---
date: 2024-11-18
type: daily
tags: [lab-notes]
---

# 2024-11-18 - Monday

## Experiments

Started [[Experiment-2024-11-18]] - [[PPI Network Analysis]] for EGFR pathway.

- Downloaded STRING [[Database]] (experimental interactions [[Only]])
- Filtered to confidence > 0.7 → 324 proteins, 1,892 edges
- Computed centrality metrics [[Using]] NetworkX
  - Degree: EGFR (47), GRB2 (38), SRC (35)
  - Betweenness: SHC1, GAB1, STAT3 [[Are]] bottlenecks

**[[Key]] insight**: Hub proteins match known cancer drivers. Betweenness identifies scaffolding proteins.

## Analysis

[[Community Detection]] [[Found]] 8 functional modules:
- RTK signaling [[Core]]
- MAPK cascade
- PI3K/AKT pathway
- JAK/STAT pathway

## [[Next Steps]]

- Validate hub proteins experimentally
- Plan [[CRISPR Knockout]] screen for Tuesday

## Papers Read

Reviewed [[Barabasi2004-Network-Biology]] for centrality interpretation.

## Notes

Network topology strongly predictive of biological function. [[High]]-degree nodes are disease-critical.
