TRANSFAC BASIC
(featuring TRANSFAC® 2.0 2025.1 and geneXplain® platform 7.6)
TRANSFAC® release 2025.1
Transcription factors · binding sites · PWMs
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), in its new release 2025.1 contains this new feature:
01
Additional interactions between transcription factors
1,900 new transcription factor interactions have been included from recent publications, covering various transcription factors, including members of the Interferon Regulatory Factor (IRF) family.
geneXplain® platform release 7.6
Bioinformatics analysis platform
The geneXplain® platform tool in its new release 7.6 contains this new feature:
01
New method: “Find DEGs in single cell data”
This release introduces the ability to process single cell RNA-seq data (scRNA-seq) and identify differentially expressed genes (DEGs). The tool compares experimental conditions using robust pseudobulk analysis and Wilcoxon test methods to detect DEGs across different cell types. It lives under Analyses → Galaxy → Single cell RNA-seq to DEGs → Find DEGs in single cell data.
A metadata file and a folder with single-cell count data, uploaded as generic files. Two formats are accepted: 10X Genomics MTX, or CSV (a matrix with genes as rows and cells as columns, or vice versa; the first row/column must contain identifiers). Thresholds for up- and down-regulated genes are given as floating point numbers. The metadata CSV must carry sample identifiers and an experimental group column valued ‘control’ or ‘experiment’; a cell_type column is optional. A pre-trained CellTypist model is required only when the metadata lacks that column.
WorkflowData loading (MTX or CSV plus metadata); data preparation, where a quality control pipeline filters low-quality genes and cells, calculates QC metrics (mitochondrial and ribosomal percentages), performs doublet detection with Scrublet, normalizes counts and log-transforms the data; optional cell typing via CellTypist; pseudobulk aggregation per sample and cell type; and differential expression, using PyDESeq2 on the pseudobulk profiles, falling back to Scanpy’s rank_genes_groups (Wilcoxon test) on the original single-cell data when PyDESeq2 fails on low sample counts.
OutputA single folder, delivered as a zip. Inside it, one CSV per cell type, named for the cell type and the method used (e.g. T_cells_pseudobulk.csv or B_cells_rank_groups.csv), plus a filtered CSV and a report.csv listing the cell types found, the number of cells of each, and which analysis was applied. Each CSV holds gene names, log2 fold changes, p-values and adjusted p-values.
TRANSFAC PATHWAYS
(featuring TRANSFAC® 2.0 2025.1, TRANSPATH® 2025.1 and the geneXplain® platform 7.6)
TRANSPATH® release 2025.1
Signal transduction · pathways · reactions
The TRANSPATH® database of mammalian signal transduction and metabolic pathways in its new release 2025.1 contains these new features:
01
Pathways integration
98 human pathways have been integrated and converted to the TRANSPATH data model. Subsequent reactions can be viewed in dedicated pathway reports, and the Pathfinder tool visualizes whole pathways with options for editing and network expansion.
02
Increase in number of reactions
4,055 new binding reactions between proteins have been added from recent publications.
TRANSFAC DISEASES
(featuring TRANSFAC® 2.0 2025.1, TRANSPATH® 2025.1, HumanPSD™ 2025.1, the geneXplain® platform 7.6 and Genome Enhancer 3.6)
HumanPSD™ release 2025.1
Genes · diseases · drugs · biomarkers
The HumanPSD™ database of gene-disease-drug-clinical trials assignments in its new release 2025.1 contains this new feature:
01
Biomarker and drug data update
The number of disease annotations increased to 418,227 and the number of unique gene/biomarker – disease assignments to 137,717. Newly FDA-approved drugs (Jan 2025 – May 2025), their indication, and their protein target information were added.
Genome Enhancer release 3.6
Automated multi-omics analysis · master regulators · drug targets · compounds
The Genome Enhancer tool in its new release 3.6 contains these new features:
01
Database updates
TRANSFAC®, TRANSPATH® and HumanPSD™ databases used in the Genome Enhancer analysis were updated to release 2025.1. Note that with the new release the analysis results might vary from the previous ones.
02
Updated demo reports
All demo reports of the Genome Enhancer pipeline were updated to the analysis results provided by Genome Enhancer release 3.6. All demo reports can be freely accessed upon login to the Genome Enhancer tool.
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