TRANSFAC products

Download of TRANSFAC data in flat files (.dat) without user interface (factor, matrix, site, gene, enhancer, cell, class, classification, reference, fragment)

Download of TRANSFAC data in JSON without user interface (factor, matrix, site, gene) e. g. for import into a PostgreSQL database

Download of TRANSCompel data in flat files (.dat) without user interface (compel, evidence)  

Download of TRANSPro data in flat files (.dat, .gtf) without user interface (promoters) 

See species list  

Command line tools (Java) for TF-binding site prediction (Match Library) in DNA sequences (FASTA)

   
Fully in-house integration into your analysis pipeline

Use of PWMs with compatible third-party tools or with your own tools

User-friendly interface (GUI)

API (Java, R, Jupyter notebook)

Partial data export via user interface or via API (excluding PWMs)

Prediction of enriched TFBSs in gene/promoter sets, in DNA sequence sets or in sets of genomic intervals

See species list 

Analysis of human genes for tissue-specific (Human Protein Atlas) and GO-specific transcription factors

Identification of regulatory DNA motifs affected by genomic variants 

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Automatic promoter extraction for TFBS prediction

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Whole genomes included at the backend allowing upload of genomic intervals

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(with option of upload of further genomes)

Visualization of predicted TF-binding sites together with other features in the included genome browser

See species list 

Tools and customizable workflows for omics data analysis

Inclusion of certain data from HumanPSD™ (Gene Ontology, tissue expression)