Find your gene regulatory pathways, biomarkers, and drug targets in a few clicks
No-coding
Bioinformatics
Academy
For molecular biologists and clinical researchers
Watch
the introductory video
Choose your training
Promoter analysis of model organisms
Q&A: Coffee break with TRANSFAC
In this session we will learn how to apply TRANSFAC to study different model organisms. We will focus on analysis of RNA-seq and ChIP-seq data from Drosophila melanogaster (GEO: GSE149116). We will identify enriched TF binding sites in promoters of DEGs and will find combinations of TFs working together. Topics to be covered:
- What is the promoter size?
- Does it depend on the genome length?
- How to integrate RNA-seq and ChIP-seq data?
- How to build your own pipeline?
Schedule
MATCH Suite
Software Demo: Coffee break with TRANSFAC
In this session we will learn how to apply the MATCH Suite component of TRANSFAC 2.0 to study gene regulation, including cases specific for particular tissues. Both: single gene analysis and gene set analysis will be performed, and the obtained results will be discussed, including the interactive user-friendly interface allowing you to fine-tune your results by applying various filters, as well as the the automatically generated analysis report. Topics to be covered:
- What is MATCH Suite and in which cases it should be used?
- What are the analysis pipelines underlying the automatised MATCH Suite workflows?
- How is the analysis launch performed in MATCH Suite?
- How to interpret the obtained results and where to use them?
Schedule
Your income and your DNA
Q&A: Coffee break with TRANSFAC
Is your level of income written in your DNA? This question will be considered in this “Coffee break with TRANSFAC” which will be hosted by Dr. Alexander Kel. You will learn how SNPs may change TF binding sites. You will see how they change enhancers in the genome that in turn affect important signaling pathways acting in the brain. You will explore the results of master regulator analysis and become curious about the potential role of oxytocin in influencing your income. Topics to be covered:
- How SNPs and SNVs are changing TF binding sites? Site gain and site loss.
- Principles of analysis of site enrichment and site combinations in enhancers.
- How enhancer analysis can help to find master regulators of signaling pathways in brain?
- How master regulators such as oxytocin can rewire the regulatory system?
Schedule
FREE geneXplain platform account
Software demo: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel together with data analysis expert Ms. Neetu Tandon will demonstrate the abilities of the geneXplain platform. The following main questions will be in the focus of this seminar:
- What is the free version of geneXplain platform?
- What methods and workflows are included in the free version?
- DEGs detection using Limma and EdgeR.
- Heatmap, PCA and t-SNE. SVM, Regression analysis and genetic algorithm.
- Site search analysis using TRANSFAC® Public.
- Pathway analysis using GeneWays and Reactome.
Schedule
Your first TRANSFAC analysis
Q&A: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will introduce to you the basic principles of promoter analysis and identification of transcription factor binding sites. You will learn how to use TRANSFAC and perform your first steps towards the understanding of gene regulation. The following main questions will be in the focus at this seminar:
- Transcription factors. Why they are important?
- What are DNA binding motifs? TRANSFAC and JASPAR.
- How to analyse promoters? Match and HOMER.
- How to start and how to interpret the obtained results?
Schedule
geneXplain platform API
Software demo: Coffee break with TRANSFAC
This session will be dedicated to the topic of Application Programming Interfaces (APIs). Prof. Dr. Alexander Kel and Kamilya Altynbekova will discuss what an API is, when it is used, and what advantages does it offer to your analysis pipeline. The following main questions will be in the focus of this seminar:
- What is an API and why is it used?
- What kind of APIs are available for the geneXplain platform?
- Where can you get the geneXplainR package?
- How to connect to your existing account in geneXplain platform via API?
- How can I use the functionalities of geneXplain platform in my R scripts?
Schedule
How to find tissue-specific transcription factor (TF) target genes
Q&A: Coffee break with TRANSFAC
In this webinar Prof. Dr. Alexander Kel will share with you the latest intriguing insights of gene regulation mechanisms. He will demonstrate how to perform tissue-specific gene regulation analysis and find enriched motifs using the TRANSFAC database and its MATCH Suite tool. The following main questions will be in the focus of this seminar:
- How to find tissue-specific TF target genes?
- Why do you need TF binding sites?
- Conserved TF binding sites – how important are they?
- PWMs – is that all? What else?
Schedule
Download TRANSFAC and do whatever you like
Software demo: Coffee break with TRANSFAC
This webseminar will give a brief overview of TRANSFAC® with the focus on the flat file download release. In the TRANSFAC® flat file download, the Match™ tool can be used in the command line or the PWMs can be used with third-party tools or with tools of the user. The following main questions will be in the focus of this seminar:
- Factor-site binding
- Factor-factor interaction
- Combinatorial gene regulation
- Gene regulatory networks
- Promoters & Enhancers
- Factor classification
- TF-binding motifs (PWMs)
- TF-binding site prediction
Schedule
Promoter hunting with TRANSFAC
Lectures and hands-on training
Become a professional promoter hunter within this four day intensive course on gene regulation analysis. Gain an understanding of the principles underlying the regulatory code of eukaryotic genes, and explore the techniques for predicting and analyzing promoters and enhancers.
