This is the accompanying website of the ISMB tutorial about epigenomics data analysis held in Prague on the 21st of July. It contains the schedule as well as information, and will be extended to contain all the data and software necessary for the tutorial.
NOTE: The final version of the tutorial material will be available at 19.07.2017 at the latest.
- Dr. Ivan G. Costa, RWTH Aachen University, Germany
- Dr. Marcel Schulz, Saarland University & Max Planck Institute for Informatics, Germany
- Dr. Matthias Heinig, Helmholtz Center Munich, Germany
One of the main molecular mechanisms controlling the temporal and spatial expression of genes is transcriptional regulation. In this process, transcription factors (TFs) bind to the promoter and enhancers in the vicinity of a gene to recruit (or block) the transcriptional machinery and start gene expression. Inference of gene regulatory networks, i.e. factors controlling the expression of a particular gene, is a key challenge when studying development and disease progression. The availability of different experimental assays (Histone ChIP-seq, Dnase1-seq, ATAC-seq, NOME-seq etc.) that allow to map in-vivo chromatin dynamics and gene expression (RNA-seq), has triggered the development of novel computational modelling approaches for accurate prediction of TF binding and activity by integrating these diverse epigenomic datasets. However, in practice researchers are faced with the problems that come with handling diverse assays, understanding the tools involved and building specific workflows that are tailored to the data they have.
This tutorial is targeted to an audience of bioinformaticians with previous experience in gene expression and next generation sequencing analysis. This Intermediary level tutorial will provide you knowledge on the use of state-of-art tools for inference of gene regulatory networks from chromatin and expression data. First, we will review tools to conduct the following analyses: 1) predict regulatory regions from different epigenetic datasets, e.g., using differential peak callers (histoneHMM - Heinig et al., 2015) or footprint methods (HINT - Gusmao et al., 2014) and 2) show how to determine cell-specific TF binding in these regions (e.g. TEPIC - Schmidt et al. 2016) and 3) build regulatory networks to study a cell type of interest (e.g. Schmidt et al. 2016, Durek et al. 2016). After introductory presentation we will guide participants through a hands on practical. Therefore, we require that all participants bring their own laptop. Software that needs to be installed before the tutorial as well as data used in the tutorial will be made available on this website.
We have created a ReadTheDocs documentation for the participants to setup the software for the tutorial and for publishing the final working examples, accessible here.
| Time | Topic | Who |
|---|---|---|
| 2:30 - 2:45 | Introduction / gene regulation / transcription / chromatin | Ivan G. Costa |
| 2:45 - 3:00 | Introduction ChIP-seq peak calling | Matthias Heinig |
| 3:00 - 3:50 | Practical peak calling | Matthias Heinig |
| 4:00 - 4:15 | Coffee break | |
| 4:15 - 4:30 | Introduction footprints | Ivan G. Costa |
| 4:30 - 4:45 | Introduction regulatory networks | Marcel Schulz |
| 4:45 - 5:50 | Practical regulatory networks | Ivan G. Costa and Marcel Schulz |
| 5:50 - 6:00 | Q & A session | all |