Release 2022.2

Release announcement

 

The geneXplain team is proud to present the new major release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2022.2, geneXplain® platform release 7.1 and Genome Enhancer release 3.1.

 

TRANSFAC® 2.0 2022.2 comes with the following new features:

Increase in enhancer – target genes relations

57,038 additional enhancer – target gene relations have been imported from the FOCS web site.

Additional interactions between human transcription factors

7,949 human transcription factor interactions have been included from a recent publication.

Integration of new human ChIP-Seq experiments from ENCODE

70 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 4 project and further publications have been integrated. The data sets comprise 603,016 fragments bound by 66 distinct transcription factors, of which 19 factors were not yet covered by ChIP-Seq data in TRANSFAC.

Match Library for TRANSFAC download package

The TRANSFAC® Match™ Library package of bioinformatics commandline programs written in Java is now available with extended documentation. It allows TRANSFAC download users to perform such commands as TF binding sites prediction in DNA sequences using Match algorithm; creation of a profile for matrix models; creation of a JSON file with binding site models from TRANSFAC dat- and/or JSON file(s), etc.

Overview of recommended TRANSFAC 2.0 Online packages

The TRANSFAC 2.0 can come in a number of online packages, each briefly summarized by its functionality here.

 

 

Select the TRANSFAC 2.0 package that fits your research needs best and immediately receive the respective price info.

For more details please explore the TRANSFAC® 2022.2 new features and database statistics.

 

TRANSPATH® 2022.2 comes with the following new features:

Increase in number of reactions

47,303 new binding reactions from recent publications between proteins in human have been added, among them e.g. from the OpenCell and the COVID19 interactome.

Update of links to Wikipathways and Reactome

Links from genes/proteins to the pathway databases Wikipathways (20220810) and Reactome (v81) have been updated.

For more details please explore the TRANSPATH® 2022.2 new features and database statistics.

 

HumanPSD™ 2022.2 comes with the following new features:

Biomarker and drug target data update

The number of disease annotations increased to 378,522 and the number of unique gene/biomarker – disease assignments to 129,784. Targets for FDA – approved drugs have been added by manual curation and the number of drug – target protein associations is now 53,034.

For more details please explore the HumanPSD™ 2022.2 new features and database statistics.

 

geneXplain® platform 7.1 release comes with the following new features:

API documentation and how-to videos

Platform APIs (genexplain-api and geneXplainR) now have extended documentation and tutorial freely available online at this page. Additional information on geneXplain platform API, as well as the how-to videos on its usage with demo scripts, can be found on here.

Support of additional species

The platform now supports the following species for performing a vast number of analyses including search for TFBS on an input gene set: FruitFly, Nematoda, Saccharomyces Cerevisiae (baker’s yeast), Schizosaccharomyces Pombe (fission yeast).

Databases update

TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2022.2.

For more details, please explore the full new features list of geneXplain® platform release 7.1.

 

Genome Enhance 3.1 release comes with the following new features:

Databases update

TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2022.2.

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 3.1.

 

Videos demonstrating our products and analysis approaches

We have united a number of biomedical data analysis masterclass videos and how-to guidances on the use of our products in a new video gallery. Explore the functionality of our tools and follow the analysis steps introduced by our experts for achieving the best results in your research.

 

 

Evaluation license

You are welcome to try out all products from this major release at once by purchasing the evaluation license. Activate now your full 1 week access to the best-in-class bioinformatics tools and biological databases.

Thank you very much for staying with us!

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