ATAC-seq, CUT&RUN and Enhancers

Q&A: Coffee break with TRANSFAC

Analysis of Epigenomics and Transcriptomics Data

This event was held on May 14th, 2024

FREE online seminar

Seminar Description

In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will provide a general introduction into epigenomics and will analyze ATAC-seq data of BPTF knockouts in Acute Myeloid Leukemia (AML) (GSE226670) and ChIP-seq and CUT&RUN data of FOXO1 knockouts in diffuse large B-cell lymphoma (DLBCL) (GSE254405) for enriched transcription factor binding sites, composite modules and upstream regulators, via combined promoter and pathway analysis with TRANSFAC master-regulators and Genome Enhancer. 

The following main topics will be in the focus of this webinar:

  • 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

What you will learn in this webseminar 

  • How to identify peaks for ATAC-seq and CUT&RUN data
  • How to join and intersect peaks/tracks
  • How to identify TF-binding motifs enriched in a differential peak set
  • What is upstream analysis (combined promoter and pathway analysis)
  • How to find master regulators as potential drug targets

Seminar Schedule

The session started on May 14 with a lecture from Prof. Alexander Kel (approx. 1 hour) and was continued with a Q&A session addressing the questions coming from the attendees of the online event (up to 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 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 and students seeking ways to analyze biological data on gene regulation


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 duly licensed 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 TRANSFAC full package accounts.

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