https://github.com/saezlab/permedcoe_summer_school_2023
PerMedCoE summer school 2023
https://github.com/saezlab/permedcoe_summer_school_2023
Last synced: over 1 year ago
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PerMedCoE summer school 2023
- Host: GitHub
- URL: https://github.com/saezlab/permedcoe_summer_school_2023
- Owner: saezlab
- Created: 2023-06-12T09:23:38.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2023-06-25T17:52:47.000Z (about 3 years ago)
- Last Synced: 2025-03-28T05:51:01.799Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 44.1 MB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# PerMedCoE Summer School 2023: From transcriptomics to mechanistic models of signalling
## Overview
Cellular signalling networks are the communication pathways that govern the behaviour of cells. They allow cells to receive and process external signals, such as growth factors and hormones, and respond appropriately by activating specific gene expression programs or inducing cellular behaviours like proliferation, migration, and differentiation. Disruptions in these signalling networks can lead to various diseases, including cancer, metabolic disorders, and immune disorders. Understanding the regulatory mechanisms of signalling networks is critical to developing effective therapies for these diseases.
One approach to discover signalling network alterations from omics data is through the use of upstream regulatory pathway analysis, which aims to identify the transcription factors and upstream signalling regulators that control the expression of downstream genes. This can be achieved through the joint analysis of omics data and the signalling network structure using methods such as CARNIVAL. By using powerful algorithms and general purpose integer optimization solvers, CARNIVAL explores the vast space of potential signalling alterations to identify a parsimonious signalling network that explains the measurements.
In this course, participants will learn how to process differential gene expression data to estimate transcription factor activities with DecoupleR, obtain and process prior knowledge networks with OmniPath and pypath, and use CARNIVAL to infer signalling networks.
## Learning outcomes
At the end of these sessions, the participants will be able to:
- Obtain custom networks of causal interactions from public databases
- Combine these networks with molecular biological activities from experimental data
- Apply causal reasoning to find the most plausible causal mechanisms that explain the observed activity patterns
- Use CARNIVAL to customise the contextualisation of signalling networks
## Trainers
- Pablo Rodriguez Mier*
- Denes Turei*
>*Saez-Rodriguez Group, Institute for Computational Biomedicine, Heidelberg University
If you have any questions or comments, you can contact Daniel Thomas López (dthlopez@ebi.ac.uk).
Visit PerMedCoE website to read about our activities, including training events, materials, and webinars.
