motifs to Regulate Gene Transcription

PLoS One
PMCID: 3707907
PMID: 23874396
DOI: 10.1371/journal.pone.0066710

[…] DISOPRED (, WebLogo (, and cisRED ( were used. […]


Statistical Approaches to Use a Model Organism for Regulatory Sequences Annotation of Newly Sequenced Species

PLoS One
PMCID: 3439465
PMID: 22984403
DOI: 10.1371/journal.pone.0042489

[…] Thaliana .We also find that some of the motifs ((for example TTTCCTGATTTG and AATGAGAAATAA) have been described in databases automatically built by a number of computational tools such as , ABS, and Phylonet ( Some motifs produced hits in high eukaryotes or bacteria sequences (not reported becaus […]


GW8510 Increases Insulin Expression in Pancreatic Alpha Cells through Activation of p53 Transcriptional Activity

PLoS One
PMCID: 3252286
PMID: 22242153
DOI: 10.1371/journal.pone.0028808

[…] following treatment with GW8510, we sought to determine whether p53 could directly trans-activate Ins2. We mined a database for genome-scale computational discovery of conserved regulatory elements, cisRED, in the mouse genome, which contains conserved sequence motifs in promoters of about 17,500 genes . Interestingly, cisRED analysis predicted a p53 response element in the promoter region of the […]


Large scale motif discovery using DNA Gray code and equiprobable oligomers

PMCID: 3244767
PMID: 22057160
DOI: 10.1093/bioinformatics/btr606

[…] tifs introduced in Hegma has effectively reduced sFP and hence improved sPPV, as mentioned in the previous subsection.We repeat the same analysis as mentioned above for the 10 most frequent motifs in cisRED (AhR, aMEF-2, POU2F1, Pax-5, DEAF-1, CREB, HNF-1α, DP-1, RSRFC4 and POU3F2). summarizes the results for these 10 motifs at the nucleotide level by averaging their statistics. The detailed resu […]


Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co regulation patterns

BMC Bioinformatics
PMCID: 3215511
PMID: 21910886
DOI: 10.1186/1471-2105-12-365

[…] pproach allowing genomewide regulatory element based searches without the need to rely on TFBS databases. Our main input dataset is the evolutionary conserved sequences of promoters obtained from the cisRED database []. Instead of using TFBS databases to narrow down the search scope, a gene of interest is selected. The methodology compares its evolutionary conserved sequences with those from all t […]


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cisRED institution(s)
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada

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