Promoter Hunting with TRANSFAC

Online Course and Hands-on Training

€299* before VAT

* FREE for TRANSFAC licensed users

June 3-6, 5 PM CEST

Course Description

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.

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)
What you will learn:
  • How to conduct gene regulation studies starting from raw omics data
  • How to construct a site search profile optimized for the biological conditions under study
  • How to perform the site search analysis and how to interpret the obtained results
  • How to identify complexes of TFBS working together
  • How to select the actual transcription factors regulating the target genes
  • How to visualize the obtained results and prepare nice images for your publications

Course Schedule

(time CEST)

June 3

17:00 – 17:15

17:15 – 18:00

18:00 – 19:15

19:15 – 20:00

Group introduction

Lecture: Prediction of promoters and enhancers. Why doing it?

Demo and hands-on: How to start my first analysis of gene expression data? Loading my data. Finding DEGs. Applying GSEA, EdgeR, Limma, Heatmap. Ready for promoter analysis and site search.

Lecture: Search for transcription factor binding sites (TFBS). Selection of site search profiles.

Homework: hands-on training. Site search on gene set.

June 4

17:00 – 17:15

17:15 – 18:00

18:00 – 19:15

19:15 – 20:00

Q&A session; Sharing experience of hands-on training

Lecture: Combinatorial analysis of gene regulation. Application of machine learning (ML) and artificial intelligence (AI).

Demo and hands-on: Loading ChIP-seq/ATAC-seq and CUT&RUN data. Peak calling; converting genome builds; track intersection; Enhancers vs promoters. Ready for enhancer analysis.

Lecture: Search for transcription factors regulating your target genes in different tissues and diseases. 

Homework: hands-on training. Combinatorial analysis of gene regulation. Enhancer analysis.

June 5

17:00 – 17:15

17:15 – 18:00

18:00 – 19:15

19:15 – 20:00

Q&A session; Sharing experience of hands-on training

Lecture: Analysis of multi-omics data inside the geneXplain platform. 

Demo and hands-on: Combining ChIP-seq data with gene expression data. Ready for identification of composite regulatory modules.

Lecture: Principles of gene regulatory code. 

Homework: hands-on training. Analysis of combined RNA-seq and ChIP-seq data and identification of composite regulatory modules.

June 6

17:00 – 19:00

Open discussion of the obtained results. Group presentations.

June 7

Whole day

Free access to TRANSFAC omics – do whatever you like and save your results

What You Get

  • Lectures on gene regulation analysis provided by one of the key opinion makers in this field
  • Personal guidance from our experts during the hands-on trainings
  • 5-day full access to TRANSFAC, geneXplain platform, and MATCH Suite
  • Course completion certificate
  • 1 month access to all course materials

* The course is FREE for all licensed TRANSFAC users, for a coupon code please contact us via [email protected]

What Others Say About Our Educational Programs and Software

Click the images to read the text

The key lecturer

Prof. Dr. Alexander Kel CEO and CSO geneXplain GmbH

  • 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

Course assistants

Kamilya Altynbekova
  • Blending her Computer Science background with a passion for life sciences, Kamilya Altynbekova works as software developer at geneXplain
  • Kamilya’s main responsibility is the development for geneXplain platform, maintenance of the existing tools and integration of the new analysis
  • As a part of geneXplain team, Kamilya also participates in research projects by conducting data analysis to extract valuable insights from biological data, often dealing with large datasets
  • Daria Stelmashenko completed her studies in Moscow State University as a master of applied mathematics and cybernetics in 2009, since then she has been working in the bioinformatics industry for almost 15 years.
  • Daria is the co-author of novel approaches towards multi-omics data analysis, together with Prof. Dr. Alexandr Kel she was at the forefront of Genome Enhancer pipeline development.
  • Daria is the co-author of 18 scientific publications, she has vast experience in successfully receiving grant funding for various biomedical projects.
  • Daria was managing the development of MATCH Suite component of TRANSFAC 2.0 and is currently responsible for further development of several products within the geneXplain’s portfolio, including the Genome Enhancer pipeline for human multi-omics data analysis.

* The course is FREE for all licensed TRANSFAC users, for a coupon code please contact us via [email protected]

To Whom It Might Be Interesting

Audience

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

Course Prerequisites

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

FAQ

No worries! Everyone who signed up for the course will get access to the video records of the sessions and the presentation materials.

Sure! All course attendees will be able to reproduce the analysis steps shown by Prof. Dr. Alexander Kel during the online sessions using their geneXplain platform and TRANSFAC accounts (respective licenses are included throughout the whole course duration).

Unfortunately, it’s not possible to shift or cancel the course and get a refund. The dates are fixed and we can’t make any changes.

Absolutely not! It’s a no-coding academy that teaches you how to perform top-level bioinformatics analysis using tools with a user-friendly graphical interface. You’re gonna love it!

Join the course to become a true gene regulation expert.

Learn how to proceed from raw omics data to the gene lists describing the biological process under study followed by the understanding of regulation mechanisms underlying the studied condition.

* The course is FREE for all licensed TRANSFAC users, for a coupon code please contact us via [email protected]