CISMAPPER specifications


Unique identifier OMICS_13381
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data CISMAPPER can take as input any set of loci from the genome of interest.
Input format BED
Output data Generates lists of the TSSs and genes that those regions may regulate.
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


No version available


  • person_outline Timothy Bailey

Publication for CISMAPPER

CISMAPPER citations


Maternal obesity programs increased leptin gene expression in rat male offspring via epigenetic modifications in a depot specific manner

PMCID: 5518658
PMID: 28752055
DOI: 10.1016/j.molmet.2017.05.010

[…] Public functional genomic data , were downloaded from Gene Expression Omnibus or the UCSC Genome Browser. The identification procedure has been detailed in . CisMapper model was used to predict the involvement of identified genomic areas in the transcriptional regulation of the leptin gene . Genomic sequences were aligned between mouse and rat by the EMBOS […]


CisMapper: predicting regulatory interactions from transcription factor ChIP seq data

Nucleic Acids Res
PMCID: 5389714
PMID: 28204599
DOI: 10.1093/nar/gkw956

[…] Thus far we have only presented results based on using the active enhancer histone mark H3K27ac in CisMapper's tissue panel. When we repeat the TSS target prediction experiment above using histone data for the active promoter histone mark H3K4me3 in place of the H3K27ac data used above, CisMapper i […]

CISMAPPER institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLB, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia; Department of Pharmacology, University of Nevada School of Medicine, Reno, NV, USA
CISMAPPER funding source(s)
This work was supported by National Institutes of Health [R01 GM103544].


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