- Search for TFs
- Search for Genes
- Search for Associations
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This utility generates a simple binary regulation matrix for input transcription factors (TFs) and regulated genes (RGs). For the input lists of TFs and RGs, the matrix summarizes which TFs regulate which genes. For each TF/Gene pair, the Regulatory Association (RA) is represented by 1 or 0, representing an existing or non-existing association, respectively.
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The utility requires a list of transcription factors and genes. Alternatively, the user can choose to construct the matrix with all the transcription factors or all the genes in the database.Back to top
By default, the matrix is generated for documented regulations.
However, user may choose to generate a regulation
matrix representing potential RAs. The dimensions of the potential regulation
matrix can be controlled by specifying the number of occurrences of each
TF binding site in the promoter region of each given gene (i.e., at least one, two or three binding sites).
Two files are given as output. The first, a semicolon separated values (CSV) file,
contains the binary regulation matrix. Depending on the size of the
regulation matrix, the second file is either an image file depicting
the regulatory associations, or a .dot file, which can be used to generate the image using the software available here.
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