TRANSFAC download webinar

TRANSFAC download

Software demo: Coffee break with TRANSFAC

This event was held on May 28th, 2024

FREE online seminar

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Seminar Description

Download TRANSFAC and do whatever you like

Introduction to the TRANSFAC flat file download release

TRANSFAC® (including TRANSCompel® and TANSPro™) contains eukaryotic transcription factors (and miRNAs), their experimentally determined genomic binding sites and consensus DNA-binding motifs (PWMs), as well as data on combinatorial gene regulation and factor-factor interaction.

Promoters, enhancers and silencers annotated with transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project and from other sources complement the manually curated binding site data.

Based on the positional weight matrices (PWMs) transcription factor binding sites can be predicted in regulatory regions (with Match™).

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.

This webseminar will give a brief overview of TRANSFAC® with the focus on the flat file download release.

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

Factor-site binding
Factor-factor interaction
Combinatorial gene regulation
Gene regulatory networks
Promoters & Enhancers
Factor classification
TF-binding motifs (PWMs)
TF-binding site prediction

What you will learn in this webseminar

Content of TRANSFAC
Data structure of the TRANSFAC flat files
Differences between the download and the online release
TF-consensus binding motifs in the form of PWMs
TF-binding site prediction using the command line with the Java Match Library

Seminar Schedule

The session started on May 28 with a lecture and software demo from Dr. Volker Matys and Kamilya Altynbekova (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 and software demo on gene regulation analysis provided by TRANSFAC experts
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 Lecturers

Prof. Dr. Alexander Kel

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

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

Dr. Volker Matys

Dr. Volker Matys, graduated in Biology at the University of Freiburg, Germany with a thesis in Molecular Biology (based on experimental research conducted at St. George’s Hospital Medical School, London)
Volker has been working on TRANSFAC for more than twenty years in various functions, initially as a database curator and editor, and later in quality control and customer support

Prerequisites

Basic knowledge of biochemistry and molecular biology. Being familiar with the use of Java-based or other command line tools. Data extraction from the flat files requires programming skills (or SQL).

To Whom It Might Be Interesting

Bioinformaticians who want to extract data on gene regulation for use with the included command line tools or with their own or third-party tools.

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 the form on this page and our experts will address them at the online event.

Sure! All duly licensed TRANSFAC download users will be able to repeat all steps of the analysis that will be shown by our experts during the online event.

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