Products overview

geneXplain products overview

 

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TRANSFAC 2.0 with MATCH Suite
HumanPSD™ + TRANSPATH®
geneXplain® platform
Genome Enhancer
Recommended TRANSFAC 2.0 packages
BRENDA
PASS
GUSAR
PharmaExpert

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.

 

 

 

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 diseases. GE is using TRANSFAC®, TRANSPATH® and HumanPSD™ databases for the performed analysis. 

 

 

BRENDA

 

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

 

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

 

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

 

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

 

 

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

Thank you very much for your interest in our tools.

 

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