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The seventeenth coffee break with TRANSFAC

This video is a record of the live session "The seventeenth Coffee break with TRANSFAC" that was held on 12th of March 2024. The event was hosted by Dr. Alexander Kel, CEO of geneXplain GmbH. The aim of this series of recurrent events titled as "Coffee break with TRANSFAC" is to provide answers to the questions of our audience in regards to the field of applied bioinformatics. You can find further info about the "Coffee break with TRANSFAC" initiative at https://genexplain.com/ask The list of questions that were addressed within this session and their time codes: 01:11 Number of different positional weight matrices (PWMs) or motifs contained in TRANSFAC for various organisms 02:56 Matrix construction for TRANSFAC database 04:08 Site enrichment analysis using TRANSFAC PWMs 06:07 Composite elements of transcription factors in gene regulation 07:16 Genetic algorithm for identification of TFBS combinations 10:45 geneXplain platform overview 13:03 Example: RNA-seq and ChIP-seq data analysis from Drosophila melanogaster (GEO: GSE149116) Spoiler: human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors acting as master transcription factors autophagy regulation! It appeared that transgenically expressed human ZKSCAN3 gene in drosophila started to regulate many drosophila genes binding to the same sites as endogenous M1BP factor. 18:20 Starting an integrated ChIP-seq and RNA-seq analysis inside the geneXplain platform: using DEGs from transgenic drosophila when compared to the wild type, and ChIP-seq peaks for the antibody for human ZKSCAN3 transcription factor from GEO: GSE149116 24:17 Is there a "proper" promoter length for performing the analysis? 28:35 What is the advantage of using the geneXplain platform to see the results of this type of experiment (integrated ChIP-seq and RNA-seq analysis) instead of using the IGV like apps? 32:39 Analysis of DEGs regulation in the geneXplain platform: filtering of a table with DEGs and selecting the ChIP-seq peaks located near the significantly differentially expressed genes using the filter one track by another function 40:38 Finding enriched motifs in tracks constructed as ChIP-seq peaks located around the upregulated genes 45:47 Results overview and interpretation for the identification of enriched motifs in tracks (site search summary and MATCH track) 50:35 Launching the CMA (Composite Module Analyst) analysis, and CMA results overview 57:53 What can TRANSFAC do in relation to enhancer sequences? 01:03:36 Are there also curated СhIP-seq datasets in TRANSFAC that can be used / compared along with own data? 01:07:33 Experimentally proven TFBS in TRANSFAC 01:09:24 The genome used for human is hg38, but is it the canonical version or the whole assembly?