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PAnDA / Protein And DNA Associations

Characterizes DNA associations with human transcription factors (TFs) using expression profiles, protein-protein interactions and recognition motifs. PAnDA predicts TF binding events with >0.80 accuracy revealing cell-specific regulatory patterns that can be exploited for future investigations. Even when the precise DNA-binding motifs of a specific TF are not available, the information derived from protein-protein networks is sufficient to perform high-confidence predictions (area under the ROC curve of 0.89).

rTRM

Predicts transcriptional regulatory modules (TRMs) by integrating genomic information from transcription factor (TF) ChIP-seq data, cell type-specific gene expression and protein-protein interaction data. A set of genomic sites identified for a specific TF by ChIP-seq is scanned for the presence of over-represented motifs, to which putative TFs are assigned by sequence similarity. Cell type-specific expression data is used to filter out candidate TFs, and in a final step only those candidates that have been reported to make interactions in the BioGRID database are retained.

jaspscan

Scans one or more DNA sequences for transcription factor binding sites from the JASPAR database. jaspscan is an Emboss package. Matches are searched for using fast sequence word-matching, optionally allowing mismatches. An output file is written with information on the matches, including sequence ID and accession number, the start and end positions of the match in an input sequence and the sequence of the region where a match has been found. Binding factor information, where available, is given at the end of the matches for each matching entry.