Release 2023.2
Release announcement
The geneXplain team is proud to present the new release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2023.2, geneXplain® platform release 7.3 and Genome Enhancer release 3.3.
TRANSFAC® 2.0 2023.2 comes with the following new features:
Integration of new human ChIP-Seq experiments from ENCODE
91 new human ChIP-Seq experiments released by the ENCODE phase 4 project have been integrated. The data sets comprise 1,029,262 fragments bound by 85 distinct transcription factors, of which 33 factors were not yet covered by ChIP-Seq data in TRANSFAC.
New matrices derived from ENCODE ChIP-Seq data
24 new positional weight matrices for yet uncovered human transcription factors have been generated from new ENCODE phase 4 ChIP-Seq data and integrated into the TRANSFAC matrix library.
For more details please explore the TRANSFAC® 2023.2 new features and database statistics.
TRANSPATH® 2023.2 comes with the following new features:
Increase in number of reactions
34,829 new protein-protein interactions from recent publications have been added. In addition, 7,531 phosphorylation reactions by human receptor tyrosine kinases (RTK) were included. This addition makes the total number of reactions in TRANSPATH over 1,186,000.
Update of links to Wikipathways and Reactome
Links from genes/proteins to the pathway databases Wikipathways (
For more details please explore the TRANSPATH® 2023.2 new features and database statistics.
HumanPSD™ 2023.2 comes with the following new features:
Biomarker and drug target data update
The number of disease annotations increased to 397,877 and the number of unique gene/biomarker – disease assignments to 133,533.
378 drugs and 2,392 protein targets were added.
For more details please explore the HumanPSD™ 2023.2 new features and database statistics.
geneXplain® platform 7.3 release comes with the following new features:
Gene regulatory networks construction via API
New Jupyter notebook Python sample code that allows construction of gene regulatory networks using the geneXplain platform API was added to the platform API description. You can view the code in Colab here and observe demo visualizations at the full new features list.
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2023.2.
For more details, please explore the full new features list of geneXplain® platform release 7.3.
Genome Enhancer 3.3 release comes with the following new features:
New Expert settings
The new Expert settings available at the analysis launch step of the wizard now also include the filter for the number of read counts per gene in at least one sample.
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2023.2.
Demo reports update
The new Genome Enhancer demo reports can be found here.
For more details, please explore the full new features list of Genome Enhancer release 3.3.
