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The twenty ninth coffee break with TRANSFAC

This video is a record of the live session "The twenty ninth Coffee break with TRANSFAC" that was held on 20th of August 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: 00:49 Gene regulation principles. Epigenetic regulation of gene expression. 04:17 Experimental methods for TF binding analysis. ChIP-seq, ATAC-seq, CUT&RUN. 10:45 Processing of ChIP-seq, ATAC-seq, CUT&RUN data. Peak calling algorithms. 15:22 Search for enriched TFBS in peaks. 17:36 geneXplain platform for analysis of ChIP-seq, ATAC-seq, CUT&RUN data 19:01 Example analysis of ChIP-seq data generated from HeLa cells with antibody to ETF1 (fastq data analysis from GSM558469 https://www.ncbi.nlm.nih.gov/geo/quer...) 21:49 Alignment of fastq file: mapping to genome using Bowtie2 23:50 BAM file visualization on genome browser 25:16 Peak calling with MACS. Finding clusters of peaks 30:09 Search for enriched TFBS in clusters of peaks 40:00 Example analysis of ChIP-seq, CUT&RUN and transcriptomics data generated for B-cell lymphoma before and after FOXO1 inhibition (data from GSE254405 https://www.ncbi.nlm.nih.gov/geo/quer...) 44:31 Modules of transcription factors working together: CMA for search of binding site compositions 45:49 How much time will an analysis take from data loading, e.g. 2GB, to receiving a result? 46:38 Applying Genome Enhancer for analysis of data from example GSE254405 (integrated CUT&RUN and transcriptomics data analysis) 51:20 Algorithm underlying the integrated analysis of transcriptomics and epigenomics data in Genome Enhancer 53:43 Analysis launch interface in Genome Enhancer 56:56 Genome Enhancer analysis report overview 01:02:51 Can we use this analysis in plant science research to develop climate-resilient crops 01:06:10 For peak calling of CUT&RUN histone reads, is SEACR better than MACS in your experience? 01:09:00 Can we use this analysis for microbe genomes? 1:12:12 What are the limitations of CUT & RUN Seq Analysis?