Tag: Regulatory Motif

oPOSSUM 3.0 – Analysis of Regulatory Motif over-representation

oPOSSUM 3.0

:: DESCRIPTION

oPOSSUM is 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.

::DEVELOPER

Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 oPOSSUM

:: MORE INFORMATION

Citation:

Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW.
oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W245-52. Epub 2007 Jun 18.

 

REMOCOD – REgulatory MOtif COmbination Detector

REMOCOD

:: DESCRIPTION

REMOCOD  is a program for the systematic identification of pairs of transcription factor binding sites (TFBSs) that tend to co-occur in promoter sequences of a set of co-regulated genes. Given a set of gene IDs, the program first detects over-represented TFBSs in the promoter sequences corresponding to these genes, and subsequently predicts regulatory motifs that show a tendency to co-occur with any of the over-represented TFBSs.

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Vandenbon A, Kumagai Y, Akira S, Standley DM.
“A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription“,
BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11

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