TRANSFAC license is included throughout the whole course duration.
The following main questions will be in the focus of this course:
- Principles of gene regulatory code
- How do I find promoters and enhancers of the genes under study?
- Basic principles of search for TFBS (Transcription Factor Binding sites)
- Combinatorial analysis of gene regulation: complexes of TFBS acting together
- Search for tissue-specific TF target genes
- Working with multi-omics data: how to compile a gene set for further promoter analysis (what you can do with RNA-seq, ChIP-seq, ATAC-seq, proteomics, metabolomics, DNA methylation, genome sequencing data)
- Mutation effect on sites: site gains and losses
- Selection of site search profiles (collection of positional weight matrices to perform the search for TFBS)
Schedule
* FREE for TRANSFAC licensed users
Don’t do pathway analysis without TRANSFAC
Q&A: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will introduce you the Upstream Analysis approach that combines robust TRANSFAC TF binding site search with the fine pathway database TRANSPATH for reconstructing the key pathways and finding master regulators in them. You will learn how to use easy online tools that will automatically analyze your gene list, build specific gene regulatory and signal transduction pathway, find master regulators, and produce nice network visualizations ready for your paper. The following main questions will be in the focus of this seminar:
- Master regulators controlling the activity of transcription factors
- Walking pathways: pathway rewiring
- Integrated transcriptomics and proteomics analysis of Myc-induced U2OS cells (data from PMID: 26538417)
- Visualization of signalling pathways and networks
Schedule
Release 2024.1 new features overview
Q&A: Coffee break with TRANSFAC
In this Coffee break with TRANSFAC Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will demonstrate the new features of the geneXplain products release 2024.1. Join this webinar to learn how MATCH Suite can now be applied for gene regulation studies of model organisms and how TRANSPATH database was updated with a big number of new pathways and reactions. The following main questions will be in the focus of this seminar:
- Release 2024.1 new features and statistics overview
- MATCH Suite now available for mouse and rat
- HOMER tool in the geneXplain platform
- TRANSPATH: new pathways and reactions; REACTOME integration
Schedule
ATAC-seq, CUT&RUN and Enhancers
Q&A: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will address the basic principles of epigenomics data analysis and will analyse ATAC-seq, ChIP-seq and CUT&RUN data for enriched transcription factor binding sites, composite modules and upstream regulators. The following main questions will be in the focus of this seminar:
- Identification of differentially accessible chromatin regions
- Analyzing differentially accessible peaks for enriched TF-binding sites and composite modules
- Finding enhancers by combining ATAC-seq with RNA-seq data
- Upstream analysis for master regulators
Schedule
“Intelligent design” of promoters
Q&A: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will delve into the roles of promoters and enhancers in gene regulation and explain why artificial promoters are essential for advancing synthetic biology. Applications of artificial promoters design in gene therapy, metabolic engineering, and synthetic biological circuits for achieving precise biological functions will be discussed. A deep dive into promoter architecture will be provided, covering elements like core promoters, upstream regulatory elements, transcription factor binding sites, and composite elements. Additionally, an overview of key databases and software tools, such as JASPAR, GTRD, TRANSFAC, and Genome Enhancer, that are crucial for promoter design, will be provided. Finally, it will be discussed how machine learning (ML) and artificial intelligence (AI) approaches can predict promoter activity. The strategies for balancing promoter strength while maximizing specificity and minimizing off-target effects will also be addressed. The following main questions will be in the focus of this seminar:
- What are promoters and enhancers? Why do we need artificial promoters?
- Application in gene therapy, metabolic engineering, and synthetic biological circuits to achieve desired biological functions
- Understanding of promoter architecture (core promoter, upstream regulatory elements, TFBS, composite elements etc.)
- Overview of databases and software tools used for artificial promoter construction (e.g., JASPAR, GTRD, TRANSFAC, Genome Enhancer)
- Machine learning and AI approaches for predicting promoter activity
- Balancing the promoter strength: maximizing cell/tissue specificity, minimizing off-target effects.
Schedule
“Intelligent design” of promoters: Practical Guide
Q&A: Coffee break with TRANSFAC
In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will show how artificial promoters can be constructed with software tools using machine learning (ML) and artificial intelligence (AI) approaches, based on data collected in TRANSFAC. After a short summary on the architecture of promoters and enhancers and on the use of artificial promoters in gene therapy and in other applications, Alexander will give a step-by-step guide for construction and evaluation of artificial promoters and their tissue- and context-specificity. The following main questions will be in the focus of this seminar:
- Summary on artificial promoters and enhancers and their application
- Machine learning and artificial intelligence approaches for predicting tissue-specific promoter activity
- Introduction into tools for construction of artificial promoters
- Demonstration of automatic promoter analysis pipeline
- Step by step demo of promoter construction and evaluation
Schedule
CRISPR Synthetic Lethality screens and TRANSFAC Pathways
Q&A: Coffee break with TRANSFAC
In this webinar Prof. Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will address the in-depth exploration of how CRISPR gene knockouts can be leveraged for TRANSFAC pathway discovery and the identification of cancer master regulators within the TRANSFAC network.
