Medizininformatik - Components Interactions and Networks

Introduction into Regulatory Genomics

Teachers

  • Carl Herrmann (carl.herrmann (at) uni-heidelberg.de)

Dates

Content

The purpose of this lecture is to provide an introduction to the concepts of regulatory genomics in the age of high throughput sequencing. We will introduce

  • the general concepts of transcriptional regulation
  • the data of sequencing data that is available (ChIP-seq, RNA-seq, Hi-C, ATAC-seq, …)
  • the role of transcription factors (TFBS binding models, position weight matrices,…)
  • the integration of different data layers (example of ChromHMM)
  • some insights into bayesian networks modelling

Practical application (30.10.2025)

  • Download the json file [here]
  • Load it into the IGV App using the Session menu on the top.

  • Try to answer the following questions

    • What kind of data is displayed in the app?
    • For each histone mark, try to characterize its shape/localization
    • What is displayed at the bottom of the window?
    • What is the difference between the two RNA-seq tracks at the bottom? (Hint: look exactly at the genes below…)
    • Search for the MYC gene in the search window (top left). Can you identify a regulatory element based on the Hi-C track (you might need to zoom out…). Is there something special at the locus of the regulatory element (histone mark,…)
    • IN the Menu, select “Tracks > ENCODE Other… > “ and search for “MCF 10A HiC”; load the “loops” track; this is another cell line, do you note differences to the K562 cell line?