Skip to content

Attendence Yichen #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
yiczhu1 wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Attendence Yichen #11

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,12 @@
# Metabolic pathway analysis for Reactome pathways

**Input:** High-throughput metabolite levels for condition and control samples
**Overview:**
MPA is an R package and application that identifies perturbed metabolic pathways from high-throughput metabolite data. It leverages pathway information from the Reactome database to score and rank pathways based on how disrupted they are under experimental conditions.

**Output:** Ranked list of Reactome pathways that perturbed in the condition under study – the rank is based on a score or p-value that results from evaluating the pathway disruption given the data and the pathway information from the Reactome database
### How It Works

1. **Input:** High-throughput metabolite levels for condition and control samples

2. **Score computation:** For each pathway, individual reaction perturbation scores are calculated using log₂ fold-change of condition vs. control metabolite levels. These are aggregated into an overall pathway perturbation score.

3. **Output:** Ranked list of Reactome pathways that perturbed in the condition under study – the rank is based on a score or p-value that results from evaluating the pathway disruption given the data and the pathway information from the Reactome database