How to find tissue-specific transcription factor (TF) target genes?

Online seminar

Free

This event was held on 6 February, 2024

Seminar Description

In this seminar Prof. Alexander Kel will share with you the latest intriguing insides in mechanisms of gene regulation. He will demonstrate how to perform tissue-specific gene regulation analysis and find enriched motifs using TRANSFAC database and its tool as: MATCH Suite.

The following topics will be addressed: 

  • 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?

Seminar Schedule

The session will start on February 6th at 6:00 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

What Others Say About Our Educational Programs and Software

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

Key learning points and questions that will be addressed:

  • How to find tissue-specific transcription factors regulating the selected genes from the tissue of your interest?
  • Position Weight Matrices (PWMs). Why they are important? What else can be used to find TF binding sites?
  • Does one PWM describe TF sites for one transcription factor only (e.g. STAT-1) or for the whole family of factors (STAT-1, STAT-2,….)? 
  • What are the algorithms for predicting TF binding sites in DNA based on positional weight matrices?    How to define the cut-offs for binding sites scores of PWMs?
  • In calculating FP (false positives) and FN (false negatives) you need to know the true binding sites. How are they determined?
  • Conserved TF binding sites. Are they the only true TF binding sites? How important are they? What is phylogenetic footprinting and how to use it while searching for TF binding sites that regulate the genes of your interest?
  • How to integrate transcriptome (RNA-seq) and epigenome (ATAC-seq) data in one TRANSFAC analysis?

Who Would Love Our Course?

  • Researchers interested in tissue-specific gene regulation principles
  • Bench biologists seeking for ways to deal with their sequencing data without any prior bioinformatics or coding experience

FAQ

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 this form 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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