This seminar will highlight the utility of CRISPR synthetic lethality screens in discovering drug targets and understanding disease mechanisms within TRANSFAC pathways. Alexander will showcase a case study where a synthetic lethal CRISPR screen identified a cancer cell-intrinsic role of PD-L1 in regulating vulnerability to ferroptosis in Homo sapiens (GSE268533). Despite the success of PD-1/PD-L1 inhibitors in cancer therapy, only a minority of patients benefit from these treatments. The presented study uses a genome-wide CRISPR screen to explore the intrinsic function of PD-L1 in head and neck squamous cell carcinoma (HNSCC). This seminar will focus on how synthetic lethality screens, combined with the TRANSFAC database, can uncover pathways and regulatory mechanisms that highlight PD-L1’s role in cancer resilience. Additionally, we’ll discuss how these insights can enhance therapeutic strategies by targeting intrinsic PD-L1 functions. The following main questions will be in the focus of this seminar:
- Genome-wide CRISPR/Cas-9 synthetic lethality screens to discover anti-cancer drug targets
- Analysis of GSE268533 dataset of head and neck squamous cell carcinoma (HNSCC)
- Mapping the results of CRISPR/Cas-9 synthetic lethality screens on TRANSFAC pathways
- Finding master-regulators to resolve resistance to PD-L1 inhibitors
Schedule
From Zebrafish to Precision Medicine: Discovering Master Transcription Factors with TRANSFAC®
Q&A: Coffee break with TRANSFAC
In this webinar Prof. Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will demonstrate how TRANSFAC® and the tools included in the geneXplain platform enable the identification of key transcription factors in model organisms like zebrafish, bridging the gap between basic research and medical applications for drug discovery. The following main questions will be in the focus of this seminar:
- Prediction of transcription factor binding sites
- Revelation of regulatory mechanisms
- Understanding disease pathways
- Advancement of drug discovery
Schedule
TRANSFAC Q&A session
Q&A: Coffee break with TRANSFAC
Join us for an exclusive online Q&A on TRANSFAC led by Prof. Dr. Alexander Kel, CEO & CSO of geneXplain GmbH. Get expert insights, troubleshoot issues, and explore key features like data integration, gene regulation analysis, and advanced functionalities. Perfect for both: beginners and experienced users. Some questions that will be addressed at the seminar:
- How can I get a p-value, or similar, for the TFBS predictions in a single promoter?
- How can I optimize my transcription factor binding site predictions?
- How can I find common transcription factors (and upstream master regulators) for a set of differentially expressed genes?
And much more, including questions coming from the audience during the live event.
Don’t miss the chance to enhance your experience with one of the top tools for gene regulation studies!
Schedule
DNA methylation signatures of diseases
Q&A: Coffee break with TRANSFAC
In this webinar Prof. Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will address the exciting topic of DNA methylation changes observed in various pathologies with a focus on DNAm signatures of Kabuki syndrome and CHARGE syndrome – two rare genetic diseases belonging to the family of chromatinopathies. The following main questions will be in the focus of this seminar:
- DNA methylation: why is it important and how to track its changes
- Identification of disease DNAm signature
- Search for prospective drug targets and treatments on the basis of DNAm data analysis
- DNAm signatures of CHARGE and Kabuki syndromes on the basis of GSE97362 dataset analysis
- Identification of shared DNAm changes between different pathologies
Schedule
Key benefits
No-coding bioinformatics
Perform cutting edge bioinformatics analysis in a user-friendly interface with no programming skills needed
Multi-omics
Learn how to process and integrate various omics data types in your analysis
Promoter analysis
Become the gene regulation expert with deep understanding of transcription factors interplay in various conditions
Pathway analysis
Discover the master regulators governing the studied biological processes through intracellular signaling pathways
Disease molecular mechanisms
Identify prospective biomarkers and drug targets for the pathologies of your interest by performing integrated promoter and pathway analysis
Gold standard tools and databases
Learn how to use the best-in-class knowledge bases on genes, proteins, transcription factors, pathways, drugs, and their targets, together with integrated tools
Testimonials
Coming soon
Promoter hunting with TRANSFAC
Hands-on training
Paid course, €299 per seat before VAT. Date and time will be announced soon.
In this course we will learn how to apply TRANSFAC and study promoters and enhancers.
The following questions will be covered:
My way from promoters to pathways
Paid course, €299 per seat before VAT. Date and time will be announced soon.
In this course we will:
Our lecturers
