Videos

Videos

 

Table of contents:

 

TRANSFAC and transcription factors
HumanPSD+TRANSPATH and gene-disease-drug assignments
geneXplain platform and omics data analysis

– geneXplain platform how-to videos

– geneXplain platform API

– Data analysis examples using the geneXplain platform

Genome Enhancer and prospective drug targets and treatments identification
PASS, GUSAR, PharmaExpert and cheminformatics
License activation instructions
The geneXplain company
Free webseminars

 

 

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TRANSFAC and transcription factors

 

This video includes a brief overview of TRANSFAC database given by its originator Prof. Dr. Edgar Wingender. (1:28 min)

 

This video is a record of free webseminar, it addresses the basic mechanism of transcription and features of transcription factors in eukaryotes, in particular their mode of recognizing regulatory DNA elements. The principles of a TF classification were outlined, their implementation as TFClass was depicted. (1:13:28 min)

 

This video demonstrates the MATCH Suite toolbox of TRANSFAC 2.0, which comprehensively addresses the syntax and semantics of gene regulation and allows identification of transcription factors regulating the gene set of your interest. (21:07 min)

 

This video gives a brief overview of the TRANSFAC® flat file download release with the included Match Library – a collection of tools that can be used via the command line interface. (8:00 min)
This video discusses principles of combinatorial regulation of genes by combinations of synergistically acting transcription factors. The basics of CMA (Composite Module Analyst) are presented, this algorithm performs search for clusters of TFBS in the promoters of studied genes (e.g. up-regulated genes).  (18:04 min)

 

This video demonstrates how to search for TFBS (Transcription Factor Binding Sites) in any eukaryotic genome using the geneXplain platform and TRANSFAC database on the example of Komagataella pastoris genome. (09:45 min)

 

This video demonstrates the analysis of important SNPs in the LZTFL1 gene which was identified in a GWAS as one of the most important genetically predisposed risk factors of COVID-19 infection. The SNPs are analyzed by searching for transcription factors which binding sites have changed because of the change of the nucleotides in this SNP. The search is performed three times using different libraries of PWMs from three different databases: (1) TRANSFAC Professional (2) TRANSFAC Public (3) JASPAR.  (11:05 min)

 

This video is a record of free webseminar, it includes the historical origins of TRANSFAC® database, basic concepts and current status of gene regulation aspects in the context of TRANSFAC® database, as well as TRANSFAC® applications for various biological research needs with focus on analysis of genomic sequences for potential transcription factor binding sites with the tools Match™ and FMatch. (1:08:38 min)

 

This video is a record of free webseminar, it shows how TRANSFAC®, geneXplain® platform, and Genome Enhancer can be applied for identification of TFBS strongly associated with SNPs linked to the severity of COVID-19 disease. Upstream analysis of identified TFs in the context of the revealed SNPs gave a clue about signal transduction pathways associated with the potential predisposition to the severe COVID-19 disease. (1:09:37 min)

 

This video is a record of the presentation given by Prof. Dr. Edgar Wingender in the scope of the World Cancer Research Day 2021 at geneXplain. (46:21 min)

 

This video demonstrates the Ontology Search tool in TRANSFAC, HumanPSD, and TRANSPATH databases, which serves as a powerful engine enabling searching for and analyzing genes, miRNAs, diseases, and drugs using various manually curated and calculated properties. (7:32 min)

 

This video is demonstrating the analysis of SNPs associated with educational attainment using the TRANSFAC database. Combinations of transcription factor binding sites in genomic enhancers marked by these SNPs are in the focus of the study. (18:06 min)

 

This video is the continuation of the previous one showing technical details of the analysis of SNPs associated with educational attainment. (17:40 min)

 

This video demonstrates the ChIP-seq data analysis taken from the publicly available dataset GSE127183. The aim of this analysis is to identify enriched TFBS in the peaks using the classical match approach. (5:54 min)
This video shows the details about the SNAIL-1 transcription factor both as a gene and as a protein. Associations of SNAIL-1 with several neoplasms as a biomarker are demonstrated. The interaction of SNAIL-1 with several FDA-approved drugs and other small molecules are reviewed. (7:50 min)

 

This video shows the analysis of regulatory SNPs associated with COVID-19 susceptibility in order to suggest the mechanisms of their action. Those SNPs that change transcription factor binding sites (TFBSs) are identified. TFBSs are identified using the library of positional weight matrices from TRANSFAC® database. This is done for both: reference and alternative alleles, and gained and lost TFBSs are identified. Motif enrichment analysis and composite module search are applied to short regions around SNPs in focus. Identification of master regulators in signalling networks upstream of the identified transcription factors is performed. (14:25 min)

