Release 2023.1
Release announcement
The geneXplain team is proud to present the new release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2023.1, geneXplain® platform release 7.2 and Genome Enhancer release 3.2.
TRANSFAC® 2.0 2023.1 comes with the following new features:
JASPAR 2022 matrix library integration
New position frequency matrices from the JASPAR 2022 release either added as matrix entries (375 cases) or hyperlinked to existing counterparts in the TRANSFAC matrix library.
Additional interactions between human transcription factors
13,100 new human transcription factor interactions have been included from BIOGRID.
Integration of new human ChIP-Seq experiments from ENCODE
162 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 4 project have been integrated. The data sets comprise 1,700,273 fragments bound by 143 distinct transcription factors, of which 39 factors were not yet covered by ChIP-Seq data in TRANSFAC.
New matrices derived from ENCODE ChIP-Seq data
12 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.
Recommended TRANSFAC 2.0 Online packages
The TRANSFAC 2.0 can come in a number of online packages, each briefly summarized by its functionality.
Select the TRANSFAC 2.0 package that fits your research needs best and immediately receive the respective price info.
For more details please explore the TRANSFAC® 2023.1 new features and database statistics.
TRANSPATH® 2023.1 comes with the following new features:
Increase in number of reactions
46,322 new binding reactions from recent publications between proteins in human have been added, amongst others from the kinase network. This addition makes the total number of reactions in TRANSPATH over 1,130,000.
Update of links to Wikipathways and Reactome
Links from genes/proteins to the pathway databases Wikipathways (20230310) and Reactome (v83) have been updated.
For more details please explore the TRANSPATH® 2023.1 new features and database statistics.
HumanPSD™ 2023.1 comes with the following new features:
Biomarker and drug target data update
The number of disease annotations increased to 390,340 and the number of unique gene/biomarker – disease assignments to 132,237.
22 recently FDA approved drugs and their protein targets were added.
More recursive search options
“Search within” option for gene expression regulator data has been enhanced.
Better performance
Server hardware update allows for faster report loading times.
For more details please explore the HumanPSD™ 2023.1 new features and database statistics.
geneXplain® platform 7.2 release comes with the following new features:
New methods and workflows:
This release of the geneXplain platform introduces a new section of the start page called “Combinatorial regulation”, which provides tools for analysis of combinations of TF binding sites in promoters, enhancers and silencers, and other regulatory genomic regions. In this section, in addition to our traditional Composite Module Analyst, we introduce a completely new branch of site search combinatorial analysis methods based on the sparse logistic regression (MEALR):
This workflow scans input sequences for tissue and cell type- specific transcription factor binding regions using the newly created library of MEALR models delivered with the TRANSFAC® database.
This method applies combinatorial regulatory models based on the MEALR affinity score to classify or scan sequences for occurrences of combinations of transcription factor binding sites represented by TRANSFAC® PWMs.
New import possibility:
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2023.1.
For more details, please explore the full new features list of geneXplain® platform release 7.2.
Genome Enhance 3.2 release comes with the following new features:
New Expert settings
The new Expert settings button is now available in the analysis launch interface of Genome Enhancer. It allows selection of logFC and p-value cutoffs that will be applied for selection of genes for further promoter analysis.
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2023.1.
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 3.2.
Videos demonstrating our products and analysis approaches
We have united a number of biomedical data analysis masterclass videos and how-to guidances on the use of our products in the video gallery. Explore the functionality of our tools and follow the analysis steps introduced by our experts for achieving the best results in your research.
