Release 2021.3

 

Release announcement

 

The geneXplain team is proud to present release 2021.3 of the TRANSFAC®, TRANSPATH® and HumanPSD™ databases as well as release 6.5 of the geneXplain® platform and release 2.5 of Genome Enhancer.

 

TRANSFAC® 2.0 2021.3 comes with the following new features:

Tissue-specific gene lists in MATCH Suite

MATCH Suite now supports new input gene list selection option: construct the input gene list from scratch based on the genes that are highly and specifically expressed in the selected tissue. Just pick the tissue of your interest and make the selection of genes that will be submitted to the gene regulation analysis using a nice graphical expression & specificity-based gene selection tool. This feature requires an active HumanPSD™ subscription.

New silencer data

31,933 human and mouse silencer sequences have been imported from the SilencerDB database and lifted over to the GRCh38 and GRCm39 genome assemblies. Silencer reports display genes with which promoters the silencer interacts, tissues and cell types/lines the silencer is active in, and genomic regions such as histone modification sequences, DNase I hypersensitivity sites, and transcription factor binding sites that overlap with the silencer.

Integration of new human ChIP-Seq experiments from ENCODE

83 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 4 project have been integrated providing 588,473 fragments bound by 79 distinct transcription factors, of which 51 factors were not yet covered by ChIP-Seq data in TRANSFAC.

Enhanced human SNP content

The 2021 dbSNP release 155 data for human has been integrated and increases the number of SNPs mapped to promoter, enhancer, and silencer sequences by more than 72,000,000 new single nucleotide variations compared to the previously used version 154.

Mouse genome assembly update

TRANSFAC® now uses the latest mouse genome assembly GRCm39 (mm39).

For more details please explore the TRANSFAC® 2021.3 new features and database statistics.

 

TRANSPATH® 2021.3 comes with the following new features:

Increase in number of reactions

24,118 new binding reactions from recent publications between proteins in human have been added.

Update of links to Wikipathways

Links from genes/proteins to the pathway database Wikipathways have been updated.

For more details please explore the TRANSPATH® 2021.3 new features and database statistics.

 

HumanPSD™ 2021.3 comes with the following new features:

Biomarker and drug target data update

The number of disease annotations increased to 363,661 and the number of unique gene/biomarker – disease assignments to 125,437. Targets for FDA – approved drugs have been added by manual curation and the number of drug – target protein associations is now 48,465.

For more details please explore the HumanPSD™ 2021.3 new features and database statistics.

 

geneXplain® platform 6.5 release comes with the following new features:

Tissue-specific gene list construction workflows

Construct a tissue-specific gene list from scratch using the new workflow that supports 61 tissues with associated gene expression data from Human Protein Atlas. A variation of this workflow allows to also specify one of the 14 supported protein functions while constructing the gene list.

Mouse genome assembly update

GeneXplain platform now supports the latest mouse genome assembly GRCm39 (mm39). Find an example here.

Databases update

TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2021.3.

API update

Platform APIs (genexplain-api and geneXplainR) were updated to provide all method parameters including expert options. JSON templates cover all platform as well as the integrated Galaxy tools of edition 6.5.

For more details, please explore the full new features list of geneXplain® platform release 6.5.

 

Genome Enhance 2.5 release comes with the following new features:

Databases update:

TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2021.3.

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 2.5.

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