Products overview

geneXplain products overview


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TRANSFAC 2.0 with MATCH Suite
TRANSFAC download
geneXplain® platform
Genome Enhancer
Recommended TRANSFAC 2.0 packages

Check out the collection of videos demonstrating the functionality of our tools.


TRANSFAC 2.0 including the MATCH Suite tool

This bundle will provide you with the best-in-class tools and knowledge library for gene regulation studies


TRANSFAC® is the database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Its library of positional weight matrices (PWM library) is a unique collection of DNA-binding models, suitable for a comprehensive analysis of genomic sequences for potential transcription factor binding sites (TFBS).

MATCH Suite is the toolbox of TRANSFAC 2.0, which allows identification of the transcription factors regulating an input gene set. MATCH Suite works with a list of human genes to identify regulation of their promoters applying integrated FMATCH and CMA analyses. A comprehensive report is generated automatically.


TRANSFAC download


The TRANSFAC® flat file download (including the databases TRANSCompel® and TANSProTM) contains eukaryotic transcription factors (and miRNAs), their experimentally determined genomic binding sites and consensus DNA-binding motifs (PWMs), as well as data on combinatorial gene regulation and factor-factor interaction. Promoters, enhancers and silencers annotated with transcription  factor  ChIP-Seq,  DNase hyper-sensitivity and histone methylated intervals from the ENCODE project and from other sources complement the manually curated binding site data.


TRANSFAC download structure

Based on the positional weight matrices (PWMs) transcription factor binding sites can be predicted in regulatory regions. In the TRANSFAC® flat file download, the tools of the MatchTM Library can be used on command line or the PWMs can be used with tools of the user.

TRANSFAC download archives



HumanPSD™ + TRANSPATH® databases


The Human Proteome Survey Database (HumanPSD) provides gene-disease-drug-clinical trial associations. The links between human proteins and diseases reflect their potential use as biomarkers. Disease similarity maps by common biomarkers are included. 



TRANSPATH® is a database of mammalian signal transduction and metabolic pathways.

With TRANSPATH® you can quickly access information about signal transduction and metabolic pathway components and their reactions, predict potential pathways targeting the genes of your interest and build customized regulatory and metabolic networks.




geneXplain® platform with TRANSFAC®, TRANSPATH® and HumanPSD™ databases connected


When connected with the TRANSFAC®, TRANSPATH® and HumanPSD™ databases, the geneXplain® platform provides its users with the ability to run Upstream Analysis – integrated promoter and pathway analysis, which allows you to study the molecular mechanisms of the studied biological processes. In its basis concept, the upstream analysis comprises of two steps:

1)Promoter analysis: search for TFBS and their combinations in promoter regions of DEGs with the use of TRANSFAC®.
2)Network analysis: Search for Master Regulators upstream of TFs identified in the previous step. The master regulator search is based on the TRANSPATH® reactions and pathways.



Genome Enhancer


Genome Enhancer (GE) is a pipeline for multi-omics data analysis in medical research. GE performs automatized identification of prospective drug targets and treatments based on the Upstream analysis approach. Proven applications of Genome Enhancer include cancerneurodegenerative diseasesinfectious diseasesdiabetes and metabolic diseaseshypertension. GE is using TRANSFAC®, TRANSPATH® and HumanPSD™ databases for the performed analysis. 





BRENDA is the most comprehensive information repository on enzymes and enzyme ligand data. Data on enzyme function are extracted manually from primary literature, and are complemented by text and data mining, data integration, and prediction algorithms. All enzymes in BRENDA are classified according to the biochemical reaction catalyzed, and are assigned to the corresponding Enzyme Commission (EC) numbers. Reaction kinetics are described in detail. 







PASS software predicts the activity profile of the given drug-like substance based on its structural formula. PASS SAR Base is based on the information about structure-activity relationships of 1,614,066 substances; the total number of experimentally determined pairwise structure-activity records is 5,174,8558,565 biological activities can be predicted with average accuracy about 0.93; by default, 1,957 activities are predicted with average accuracy 0.97.






GUSAR is a tool to create models on quantitative structure-activity relationships. The acronym stands for “General Unrestricted Structure-Activity Relationships”. The input of the program is your training set of chemical structures and quantitative data on biological activities. The output is a reliable quantitative SAR/SPR (Structure Activity and Property Relationship) model.


GUSAR intro video





PharmaExpert analyzes the relationships between biological activities, drug-drug interactions and multiple targeting of chemical compounds and selects compounds that have a pre-defined biological activity. Its knowledgebase contains over 15 thousand of known interactions between biological activities, as well as the relationships between proteins, signalling/regulatory pathways (KEGG or Reactome), Gene Ontology biological processes and therapeutic and adverse effects.



PharmaExpert interface

PharmaExpert knowledgebase



All our customers enjoy the following advantages or our products:

–       Technical and scientific support or your research: rapid answers to your questions from our professional support team will be always provided

–       Secure cloud space connected with online licenses that can be accessed from any location

–       Extensive manuals, documentation, examples, and tutorials available for all our products

–       Frequent releases and updates of our databases contents and software functionality

–       Ability to request personal training sessions

–       All our servers are running on CO2-neutral water or wind power


Got any questions? We will be glad to help. Just send your request to and we will come back to you shortly.

Thank you very much for your interest in our tools.