Release announcement

The geneXplain team is proud to present the new release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2025.1, geneXplain® platform release 7.6 and Genome Enhancer release 3.6, all coming in respective TRANSFAC 2.0 packages.

TRANSFAC BASIC

(featuring TRANSFAC® 2.0 2025.1 and geneXplain® platform 7.6)

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:

• 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.

For more details please explore the TRANSFAC® 2025.1 new features and database statistics.

The geneXplain® platform tool in its new release 7.6 contains this new feature:

New method: 

This release of the geneXplain platform introduces ability to process single cell RNA-seq data (scRNA-seq) and identify the differentially expressed genes (DEGs) using the newly developed method “Find DEGs in single cell data”. 

You will find the new method for DEGs identification from scRNA-seq under the:

Analyses → Galaxy → Single cell RNA-seq to DEGs → Find DEGs in single cell data

This new tool identifies differentially expressed genes in single-cell RNA-seq data by comparing experimental conditions. It uses robust pseudobulk analysis and Wilcoxon test methods to accurately detect DEGs across different cell types, ensuring reliable biological insights.

Input:

As input for this method a metadata file and a folder with single-cell count data should be provided. A cell-typing model is mandatory if cell types are not provided in the metadata file. All files should be uploaded as generic files.

The tool accepts two formats of single-cell RNA Sequencing Data:

  • 10X Genomics MTX Format
  • CSV Format (a matrix with genes as rows and cells as columns, or vice-versa; the first row/column must contain identifiers)

Thresholds for up/down regulated genes should be provided as a floating pointer number which is used for filtering up and down regulated genes

Sample metadata should be provided in the format of a CSV file. The obligatory columns include:

– Sample identifiers
– An experimental group column with the values ‘control’ or ‘experiment’
– An optional cell_type column for annotations.

Model for Cell-Typing is a required input only if the metadata file lacks a cell_type column. A pre-trained CellTypist model can be selected to automatically annotate cell types.

Workflow:

The tool follows a sequential workflow from data loading to analysis.

  • Data Loading: Reads the input single-cell data (MTX or CSV) and metadata file.
  • Data Preparation: A quality control pipeline filters low-quality genes and cells, calculates QC metrics (mitochondrial/ribosomal percentages), performs doublet detection with Scrublet, normalizes counts, and log-transforms the data.
  • Cell Typing (Optional): If the cell_type column is missing, the tool uses the selected CellTypist model to predict cell types.
  • Pseudobulk Aggregation: Gene counts are aggregated for all cells belonging to the same sample and cell type, creating pseudobulk profiles.
  • Differential Expression: For each cell type, the tool performs DEG analysis.
  • Primary Method: Uses PyDESeq2 on pseudobulk profiles to compare ‘experiment’ vs ‘control’.
  • Fallback Method: If PyDESeq2 fails (e.g., due to low sample counts), it defaults to Scanpy’s rank_genes_groups (Wilcoxon test) on the original single-cell data.
  • Output Generation: The final DEG results are saved into separate CSV files for each cell type. The tool also generates a filtered csv file and a report.csv file which contains found cell types, number of cells corresponding to each type, and the type of analysis which was used.

Output:

The tool returns a single folder containing the analysis results.

Inside the zip file there is one CSV file per cell type. The filenames indicate the cell type and the analysis method used (e.g., T_cells_pseudobulk.csv or B_cells_rank_groups.csv). The tool also generates a filtered csv file and a report.csv file which contains found cell types, number of cells corresponding to each type, and the type of analysis which was used.

Each CSV file includes:

  • Gene names
  • Log2 fold changes
  • P-values
  • Adjusted p-values

For more details, explore the full new features list of geneXplain® platform release 7.6.

TRANSFAC PATHWAYS

(featuring TRANSFAC® 2.0 2025.1, TRANSPATH® 2025.1 and the geneXplain® platform 7.6)

The TRANSPATH® database of mammalian signal transduction and metabolic pathways in its new release 2025.1 contains these new features:

• 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 e.g. editing and network expansion.

• Increase in number of reactions

4,055 new binding reactions from recent publications between proteins have been added.

For more details please explore the TRANSPATH® 2025.1 new features and database statistics.

TRANSFAC DISEASES

(featuring TRANSFAC® 2.0 2025.1, TRANSPATH® 2025.1, HumanPSD™ 2025.1, the geneXplain® platform 7.6 and Genome Enhancer 3.6)

The HumanPSD™ database of gene-disease-drug-clinical trials assignments in its new release 2025.1 contains these new features:

• 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.

For more details please explore the HumanPSD™ 2025.1 new features and database statistics.

The Genome Enhancer tool in its new release 3.6 contains these new features:

• Database updates

TRANSFAC®, TRANSPATH® and HumanPSD™ databases used in the Genome Enhancer analysis were updated to the release 2025.1. 
Please note that with the new release the analysis results might vary from the previous ones.

• Updated demo reports

All demo reports of 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. 

For more details please explore the full new features list of Genome Enhancer release 3.6.

The customers of PROTEOME™ integrated database (HumanPSD™+TRANSPATH®) can refer to the full release 2025.1 features and statistics documents for the release details.