Below you will find pages that utilize the taxonomy term “network clustering”
Blog
GO Enrichment of Network Clusters
In my previous post, I mentioned how I clustered the network we obtained at the end. For functional annotation gene ontology (GO) enrichment has been done on these clusters.
There were 20 clusters and the HGNC names are obtained separately for each cluster and using DAVID functional annotation tool API, GO and pathway annotations are collected per cluster and these are saved separately.
http://david.abcc.ncifcrf.gov/api.jsp?type=OFFICIAL_GENE_SYMBOL&tool=chartReport&annot=GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,BBID,BIOCARTA,KEGG_PATHWAY&ids=HGNC_NAME1,HGNC_NAME2,HGNC_NAME3,... Above URL was used to obtain chart report for some GO and pathways chart records.
Blog
Network Clustering with NeAT - RNSC Algorithm
As we have obtained proteins at different times points from the experimental data, then we have found intermediate nodes (from human interactome) using PCSF algorithm and finally with a special matrix from the network that PCSF created, we have validated the edges and also determined edge directions using an approach which a divide and conquer (ILP) approach for construction of large-scale signaling networks from PPI data. The resulting network is a directed network and will be used and visualized for further analyses.