The geneXplain team is proud to present the new major release of its products: TRANSFAC®, TRANSPATH® and HumanPSD™ databases release 2022.1, geneXplain® platform release 7.0 and Genome Enhancer release 3.0.
TRANSFAC® 2.0 2022.1 comes with the following new features:
Single gene analysis in MATCH Suite
MATCH Suite now supports gene regulation analysis for single genes in addition to the previously introduced gene set studies. Specify the gene of your interest and find transcription factors responsible for its regulation via promoter and enhancers/silencers. Optionally select the tissue of your interest, the promoter type and region to be used for the analysis, or the GO terms to narrow down the identified transcription factors to the ones belonging to the chosen biological processes. The generated report will provide you with comprehensive information on the performed analysis, while the interactive visualisation of the obtained results in user-friendly interface will give you the look-and-feel of the identified factors and binding models, including their on-the-fly filtering and genome browser visualisation.
Extended options to use search results as input for further queries
Transcription factors that bind to regulatory regions of specific genes in ChIP-Seq experiments, can now be queried directly from a gene/protein search result. This extends the possibility to identify regulatory factors for a gene beyond the ones found through DNA binding sites from low-throughput experiments.
Integration of new human ChIP-Seq experiments from ENCODE
17 new human transcription factor binding site ChIP-Seq experiments released by the ENCODE phase 4 project have been integrated providing 38,319 fragments bound by 17 distinct transcription factors, of which 10 factors were not yet covered by ChIP-Seq data in TRANSFAC. For 14 of the sets, an existing positional weight matrix for the respective transcription factor was used together with the MATCH tool to predict altogether 28,204 best binding sites inside the fragments.
TRANSPATH® 2022.1 comes with the following new features:
Increase in number of reactions
57,268 new binding reactions from recent publications between proteins in human and mouse have been added.
Update of links to Wikipathways and Reactome
HumanPSD™ 2022.1 comes with the following new features:
Quantitative tissue expression diagram in human locus reports
Normalized transcript expression levels from Human Protein Atlas (v20) are displayed in a histogram across 61 different cell types / tissues. There are several sorting and grouping options, e.g. cell/tissue by organ. In addition, a value for the relative tissue specificity as indicator for expression ubiquity of the respective human gene is given.
Extended options to use search results as input for further queries
The added options include the possibilities to query for drugs approved or under research for a certain condition from a search result of diseases and vice versa.
Biomarker and drug target data update
The number of disease annotations increased to 369,215 and the number of unique gene/biomarker – disease assignments to 126,804. Targets for FDA – approved drugs have been added by manual curation and the number of drug – target protein associations is now 51,827.
geneXplain® platform 7.0 release comes with the following new features:
- Fully automatic pipelines for paired RNA-seq libraries
- 2 new workflows for analyzing multiple BAM files
- 8 new and enhanced workflows for DEGs estimation from raw RNA-seq data, counts or normalized transcriptomic data
- Support of new species Zebrafish and Arabidopsis for analyzing RNA-seq data or genes and sequences for transcription factor binding sites in over 20 workflows
- Support of Affymetrix miRNA-4.1 microarray chip & Agilent miRNA microarray chips
- Enabled multiple miRNA ID support and conversion handling
- Investigation of tissue- or cell-line specific miRNA promoter regions with TRANSFAC®
- Identification of miRNA binding sites in tissue-specific genes with HumanPSD™
- New pipeline to analyze SNPs with TRANSFAC® and TRANSPATH® at once
- New features: MATCH™ for tracks, Convert table to VCF track, Filter VCF by genotype
- Start page update with new features and > 30 enhanced or new workflows
- TRANSFAC®, TRANSPATH® and HumanPSD™ databases update to release 2022.1
For more details, please explore the full new features list of geneXplain® platform release 7.0
Genome Enhance 3.0 release comes with the following new features:
Integration of somatic variants info into the analysis report
New ‘Somatic variants’ column was introduced in FDA approved and repurposed drugs tables for cases when somatic mutations/variations in tumor DNA are analyzed and significant association between predicted drugs and identified DNA variations is revealed. Provided info includes the gene, in which the mutation was found, the mutation/variant(s) ID, the predicted type of associated drug action (resistance / response) and the level of clinical evidence.
New table of prospective drugs approved for the studied oncology
If all input diseases are neoplasms, a new drug table ‘Drugs approved in clinical trials for Oncology’, containing only the drugs that were clinically approved for the pathologies under study, will be constructed in addition to the standard drug tables provided by Genome Enhancer report.
Extended list of drugs approved for neoplasms with predicted drug scores assigned
If at least one of the input diseases is a neoplasm, a new ‘Supplementary drug info’ table will be provided. It includes an extended list of drugs generally used in clinic for treatment of neoplasms with predicted drug scores for the studied case. If MTB report was generated and any of the drugs from supplementary table received a matching gene-drug predictive association, the‘Somatic variants’ column will provide respective info.
Extended clinical trials info
New columns with clinical trials info were added to the drug tables in Genome Enhancer report: the ‘Disease trial phase’ column displays the maximum clinical trials phase in which the drug was tested for the studied pathology and the ‘Maximum trial phase’ column displays the maximum clinical trials phase in which the drug was tested for any pathology.
Epigenomics analysis launch on CpG loci identifiers
Genome Enhancer is now able to analyze DNA methylation data provided in the format of CpG loci IDs with respective numerical values without any additional omics data needed for the analysis. Details on processing of such data can be found in the new demo report on Hypertension or in the extended description of Genome Enhancer analysis algorithm.
Improvement of genomics data analysis algorithm
If genomics data was analyzed, additional weights reflecting the transcription factor binding affinity change caused by the mutation will be calculated. Obtained weights will be used to find the regulatory regions of genes most affected by variations and associated binding models will be taken into the composite modules search (CMA algorithm).
TRANSFAC®, TRANSPATH® and HumanPSD™ databases were updated to the release 2022.1. The CIViC database used for MTB report construction was updated to version 01 March 2022.
New and updated demo reports
The new and updated Genome Enhancer demo reports can be found here.
For more details, please explore the full new features list of Genome Enhancer release 3.0.