微信公眾號: geneXplain

The geneXplain team is proud to present release 2023.1 of the?TRANSFAC?,?TRANSPATH??and?HumanPSD??databases as well as?release 7.2 of the?geneXplain? platform?and release 3.2 of?Genome Enhancer.

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.

For more details please explore the TRANSFAC? 2023.1?new features (https://genexplain.com/wp-content/uploads/2023/07/Release_news_TRANSFAC.pdf) and database statistics (https://genexplain.com/wp-content/uploads/2023/07/TRANSFAC_stats.pdf).

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.

For more details please explore the HumanPSD? 2023.1?new features (https://genexplain.com/wp-content/uploads/2023/07/Release_news_HumanPSD_TRANSPATH.pdf) and?database statistics (https://genexplain.com/wp-content/uploads/2023/07/HumanPSD_TRANSPATH_stats.pdf).

The new 7.2 release of geneXplain? platform is available now!

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):

• Combinatorial regulation analysis of genomic or custom sequences

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.

• MEALR combinatorial regulation analysis

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.

• Extract TRANSFAC(R) PWMs from combinatorial regulation analysis

This tool extracts TRANSFAC? PWMs from a result table generated by the?MEALR combinatorial regulation analysis.??

New import possibility:

The files from the?Sequence Read Archive (SRA)?can be now uploaded to the geneXplain platform directly by the SRR ID.

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. (https://genexplain.com/wp-content/uploads/2023/07/geneXplain-platform-release-7.2.pdf)

The new 3.2 release of Genome Enhancer is available now!

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. (https://genexplain.com/genome-enhancer/#section5)

For more details, please explore the?full new features list?of?Genome Enhancer release 3.2. (https://genexplain.com/wp-content/uploads/2023/07/Genome-Enhancer-release-3.2.pdf)