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Transcriptional regulatory module prediction software tools | Protein analysis

Transcription factors (TFs) combine with co-factors to form transcriptional regulatory modules (TRMs) that regulate gene expression programs with spatiotemporal specificity.Source text:(Diez et al., 2014) Systematic identification of transcriptional…
PAnDA
Web

PAnDA Protein And DNA Associations

Characterizes DNA associations with human transcription factors (TFs) using…

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…

rTRM
Desktop
Web

rTRM

Predicts transcriptional regulatory modules (TRMs) by integrating genomic…

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…

DACO
Desktop

DACO Domain-Aware Cohesiveness Optimization

Combines protein–protein interaction networks and domain–domain interaction…

Combines protein–protein interaction networks and domain–domain interaction networks with the cluster-quality metric cohesiveness. The metric is locally maximized on the holistic level of protein…

jaspscan
Desktop

jaspscan

Scans one or more DNA sequences for transcription factor binding sites from the…

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…

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