OncoSignature - Drug response prediction on Acute Myeloid Leukemia

Copyright (C) 2019 Nicolàs Palacio
Contact: nicolas.palacio@bioquant.uni-heidelberg.de

Please, use the Github Issue page for questionts.

GNU-GLPv3:

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

A full copy of the GNU General Public License can be found on http://www.gnu.org/licenses/.

This repository contains the scripts used to analyze and extract phosphorylation signatures of drug response in AML samples.

1) Data normalization pipeline

Data cleaning + normalization + batch correction

2) Differential expression analysis

This script analyzes the differential expression between treated vs. untreted samples (responders and non-responders seperatedly) and between responders vs. non-responders before treatment

2.1) Differential expression plots

This script generates the volcano plots to visualize the differential expression results

2.2) Biomarkers of interest

This script tries to find interesting biomarkers based on the differential expression results. Phosphosites of interest are defined as follows:

2.3) Significant differential phosphorylation

This script subsets the differential expresssion results and saves a table for each contrast containing only the significantly differentially expressed p-sites.

3) Gene Set Enrichment Analysis

This script computes the GSEA with 11 different methods and generates a consensus score based on ranking

3.1) Gene set enrichment analysis plots

This script generates the plots to visualize the results of the GSEA

4) Kinase-substrate enrichment analysis

This script computes the kinase enrichment based on the differential phosphoproteomics data