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The twenty first coffee break with TRANSFAC

This video is a record of the live session "The twenty first Coffee break with TRANSFAC" that was held on 16th of April 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: 00:21 Why do you need to analyze anything using TRANSFAC? Why do you need to predict TFBS? 02:57 Starting TRANSFAC analysis from scratch: TRANSFAC database overview 10:00 Observing the geneXplain platform tools 17:47 Uploading a gene list to the geneXplain platform 23:35 Transcription factors, their binding sites and models for their prediction 31:14 Does TRANSFAC DB include data on all the three layers about a specific TF (means adaptor, co-activator)? 33:08 Motif scanning: how scores are calculated (Sum of the contribution of each nucleotide calculated independently (like in HOMER) versus sum of the contribution of each nucleotide multiplied by an information vector (like in MATCH)) 38:20 Calculation of optimized cut-offs for PWMs 43:02 Why a NO set (control) is needed for searching for TFBS. Enrichment analysis. 45:37 Site search on gene set in the geneXplain platform (MATCH): analysis launch and results overview 01:02:27 Visualization of found sites in the genome browser 01:04:10 HOMER and other Galaxy tools in the geneXplain platform 01:07:34 Whatever analysis is done, is there a summary report generated? 01:10:16 Will there be any sessions on miRNA target prediction in future?