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CisGenome specifications


Unique identifier OMICS_00423
Name CisGenome
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


  • Invertebrates
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


No version available


  • person_outline Wing Hung Wong
  • person_outline Hongkai Ji
  • person_outline Wenxiu Ma

Additional information

Publication for CisGenome

CisGenome citations


Megakaryocyte lineage development is controlled by modulation of protein acetylation

PLoS One
PMCID: 5919413
PMID: 29698469
DOI: 10.1371/journal.pone.0196400
call_split See protocol

[…] Life Technologies, Carlsbad, CA, USA). Sequencing reads were mapped against the reference genome (hg19,NCBI3) using the BWA package (-c–l 25 –k 2 –n 10) []. Non-uniquely placed reads were discarded. Cisgenome v2.0 software package [] was used for the peak calling from the ChIP-seq data with settings–e 50 –maxgap and further analysis. Cisgenome 2 was used with settings: -e 50, -maxgap 200 and -min […]


The regulon of the RNA chaperone CspA and its auto regulation in Staphylococcus aureus

Nucleic Acids Res
PMCID: 5815144
PMID: 29309682
DOI: 10.1093/nar/gkx1284

[…] resent RNA regions protected by CspA binding.Next, peak calling was performed using two complementary methods (see Material and Methods). In total, we identified 570 and 355 peaks by Thresholding and CisGenome, respectively. The difference in the number of peaks detected by both bioinformatics approaches can be explained by their distinct data processing procedures. Thresholding method considers a […]


Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources

PMCID: 5919752
PMID: 29208650
DOI: 10.1534/g3.117.300138

[…] to have recognition sequences within gene bodies. However, 1083 out of 1136 narrow peak regions (defined in the Materials and Methods and supplemental material) of Yrr1 ChIP enrichment identified by CisGenome and MACS2 overlap with annotated genes in the published S288c genome. False-positive ChIP peaks have been previously identified within highly expressed genes, i.e., “hyper-ChIPable” regions […]


JUNB governs a feed forward network of TGFβ signaling that aggravates breast cancer invasion

Nucleic Acids Res
PMCID: 5814809
PMID: 29186616
DOI: 10.1093/nar/gkx1190

[…] using MACS software (Model based analysis of ChIP-seq) (version 1.4.2) () with a P-value threshold of 1e-5. Assigning a binding site to the nearest gene within 100 kb from a peak was performed using CisGenome ver2 (). De novo motif prediction was performed by MEME-ChIP with a slight modification of the default settings (maximum width: 10) (MEME-ChIP version 4.10; […]


C State: an interactive web app for simultaneous multi gene visualization and comparative epigenetic pattern search

BMC Bioinformatics
PMCID: 5606219
PMID: 28929968
DOI: 10.1186/s12859-017-1786-6

[…] fication such as CHROMATRA [], a plug-in specific for the Galaxy platform or PAVIS [], which links to the UCSC browser and uses a chromosome-centric approach. Complete ChIP-seq analysis packages like CisGenome [] and recently developed visualization tools such as VisPIG [] and Epiviz [] offer options for peak visualization but cannot directly screen and display user-defined patterns across multipl […]


Effects of distinct drugs on gene transcription in an osteosarcoma cell line

PMCID: 5649527
PMID: 29085469
DOI: 10.3892/ol.2017.6767

[…] l-based analysis of ChIP-Seq 2 was applied to identify peaks of transcription factor p53-binding regions (). The two procedures used the default value as parameter. Peak annotations were processed by CisGenome (version 2.0; (), an integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. Any genes presenting with a peak lo […]


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CisGenome institution(s)
Department of Biostatistics Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Computational and Mathematical Engineering Stanford University Durand Building, Stanford, CA, USA; Department of Computer Science Stanford University 353 Serra Mall Stanford, CA, USA; Department of Genetics Stanford University School of Medicine, Stanford, CA, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Statistics Stanford University Sequoia Hall, Stanford, CA,USA; Department of Health Research and Policy Stanford University Sequoia Hall, Stanford, CA, USA
CisGenome funding source(s)
Supported by NIH grant HG003903 (WHW), and by NHGRI's ENCODE project (RMM), and partially by the JHSPH Richard L. Gelb Cancer Research Fund.

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