 

This video provides instructions on how to perform search for transcription factor binding sites in a FASTA sequence by using the geneXplain platform and the TRANSFAC database. (5:09 min)

 

This video is dedicated to TRANSFAC 30 years anniversary: Dr. Alexander Kel, CSO geneXplain GmbH, is performing “TRANSFAC Chastushki”(4:28 min)

 

HumanPSD+TRANSPATH and gene-disease-drug assignments

 

This video gives a brief overview of HumanPSD and TRANSPATH databases given by CSO geneXplain GmbH Dr. Alexander Kel. (2:32 min)

 

This video demonstrates the Ontology Search tool in TRANSFAC, HumanPSD, and TRANSPATH databases, which serves as a powerful engine enabling searching for and analyzing genes, miRNAs, diseases, and drugs using various manually curated and calculated properties. (7:32 min)

 

This video shows how two students were searching for hypertension biomarkers involved in the disease molecular mechanism, as well as hypertension biomarkers that correlate with the disease and can be found in urine. (2:22 min)

 

 

geneXplain platform and omics data analysis

 

This video gives a brief overview of geneXplain® platform – an online toolbox and workflow management system for a broad range of bioinformatics and systems biology applications. (1:59 min)

geneXplain platform how-to videos

 

This video provides instructions on how to create a new workflow in the geneXplain® platform that would allow performing a joint analysis of gene expression (Transcriptomics) and DNA methylation (CGmethylation) data(42:40 min)

 

This video provides instructions on how to convert gene identifiers from Ensembl to Entrez or to Uniprot in the geneXplain platform. (3:03 min)

 

This video provides instructions on how to annotate and add additional columns of gene symbol and gene description to a table with only gene identifiers in the geneXplain platform. (2:58 min)

 

This video provides guidance on the FASTQ file format, base call quality scores, and provides instructions on how to assess the quality of raw RNA-seq data using the geneXplain platform. (4:44 min)

 

This video provides instructions on how perform read alignment in the geneXplain platform. (6:30 min)

 

This video provides instructions on how perform RNA-seq read quantification in the geneXplain platform. (6:54 min)

 

This video provides instructions on how to perform search for transcription factor binding sites in a FASTA sequence by using the geneXplain platform and the TRANSFAC database. (5:09 min)

 

This video demonstrates how to search for TFBS (Transcription Factor Binding Sites) in any eukaryotic genome using the geneXplain platform and TRANSFAC database on the example of Komagataella pastoris genome. (09:45 min)

 

geneXplain platform API

 

This video demonstrates geneXplain Java API that allows integration of the platform’s functionalities into Java programs and provides a JSON interface to configure and execute individual analysis tasks as well as complex workflows. (9:23 min)

 

This video demonstrates the R-based API of the geneXplain platform. GeneXplainR package provides interface for easy integration of geneXplain platform and TRANSFAC functionalities into the R pipelines. Execution of the “Identify enriched motif in promoters (TRANSFAC)” workflow is shown in details. (9:29 min)

 

Data analysis examples using the geneXplain platform

 

This video demonstrates the ChIP-seq data analysis taken from the publicly available dataset GSE127183. The aim of this analysis is to identify enriched TFBS in the peaks using the classical match approach. (5:54 min)

 

This video shows the details about the SNAIL-1 transcription factor both as a gene and as a protein. Associations of SNAIL-1 with several neoplasms as a biomarker are demonstrated. The interaction of SNAIL-1 with several FDA-approved drugs and other small molecules are reviewed. (7:50 min)

 

This video shows identification of master regulatory molecules in breast cancer triple negative cells based on FASTQ files taken from GSE188914. The FASTQ files are submitted to the pre-defined workflow in the geneXplain platform that includes subread-align, featurecounts, and Limma voom methods for FASTQ files processing. The workflow output contains a gene table with calculated LogFold Changes and P-values. (6:19 min)

 

This video shows the output files of the pre-defined workflow of the geneXplain platform that includes subread-align, featurecounts, and Limma voom methods for FASTQ files processing. Aligned and mapped to genes BAM files are visualized on the inbuilt genome browser. The differentially expressed genes generated by limma_voom are shown with the calculated LogFold Changes and adjusted P-values. (6:01 min)

 

This video shows further processing of the upregulated genes, their mapping to GO terms, to pathways, to disease ontology. Functional groups of genes are identified that can be further used for regulatory transcription factors identification as well as master regulators identification. (6:17 min)

 

This video shows how to apply upstream analysis to the genes expressed in breast cancer in order to identify master regulatory molecules that potentially play a role in breast neoplasms. (6:09 min)

 

