Release announcement
The geneXplain team is proud to present the new release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2026.1, geneXplain® platform release 7.8, Pathway Omics Suite release 3.8, and Genome Enhancer release 3.8, all coming in respective TRANSFAC 2.0 packages.
TRANSFAC BASIC
(featuring TRANSFAC® 2.0 2026.1 and geneXplain® platform 7.8)
TRANSFAC® release 2026.1
Transcription factors · binding sites · PWMs
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), in its new release 2026.1 contains these new features:
01
1,346 new CAP-SELEX- and HT-SELEX-derived PWMs
1,334 represent binding specificities of human transcription factor heterodimer complexes, covering combinations across 19 different TFClass classes. A new MATCH™ profile set, factor_pairs_capselex, makes them searchable in the geneXplain® platform.
02
517 new transcription-factor interactions from recent publications.
geneXplain® platform release 7.8
Bioinformatics analysis platform
The geneXplain® platform in its new release 7.8 contains these new features:
01
New method: “Construct Composite Modules on Track — Weighted Correlation”
A regulatory analysis method that finds composite modules of co-occurring TF binding sites associated with a continuous experimental signal:
Promoter track, where each promoter carries a continuous experimental value (e.g. logFC) and an optional reliability value (e.g. a p-value). Unlike the standard Composite Module Analyst [Waleev et al. 2006], it needs no foreground-vs-background sets.
WorkflowEach promoter gets a composite score for co-occurring TF binding sites whose collective strength correlates with the signal (weighted rank correlation, robust to outliers). Candidate composite models are optimized with a genetic algorithm; model fitness = correlation strength − complexity penalty + an optional bonus for known TF–TF interactions.
OutputA promoter level table ranked by composite model score; genome browser links; per promoter TF binding site models; a graphical model representation; a scatter plot (signal vs composite score); model statistics; and a JSON representation for programmatic reuse. Ships with a glioblastoma RNA-seq demo project (GSE59612).
02
Minfi (Bioconductor) method for IDAT processing
Process raw Illumina Infinium DNA methylation array (IDAT) files in the platform (supports Infinium HumanMethylation450 (450K, hg19), MethylationEPIC v1 (hg19), MethylationEPIC v2 (hg38) arrays). Computes Beta and M values and identifies DMPs and DMRs.
TRANSFAC PATHWAYS
(featuring TRANSFAC® 2.0 2026.1, TRANSPATH® 2026.1, Pathway Omics Suite 3.8, and the geneXplain® platform 7.8)
TRANSPATH® release 2026.1
Signal transduction · pathways · reactions
The TRANSPATH® database of mammalian signal transduction and metabolic pathways in its new release 2026.1 contains these new features:
01
Increase in reactions and pathways
13,942 new reactions and 36 new pathways added from over 7,250 recent publications.
02
Protein genome map update
Now contains 222,999 posttranslational modifications (PTMs) for 18 different modification types in 970 Drosophila, 22141 human, 5069 mouse, and 33 rat protein isoforms from TRANSPATH® and BioGRID, as well as their genomic locations in assemblies BDGP6.54, GRCh38, GRCm39 and GRCr8.
These PTM data are drawn from TRANSPATH® and BioGRID (Stark et al. 2006; Oughtred et al. 2021). The BioGRID attribution must travel with this figure wherever it is used.
03
Pathway Omics Suite 3.8
The Pathway Omics Suite has been updated to version 3.8 featuring new advanced expert settings and support of raw IDAT files processing.
TRANSFAC DISEASES
(featuring TRANSFAC® 2.0 2026.1, TRANSPATH® 2026.1, HumanPSD™ 2026.1, the geneXplain® platform 7.8 and Genome Enhancer 3.8)
HumanPSD™ release 2026.1
Genes · diseases · drugs · biomarkers
The HumanPSD™ database of gene-disease-drug-clinical trials assignments in its new release 2026.1 contains these new features:
01
Biomarker and drug data update
Disease annotations increased to 443,444; unique gene/biomarker-disease assignments increased to 142,640.
02
Disease vicinity update
Disease similarity maps re-inferred from updated HumanPSD™ curation. The disease network and heatmap visualisations now offer interactive access to disease/gene reports and downloadable causal biomarker subsets
Genome Enhancer release 3.8
Automated multi-omics analysis · master regulators · drug targets · compounds
The Genome Enhancer tool in its new release 3.8 contains these new features:
01
IDAT DNA methylation files processing
Support of raw IDAT files from Illumina BeadChip methylation arrays (450K, hg19; EPIC v1, hg19; EPIC v2, hg38).
02
New expert settings
An extended set of user-configurable parameters across preprocessing, differential expression, and regulatory network reconstruction.
03
Updated and new demo reports
All demo reports updated for databases release 2026.1, including a new demo report showcasing analysis of host response to bacteria stimulus (staphylococcus aureus 6 h exposure, PMID 37277347).
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