geneXplain platform news


  • New start page icons in any of the platform’s research categories
  • Pre-release of TRANSFAC®, TRANSPATH® and HumanPSD databases (version 2018.2)
  • Update to Ensembl 91 database
  • Update to Reactome 63 database


The geneXplain platform toolbox for bioinformatics data analysis contains these new functional features in the current release:


  • New analysis methods

Construct composite modules on track (correlation) – method predicts composite module using the result of the “Site search on gene set” analysis.

Cluster track – method clusters sites in a track, what is useful for merging of closely spaced sites into one big cluster.

Compute profile thresholds – method computes profile thresholds minimizing either false negatives(minFN) or false positive(minFP) on the random DNA sequence.

Create miRNA promoters – method extracts miRNA promoters from mirprom database for a given list of miRNAs

Get transcripts track – method extracts track from a database by a transcript ID

Recalculate composite module score on new track – method takes best composite model from the given CMA result and calculates its scores on all sites of a given track.

Continue CMA – method continues prediction of composite module using results of the previous prediction as a start point. Prediction parameters are customizable.

Table Imputation – method replaces missing data in the given input table with row means.


  • New HTML report for site search analysis

You can now create a summary of your site search analysis including visualization of input promoters together with identified enriched transcription factor binding sites (TFBSs) in HTML format, which can be exported to your local computer. These results can be easily used for presentations or publications.


  • New toolbar buttons

Check out our new toolbar icons which will lead you to remarkable results in your research simply by a couple of clicks.


  • Integration with updated TRANSFAC®, TRANSPATH® and HumanPSDTM databases in release 2018.1

The TRANSFAC® database of transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), TRANSPATH® database of mammalian signal transduction and metabolic pathways and Human Proteome Survey Database (HumanPSDTM) with focus on human proteins as disease biomarkers and drug targets in their 2018.1 release versions are currently integrated with the geneXplain platform.


Installation of TRANSFAC 2017.3 (information download)

– Annotation of transcription factor binding sites based on sequence conservation

ChIP-Seq experiment browse pages

– Reorganization of the in vivo transcription factor bound fragment section on a Locus Report

HOCOMOCO v10 matrix library integration

Enhanced human SNP content

Ensembl version update

Installation of TRANSPATH & HumanPSD 2017.3 (information download)

– Integration of new clinical trial (CT) data sources

– Improved user data management

– Quick search for disease and drug entries

– Link-out to BRENDA professional – the comprehensive enzyme information system

New phosphorylation targets content


New method: LRPath is a Gene Set Enrichment Analysis (GSEA) method that uses logistic regression models to discover categories that are significantly correlated with a predictor.

New protein category (TRANSPATH® isogroups) to enhance identification of master regulators.


Installation of TRANSFAC public:

– Available for everyone

– 219 profiles (matrices) for site search tools

– Search function implemented

DESeq tool:

– Bug fixed that prevented analysis from completing correctly

– Added option to run DESeq or DESeq2


– New versions of PROTEOMETM data now named HumanPSDTM database

– Latest release 2017.2 available in the geneXpain platform

– Platform Java API available from

– Executable jar can be configured with JSON config files to invoke platform processes from the command line