Release announcement

01

JASPAR 2024 matrix library integration

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.

02

New enhancer data

2,045 new human and mouse enhancers have been integrated together with 2,693 high confidence enhancer – promoter interactions (EPI).

03

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 variations compared to the previously used version 155.

04

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.

05

Rat genome assembly update

TRANSFAC now uses rat genome assembly mRatBN7.2.

06

Additional interactions between human transcription factors

1,299 new human transcription factor interactions have been included from recent publications.

07

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. Gene sets coming from Zebrafish, Arabidopsis, Nematoda, Fruit fly or Baker’s yeast can now be analyzed based on functional categorization. You can narrow the site search down by selected transcription factors, or select the functional categories of your interest and restrict the search to transcription factors belonging to those GO terms. As usual, a comprehensive report is generated automatically with a detailed description of the performed analysis steps, and the interactive results visualization mode allows you to fine-tune the obtained results by applying additional filters.

01

Increase in number of reactions

18,474 new binding reactions between proteins in human have been added from recent publications, e.g. from the chromosome 21 interactome.

01

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.

01

GO functional classification for model organisms

This release introduces the ability to launch Gene Ontology (GO) functional classification on Zebrafish, Arabidopsis, Nematoda, Fruit fly or Baker’s yeast gene lists, and to visualize the obtained results with a tree map diagram.

02

Databases update

TRANSFAC®, TRANSPATH® and HumanPSD™ databases are updated to release 2024.2, and the Ensembl datasets to release 112. Note that with the new release the analysis results might vary from the previous ones.

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)

01

Databases update

TRANSFAC®, TRANSPATH® and HumanPSD™ databases are updated to release 2024.2, and the Ensembl Human database to release 112 (hg38). Note that with the new release the analysis results might vary from the previous ones.

02

Demo reports update

New Genome Enhancer demo reports are available with this release.