Network biology lab
Nov 20, 2014
Lab materials (files)
• Parent_PPI: This is a highly-curated human protein
interaction network
• HT.pvals.out: Gene-based p-values (VEGAS) from a
GWAS in hypertension (HT)
• MS.pvals.out: Gene-based p-values (VEGAS) from a
GWAS in multiple sclerosis (MS)
• Cytoscape_import_attributes.txt: Gene-based pvalues from both GWAS and known associated genes
for importing into Cytoscape
Lab materials (code)
• qqplot.r: Script to run gene-wise Qqplot from each
• Manhattan plot.r: Script to run gene-wise Manhattan
plots from each GWAS
• Make_block.r: Script to compute association blocks
from both GWAS and plot them side by side
• Pathway_permutation.r: script to run background
distributions of networks of different sizes with
randomly selected nodes from the parent PPI. This
code also plots the distributions and the actual
number of significant genes (nodes) in the first order
Lab materials (software)
• Cytoscape 3.2
– Network analyzer (Core plugin)
– BINGO plugin
1. After exploring the Manhattan plots, qq-plots and association blocks from each
GWAS, what can you tell about the power of each study?
2. Using Cytoscape, analyze the PPI and describe its main network properties
3. Using Cytoscape, find the first order networks (p<0.05) for each GWAS
4. Are the first order networks from both GWAS more connected than expected?
What does this mean?
5. Run BINGO App on all nodes. nodes from largest connected component. What
biological processes emerge from the first order networks?
6. Run BINGO App on nodes from largest connected component. Interpret the results
7. Map and color known MS and HT genes onto their respective first order nets.
Interpret results.

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