Videos

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TRANSFAC and transcription factors

TRANSFAC® database of transcription factor binding sites

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

Transcription factors and their classification

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)

MATCH Suite introduction

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)

TRANSFAC download: PWMs, Transcription factor binding site prediction

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)

TRANSFAC for identification of composite modules – combinations of TFBS

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)

How to find TFBS of one transcription factor in your gene set

This video demonstrates how a site search profile can be created for one specific transcription factor, and how the respective profile can be then used for performing the site search on gene set. Filtering of the obtained results based on the number of sites in the promoters of target genes is demonstrated. Graphical visualization of found sites in the promoters of target genes is shown. (09:13 min)

Search for TFBS in any eukaryotic genome using the geneXplain platform and TRANSFAC database

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)

SNP analysis in COVID-19 with TRANSFAC Public, TRANSFAC Professional, and JASPAR

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)

TRANSFAC® database and its applications

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)

Regulatory SNPs in TRANSFAC® sites. Severe COVID-19 patients versus non-symptomatic.

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)

TRANSFAC 2.0: the fresh look at the gold standard of gene regulation studies

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)

Ontology Search Introduction

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)

Analysis of SNPs associated with educational attainment using the TRANSFAC database

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)

Educational attainment SNPs analysis in the geneXplain platform

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

ChIP-seq Data Analysis (part-1) Identification of Enriched TFBS

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)

ChIP-seq Data Analysis (part-2) SNAIL-1 in the TRANSFAC database

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)

Concept of regulatory SNP analysis to reveal gained and lost binding sites for transcription factors

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)

Search for TFBS in FASTA sequences

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)

How transcription factor binding affinity is computed

In this video Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, explains how binding affinity of a transcription factor to the DNA sequence can be computed.(22:04 min)

TRANSFAC Chastushki

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

Coffee break with TRANSFAC

This video is a record of the first Coffee break with TRANSFACsession, where geneXplain’s CEO Dr. Alexander Kel is answering your questions on the topic of applied bioinformatics in a format of a live Q&A session. (1:24:22 min)

HumanPSD+TRANSPATH and gene-disease-drug assignments

HumanPSD™ and TRANSPATH® databases

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

Ontology Search Introduction

Search for hypertension biomarkers by Liz and Mark

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

geneXplain® platform for multi-omics

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

Workflow creation for analysis of Transcriptomics and CGmethylation data in the geneXplain® platform

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)

How to convert gene identifiers from Ensembl to others in the geneXplain platform

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

Annotate table in geneXplain platform

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)

RNA-seq preprocessing in geneXplain platform: quality control

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)

RNA-seq preprocessing in geneXplain platform: read alignment

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

RNA-seq preprocessing in geneXplain platform: read quantification

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

Search for TFBS in FASTA sequences

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)

Search for TFBS in any eukaryotic genome using the geneXplain platform and TRANSFAC database

geneXplain platform API

The geneXplain platform Java API introduction

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)

geneXplainR: An R interface for the geneXplain platform

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

ChIP-seq Data Analysis (part-1) Identification of Enriched TFBS

ChIP-seq Data Analysis (part-2) SNAIL-1 in the TRANSFAC database

PART1: RNA-seq data analysis from FASTQ files to master regulators

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)

PART2: RNA-seq data analysis from FASTQ files to master regulators

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)

PART3: RNA-seq data analysis from FASTQ files to master regulators

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)

PART4: RNA-seq data analysis from FASTQ files to master regulators

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)

PART5: RNA-seq data analysis from FASTQ files to master regulators

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)

Analysis of SNPs associated with educational attainment using the TRANSFAC database

Educational attainment SNPs analysis in the geneXplain platform

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

Concept of regulatory SNP analysis to reveal gained and lost binding sites for transcription factors

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

Genome Enhancer – the new era of precision medicine

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

Genome Enhancer: the new era of precision medicine

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

Genome Enhancer – the new era of precision medicine

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)

Genome Enhancer used for predicting VEGFA-targeted treatment response of colorectal cancer patients

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)

Genome Enhancer: from raw omics data to personalised drug targets and treatments

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)

Personalized selection of cancer treatment using RNA-seq and integrated promoter & pathway analysis

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)

Omics data analysis and modeling using Genome Enhancer

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)

Introducing Genome Enhancer

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

PASS – Prediction of Activity Spectra for Substances

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)

GUSAR – General Unrestricted Structure Activity Relationships

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)

In silico approach to finding potential anti-SARS-CoV-2 agents among one billion molecules

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)

In silico evaluation of the pharmacological potential of natural compounds

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

GeneXplain classroom license

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

geneXplain GmbH

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)

The sites of beautiful Wolfenbüttel – home of geneXplain GmbH

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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