geneXplain products overview
TRANSFAC 2.0 with MATCH Suite
HumanPSD™ + TRANSPATH®
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.
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.
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:
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 cancer, neurodegenerative diseases, infectious diseases, diabetes and metabolic diseases. 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 5,174,855. 8,565 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.
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.
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