Lecture 9
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- Title: what to do with the networks!?!
Contents
MCODE
- Vertex weighting: weight is high if has high core
- module detection - specify threshold (e.g. 2), decision which modules are included
- post processing - filter out, look at density, modules may overlap; haircut, remove vertices that are singly connection
other algorithms
- MCL
- k-means - divide into k groups
- pinnacle-z
function prediction
- predict function by looking at the neighbors
- Biological roles
- GO - divide processes, cellular component, molecular function - Ashburner, nature genetics 2000
- KEGG - manually curated biological processes
- MIPS
function-prediction methods
- majority-rule - consider neighbors and take most frequent annotation.
- neighborhood enrichment - look at all proteins within a particular radius
- minimum-multiway cut - find multicut minimizing crossing edges
- helps decide which nodes belong to which modules
- functional flow - choose start module and push water through the network, helps decide
- this one looks good!
networks and gene expression
- party hub - multiple proteins at once - high correlation of expression with neighbors
- date hub - one interaction at a time - lower correlation, most likely a regulator
- if presence highly correlated, may not interact but may be part of similar pathway
networks and disease
- scale-free networks, most nodes low degree, a few hubs, very robust
- disease perturbed subnetworks
SECTION 2: CYTOSCAPE
- MCODE plug in to cytoscape to help figure out subnetworks/modules
- BiNGO - enrich networks with gene ontology