topic02_team04

Project description

In this project, we used RNASeq and protemics data from The Cancer Genome Atlas (TCGA) to analyze the activity of cancer hallmark and metabolic pathways across 33 cancer types with a focus on prostate adenocarcinoma (PRAD). After identifying and filtering pathway gene sets, we assessed pathway activity using GSVA and limma to compare and cluster samples and cancer types. Similarly, we compared pathway activities between tumor and normal tissue in PRAD samples and examined the correlation of RNA-level pathway activity with proteome data. To classify PRAD samples as tumor or normal based on pathway activity scores, we trained and evaluated a logistic regression model.

Repo structure

• FINAL MARKDOWN.Rmd in the root directory contains the analysis scripts for all objectives
• FINAL MARKDOWN.html and FINAL MARKDOWN.pdf contain the knitted analysis script
• the data folder contains raw and processed data (see below for setup instructions)
• the figures folder contains a folder for each objective with the main figures saved as .png or .pdf
• the scripts folder contains analysis scripts for each objective, in part with additional steps and biological interpretation

Data setup

Due to file size, raw data are not included in this repository. Before running the code, please follow these steps for setup.

1. Clone and pull the repo.
2. Please download the TCGA .rds files and place them in : data/raw/ using the default file names given in the official project description .README. The analysis script assumes this structure.
3. Open the R project topic02_tem04.Rproj using RStudio and run FINAL MARKDOWN.Rmd from the Files tab.

Affiliation and AI usage

This project is part of the "Methoden der Bioinformatik" course in the summer term 2026 for the bachelor's program in molecular biotechnology at Heidelberg University.
The following AI / LLM tools were used during the project:

Model	Scope	Purpose of use
Claude Sonnet 4.6 / 5 (Anthropic)	entire code	literature search, code generation and improvement, including plots and analysis functions
ChatGPT 5.5 (OpenAI)	entire code	literature search, code generation and improvement, including plots and analysis functions