CreateNetwork

Background

Analysis using TOBIAS BINDetect provides a prediction of bound transcription factors. Due to the possibility of annotating TFBS, we can use the combined pool of binding sites to unravel transcription factor binding networks. The concept of TF-TF binding networks is illustrated here:

TOBIAS CreateNetwork is a tool taking annotated transcription factors and gene-TF pairs to identify TF-binding cascades.

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Example command

$ TOBIAS CreateNetwork --TFBS test_data/annotated_tfbs/* --origin test_data/motif2gene_mapping.txt 

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Input parameters

• --TFBS
  A list of .bed-files containing annotated TFBS sites, e.g. output from TOBIAS BINDetect. "Annotated" means that there should be a column in each .bed-file specifying the target gene. By using TOBIAS BINDetect with --peaks containing annotation information, this information is automatically brought into the output files. The columns to use will be automatically estimated based on the content of --origin.

• --origin
  This is a file containing information of the origin gene for each TF. By "origin", what is meant is the gene from which the transcription factor is coded. The example-file 'motif2gene_mapping.txt' within the test data gives a good impression of how such a file should look.