Promoter analysis of model organisms

Q&A: Coffee break with TRANSFAC

Event was held on March 12, 2024

FREE online seminar

Seminar Description

In this “Coffee break with TRANSFAC” we will apply TRANSFAC to study different model organisms.

We will analyse 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 (using CMA – Composite Module Analyst and fly genome integrated into the geneXplain platform).

As usual, the event will be hosted by Prof. Dr. Alexander Kel.

The following main questions will be in the focus at this seminar:

  • 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?

What you will learn in this webseminar 

  • TRANSFAC database and geneXplain platform – brief overview.
  • Principles of site enrichment analysis.
  • Site combinations: complexes of transcription factor binding sites; composite modules.
  • To which extend can we apply TRANSFAC for different model organisms?
  • Example of analysis of drosophila genes from GEO:GSE149116 – combination of RNA-seq and ChIP-seq data.
  • Intersection of RNA-seq data with ChIP-seq data.
  • How site search summary looks like in the geneXplain platform?
  • Identification of “master” transcription factors working together in combinations; CMA (Composite Module Analyst) analysis in the geneXplain platform.
  • Can we use other genomes (other than human) for TFBS analysis with TRANSFAC in the geneXplain platform?

Seminar Schedule

The session will start on March 12, 6 PM CET with a lecture from Prof. Alexander Kel (approx. 1 hour) and will be continued with a Q&A session addressing the questions coming from the attendees of the online event (approx. 30 minutes).

What You Get

  • 1 hour lecture on gene regulation analysis provided by one of the key opinion makers in this field
  • 30 minutes interactive Q&A session addressing your questions regarding tissue specific search for TFBS
  • Time-unlimited access to the video record of the session

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The Lecturer

  • Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990 and has has over 35 years of research experience in Bioinformatics
  • He studied at Novosibirsk State University, obtaining an M.S. in biology with a focus on mathematical biology in 1985
  • His work spans numerous bioinformatics branches (sequence analysis, gene recognition, promoter/enhancer analysis and prediction, prediction of RNA secondary structure, analysis of signal transduction pathways, identification of drug targets, systems biology and systems medicine)
  • He is the originator of the “fuzzy puzzle” concept for gene regulatory regions modeling
  • Developed “upstream analysis” for identifying biomarkers and drug targets in various diseases
  • Participated in over 20 national and international research projects
  • Author of more than 130 scientific publications and several book chapters on bioinformatics and systems biology
  • CEO and CSO of geneXplain GmbH, Wolfenbüttel, Germany
  • Visiting Professor at Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland


Basic knowledge of biochemistry and molecular biology. No programming skills are required.

To Whom It Might Be Interesting

  • Bench biologists seeking for ways to deal with sequencing data in order to discover what is hidden there in terms of genes, promoters, and repressors


That’s ok! All registered course attendees will receive access to the video record of the session together with the presentation materials. 

You can ask your questions live during the online event using the Q&A section of the online webinar, or you can send us your questions in advance using the form on this page and Prof. Dr. Alexander Kel will address them at the online event.

Sure! All licensed TRANSFAC users will be able to repeat all steps of the analysis that will be shown by Prof. Dr. Alexander Kel during the online event using their geneXplain platform and TRANSFAC accounts.

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