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MatrixREDUCE

eagle-i ID

http://shared.eagle-i.net/i/0000013a-0e94-7f1d-e36c-637980000000

Resource Type

  1. Software

Properties

  1. Resource Description
    "Regulation of gene expression by a transcription factor requires physical interaction between the factor and the DNA, which can be described by astatistical mechanical model. Based on this model, the MatrixREDUCE algorithm uses genome-wide occupancy data for a transcription factor (e.g.ChIP-chip or mRNA expression data) and associated nucleotide sequences to discover the sequence-specific binding affinity of the transcription factor. The sequence specificity of the transcription factor's DNA-binding domain is modeled using a position-specific affinity matrix (PSAM), representing the change in the binding affinity (Kd) whenever a specific position within a reference binding sequence is mutated. The PSAM can be transformed into affinity logo for visualization using the utility program AffinityLogo, and a MatrixREDUCE run can be summarized in an easy-to-navigate webpage using HTMLSummary." Development stage: Extensively tested in lab. Release date: July 10, 2006 Keywords: position-specific affinity matrix, binding affinity, cis-regulatory element, transcription factor
  2. Contact
    Bussemaker, Harmen J.
  3. Used by
    Center for Multiscale Analysis of Genomic and Cellular Networks
  4. Version
    Version 1.0
  5. Data Input
    gene expression dataset
  6. Software purpose
    Gene expression analysis
  7. Website(s)
    http://www.bussemakerlab.org/software/MatrixREDUCE
  8. Related Technique
    ChIP-chip assay
 
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Provenance Metadata About This Resource Record

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