Release 2024.2
Release announcement
The geneXplain team is proud to present the new release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2024.2, geneXplain® platform release 7.5 and Genome Enhancer release 3.5.
TRANSFAC® 2.0 2024.2 comes with the following new features:
New position frequency matrices from the JASPAR 2024 release either added as matrix entries (446 cases) or hyperlinked to existing counterparts in the TRANSFAC matrix library.
· New enhancer data
2,045 new human and mouse enhancers have been integrated together with 2,693 high confidence enhancer – promoter interactions (EPI).
· Enhanced human SNP content
The 2023 dbSNP release 156 data for human has been integrated and increases the number of SNPs mapped to promoter, enhancer, and silencer sequences by more than 13,800,000 new single nucleotide variatons compared to the previously used version 155.
· Ensembl version update
Genomic information for genes, promoters, and ChIP fragments for the species human, mouse, rat, pig, macaque, Drosophila, and Arabidopsis is now based on Ensembl release 112.
· Rat genome assembly update
TRANSFAC now uses rat genome assembly mRatBN7.2.
· Additional interactions between human transcription factors
1,299 new human transcription factor interactions have been included from recent publications.
· MATCH Suite update
In its new 3.1 release, the MATCH Suite toolbox of TRANSFAC 2.0 was updated with the functionality of extended model organisms’ gene regulation analysis. Now, gene sets coming from Zebrafish, Arabidopsis, Nematoda, Fruit fly or Baker’s yeast can be analyzed based on functional categorization. You can narrow down the site search by selected transcription factors, or you can select the functional categories of your interest and restrict search for transcription factors belonging to those GO terms. As usual, a comprehensive report will be automatically generated with detailed description of the performed analysis steps, and the interactive results visualization mode will allow you to fine-tune the obtained results by applying additional filters.
For more details please explore the TRANSFAC® 2024.2 new features and database statistics.
TRANSPATH® 2024.2 comes with the following new features:
Increase in number of reactions
18,474 new binding reactions from recent publications between proteins in human have been added, e.g. from the chromosome 21 interactome.
For more details please explore the TRANSPATH® 2024.2 new features and database statistics.
HumanPSD™ 2024.2 comes with the following new features:
Biomarker and drug target data update
The number of disease annotations increased to 414,870 and the number of unique gene/biomarker – disease assignments to 137,060.
Newly FDA-approved drugs (Apr 2024 – Aug 2024), their indication, and their protein target information were added.
For more details please explore the HumanPSD™ 2024.2 new features and database statistics.
geneXplain® platform 7.5 release comes with the following new features:
GO functional classification for model organisms
This release of the geneXplain platform introduces ability to launch Gene Ontology (GO) functional classification on Zebrafish, Arabidopsis, Nematoda, Fruit fly or Baker’s yeast gene lists and to further visualize the obtained results with a tree map diagram.
You will find the functional classification tool under the:
Analyses –> Methods –> Functional classification:
– Functional classification – for performing the GO-based classification of the studied gene set
– TreeMap on Functional classification – for visualizing the results of functional classification in a form of a colorful tree map
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases are updated to release 2024.2.
Ensembl datasses update to the following versions:
- Ensembl Human 112 (hg38)
- Ensembl Mouse 112 (mm10)
- Ensembl Rat 112 (mRatBN7.2)
- Ensembl Zebrafish 112 (GRCz11)
- Ensembl Nematoda 112 (wbcel235)
- Ensembl Fruit fly 112 (dm6)
- Ensembl Saccharomyces Cerevisiae 112 (sacCer3)
- Ensembl Schizosaccharomyces Pombe 112 (ASM294v2)
- Ensembl Arabidopsis Thaliana 112 (TAIR10)
Please note that with the new release the analysis results might vary from the previous ones.
For more details, explore the full new features list of
Genome Enhancer 3.5 release comes with the following new features:
Databases update
TRANSFAC®, TRANSPATH® and HumanPSD™ databases are updated to release 2024.2.
Enseml Human database was updated to the release 112 (hg38).
Please note that with the new release the analysis results might vary from the previous ones.
Demo reports update
The new Genome Enhancer demo reports can be found here.
For more details, explore the full new features list of
Licensing info
Interested in licensing our products? Find out the prices for the products of your interest here.