This video shows the result of promoter analysis. 437 promoters of genes upregulated in triple negative breast cancer cells were analysed. Visualization of identified TFBS on these promoters is shown. (5:18 min)

 

This video is demonstrating the analysis of SNPs associated with educational attainment using the TRANSFAC database. Combinations of transcription factor binding sites in genomic enhancers marked by these SNPs are in the focus of the study. (18:06 min)

 

This video is the continuation of the previous one showing technical details of the analysis of SNPs associated with educational attainment. (17:40 min)

 

This video shows the analysis of regulatory SNPs associated with COVID-19 susceptibility. Those SNPs that change transcription factor binding sites (TFBSs) are identified using the library of positional weight matrices from TRANSFAC® database. Motif enrichment analysis and composite module search are applied to short regions around SNPs in focus. Identification of master regulators in signalling networks upstream of the identified transcription factors is performed. (14:25 min)

 

Genome Enhancer and prospective drug targets and treatments identification

 

This video gives a brief overview of Genome Enhancer tool given by CSO geneXplain GmbH Dr. Alexander Kel. (2:57 min)

 

This video provides a short promo introduction to the Genome Enhancer tool and its capabilities. (2:13 min)

 

This video provides promo introduction to the Genome Enhancer tool and its capabilities, as well as the basic principles of underlying the Genome Enhancer analysis. (4:03 min)

 

This video shows how Genome Enhancer results can be interpreted for further use in clinic on the example of sensitivity prediction towards VEGFA-targeted therapy for three colorectal cancer patients. (5:51 min)

 

 

This video is the record of the presentation given by Dr. Alexander Kel (CSO of geneXplain GmbH) in the scope of the World Cancer Research Day 2021 at geneXplain. (47:36 min)

 

 

This video is the record of the presentation given by Daria Stelmashenko (product manager Genome Enhancer) in the scope of the World Cancer Research Day 2021 at geneXplain. (35:23 min)

 

 

This video is a record of a live webinar from 21.01.2020 organized jointly by Optogenerapy EU project and geneXplain GmbH. Reviews of the basic principles of intracellular regulation are given and Upstream Analysis application for reconstruction of molecular mechanisms of the studied pathology is shown mostly on the example of Multiple Sclerosis. The geneXplain platform and Genome Enhancer tools are demonstrated as powerful resources for performing the Upstream Analysis for identification of prospective drug targets and biomarkers. (50:24 min)

 

This video is an interview with geneXplain’s CSO Dr. Alexander Kel, who is introducing Genome Enhancer – a new tool for completely automatized drug target identification and prospective therapy selection. (7:58 min)

 

PASS, GUSAR, PharmaExpert and cheminformatics

 

This video demonstrates PASS program for prediction of biological activities spectra of organic drug-like compounds. The input is the structural formula of a chemical compound, and the output is a list of biological activities with respective probability values. (4:58 min)

 

This video demonstrates GUSAR tool for creation of quantitative structure-activity relationship (QSAR) models. It uses a customized training set of chemical structures and quantitative data on biological activities to create a highly specific QSAR model. (5:35 min)

 

This video is a record of geneXplain’s live webseminar which was held on May 13th, 2020. In this video Prof. Vladimir Poroikov from Institute of Biomedical Chemistry (IBMC) Moscow, Russia, is showing how to apply artificial intelligence and machine learning methods to in silico screening of hits with the desired biological activity in chemical libraries of synthesized or virtual molecules. Particular emphasis is placed on PASS – one of the earliest and most widely used tools for the elucidation of hidden pharmacological potential of drug-like molecules. (1:00:14 min)

 

This video is a record of geneXplain’s live webseminar which was held on November 24th, 2020. In this video Prof. Vladimir Poroikov from the Institute of Biomedical Chemistry (IBMC), Moscow, Russia, demonstrates how new medical indications for medicinal plants’ phytoconstituents may be identified by applying bio- and chemoinformatics methods. (47:15 min)

 

 

License activation instructions

 

This video shows how to activate the 1 week evaluation licence for geneXplain’s best-in-class bioinformatics tools and biological databases. (4:31 min)

 

This video shows how to activate the classroom licence for geneXplain’s best-in-class bioinformatics tools and biological databases. (5:54 min)

 

The geneXplain company

 

This video gives a brief overview of geneXplain GmbH as a leading bioinformatics company providing the research community worldwide with the best-in-class tools and databases for biomedical research. The company is presented by its CEO and founder Prof. Dr. Edgar Wingender. (1:24 min)

 

This video takes you through a short tour on the beautiful views of Wolfenbüttel – the home of geneXplain GmbH. (3:26 min)

Free webseminars

 

Explore the full list of the video records of our free webseminars with their short summaries and speaker info at this page.

 

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