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oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

G3 (Bethesda, Md.) | 2012

oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca.

Pubmed ID: 22973536 RIS Download

Research resources used in this publication

None found

Antibodies used in this publication

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Associated grants

  • Agency: NIGMS NIH HHS, United States
    Id: R01 GM084875
  • Agency: NIGMS NIH HHS, United States
    Id: 1R01GM084875
  • Agency: CIHR, Canada

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This is a list of tools and resources that we have found mentioned in this publication.


GitHub (tool)

RRID:SCR_002630

A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.

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oPOSSUM (tool)

RRID:SCR_010884

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

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ChIP-seq (tool)

RRID:SCR_001237

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

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TFBS (tool)

RRID:SCR_015774

Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites.

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