Release 2021.2 introducing TRANSFAC 2.0
Introducing TRANSFAC 2.0 and much more
The geneXplain team is proud to present release 2021.2 of the TRANSFAC®, TRANSPATH® and HumanPSD™ databases as well as release 6.4 of the geneXplain® platform and release 2.4 of Genome Enhancer! The new release introduces TRANSFAC® 2.0 – a fresh look on the gene regulation studies.
Please welcome TRANSFAC® 2.0
The TRANSFAC® database on transcription factors, their genomic binding sites and DNA-binding motifs (PWMs), in its 2021.2 release is introducing the TRANSFAC® 2.0 – a fresh look to the gold standard resource in the area of transcription regulation. TRANSFAC® 2.0 provides you with a range of new content as well as new software.
New tool – MATCH Suite
This software has been developed to identify transcription factors and their combinations that regulate the genes of your interest. MATCH Suite accepts human gene lists as input. It initializes a fully automatized sophisticated workflow that considers the biological context of the input data and returns a thoroughly selected list of most likely regulators of your gene set. The automatically generated results report is available as PDF file as well as interactive tables of the identified factors and their binding sites. On-the-fly filtering by different criteria as well as an in-built genome browser are a part of the interface. You are welcome explore the user guide here.
New enhancer reports
This is a new type of reports in TRANSFAC 2.0. 199,183 human enhancer sequences have been imported from FANTOM5 and the HACER database and lifted over to the GRCh38 genome assembly. The enhancer reports display regulated genes, tissues and cell types the enhancer is active in, and some other functional genomic regions that overlap with the enhancers.
Additional transcription factor interactions
3,888 new interactions between human transcription factors fromthe recently published BIOPLEX 3 data set and the human reference interactome (HuRI) have been included.
Integration of new human ChIP-Seq experiments from ENCODE
15 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 4 project have been integrated. The data sets comprise 197,893 fragments bound by 13 distinct transcription factors, of which 5 factors were not yet covered by ChIP-Seq data in TRANSFAC.
For more details please explore the TRANSFAC® 2021.2 new features and database statistics.
TRANSPATH® 2021.2 comes with the following new features:
BIOPLEX 1 and 3 interactome data imported
Integration of BIOPLEX human interaction data from release 1 and 3 resulted in 131,566 new and 60,151 reactions updated with additional experimental evidence.
Human Reference Protein Interactome (HuRI) integrated
45,468 new reactions were imported from the HuRI mapping project. In addition, 6,371 existing reactions were updated with experimental evidence from HuRI.
Additional increase in number of reactions
29,662 new binding reactions between proteins in human have been added.
Update of links to pathway databases
Links from genes/proteins to the pathway databases Reactome (version 77) and Wikipathways (20210610) have been updated.
For more details please explore the TRANSPATH® 2021.2 new features and database statistics.
HumanPSD™ 2021.2 comes with the following new features:
Biomarker and drug data update
The number of disease annotations increased to 358,353 and the number of unique gene/biomarker – disease assignments to 123,948. New FDA-approved drugs have been added and the number of drug-target protein associations is now 47,504.
For more details please explore the HumanPSD™ 2021.2 new features and database statistics.
The new 6.4 release of geneXplain® platform is available now!
Orthologous and paralogous extension:
Transfac ‘Matrix to Ensembl’ matching was extended by links from matrices to orthologous and paralogous Ensembl identifiers. These links are used in hub, which converts Matrices to Ensembl genes in Convert table analysis.
Support of hg19 build for genome variants analysis:
Detection of Genome variants and indels from RNA-seq data can now be processed for both hg19 and hg38 builds.
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2021.2.
New proteomics example with Gene Expression Omnibus data (GSE66789). Extended descriptions for other examples were added.
For more details, please explore the full new features list of geneXplain® platform release 6.4.
The new 2.4 release of Genome Enhancer is available now!
TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2021.2
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 2.4.