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Protocols

CIS-BP specifications

Information


Unique identifier OMICS_10990
Name CIS-BP
Alternative names Catalog of Inferred Sequence Binding Preferences, CIS-BP motif database
Restrictions to use None
Data access File download, Browse
Version 1.02
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus tropicalis

Maintainer


  • person_outline Timothy Hughes

Publication for Catalog of Inferred Sequence Binding Preferences

CIS-BP citations

 (25)
library_books

Chromatin Accessibility Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood Stage Development

2018
PMCID: 5899830
PMID: 29649445
DOI: 10.1016/j.chom.2018.03.007

[…] if search using GimmeMotifs and seqGL (; , ). These de novo predicted motifs were combined with previously predicted Plasmodium motifs () and known vertebrate, invertebrate, and plant motifs from the CIS-BP database (), yielding a comprehensive library of putative cis-regulatory sequences. Next we identified gene sets with clear stage-specific accessibility/expression profiles by selecting all acc […]

library_books

Degenerate Pax2 and Senseless binding motifs improve detection of low affinity sites required for enhancer specificity

2018
PLoS Genet
PMCID: 5902045
PMID: 29617378
DOI: 10.1371/journal.pgen.1007289

[…] cts SRP029908 [] and SRP002575 []); assessing read quality with FASTQC [] (–); mapping to the mm10 genome using Bowtie 2 []; and calling and scoring peaks using MACS2 [].PBM data were downloaded from CIS-BP (D. rerio Pax2b, M1499_1.02) and UniPROBE (H. sapiens Gfi1b, UP00592) [, ]. AUROC analysis was done on PBM probes binned by fluorescence (top 0.25%, top 0.5%-0.25%, top 1%-0.5%, top 2.5%-1%, to […]

library_books

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

2018
Mol Syst Biol
PMCID: 5822049
PMID: 29472273
DOI: 10.15252/msb.20177902

[…] he number of bases matching the top 10mer, then constructed a frequency matrix from these alignments, and, finally, used this frequency matrix to align the retained SELEX probes. For the UniPROBE and CIS‐BP PBM datasets, we selected the 100 probes with the strongest binding signal and aligned these to the curated scoring matrix. We finally used the pentamer tables to compute the mean shape‐paramet […]

library_books

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

2018
Nat Commun
PMCID: 5823854
PMID: 29472540
DOI: 10.1038/s41467-018-03082-6

[…] We examined the genome-wide impact of discSNPs on GATA1 binding as an unbiased means to define in vivo genetic determinants of GATA1 chromatin occupancy. We used the MEME suite and CIS-BP motif database to identify discSNP pairs that fall within a TF motif and are predicted to disrupt binding to that motif (detailed in Methods). We found that 67% of all discSNPs in GATA1 peaks d […]

library_books

Identification of Single Nucleotide Non coding Driver Mutations in Cancer

2018
Front Genet
PMCID: 5801294
PMID: 29456552
DOI: 10.3389/fgene.2018.00016

[…] P) followed by next generation sequencing (ChIP-seq) (; ; ). Currently, DNA binding specificities have been determined for nearly half of human TFs, which are available in different repositories such CIS-BP, Jaspar, Uniprobe, and Transfac (; ; ; ) (Table ). Differences in TF binding between SNV alleles can be predicted using position weight matrices (PWMs), probabilistic representations of DNA bin […]

call_split

Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10 clade

2017
BMC Plant Biol
PMCID: 5735953
PMID: 29258424
DOI: 10.1186/s12870-017-1210-4
call_split See protocol

[…] s applied to the resulting MEME motifs using “Complete scoring” (which takes non-matching parts into account), and MEME motifs were compared with the JASPAR Core plant motif database [], and with the CIS-BP Arabidopsis thaliana database [].In addition to the de novo motif search, a set of potentially relevant existing motifs were obtained from literature [, ] and from the JASPAR database (BZR1, MA […]


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CIS-BP institution(s)
CisBP is a collaborative effort between the labs of Tim Hughes (University of Toronto) and Matt Weirauch (Cincinnati Children’s Hospital). It originated while Matt was a postdoc in Tim’s lab. In addition to Matt and Tim, extensive contributions have been made by Ally Yang (experimental) and Mihai Albu (database/web server).

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