Functionality

Functionality implemented in the Reactome FI Cytoscape plugin

2009 Network URL: http://reactomews.oicr.on.ca:8080/caBigR3WebApp/FIService/ 2012 Network URL: http://reactomews.oicr.on.ca:8080/caBigR3WebApp2012/FIService/

Gene set/mutation analysis

• Load file
  • simple gene set (one line per file)
  • gene/sample number pair
  • NCI MAF
• Specify sample count cutoff
• Construct FI network
  • path: /queryAllFIs
  • produces: text
• Fetch FI annotations
• Analyze network functions
  • path: /annotateGeneSet/{type}
  • type one of {Pathway, BP, CC, MF}
  • consumes: text
  • produces: XML, JSON
• Cluster FI network
  • path: /cluster
  • consumes: text
  • produces: XML, JSON
• Analyze module functions
  • path: /annotateGeneSet/{type}
  • type one of {Pathway, BP, CC, MF}
  • consumes: text
  • produces: XML, JSON

HotNet mutation analysis

• Select FI network version
• Load file (NCI MAF only)
• Set Options
  • delta (float/auto,FDR)

  • permutations (max 1000)

• Generate network modules
• Set size cutoff, FDR cutoff
• Generate subnetwork

Microarray data analysis

• Load file (TSV, genes in first column, sample gene expression in others)
• Set options
  • inflation parameter
  • use absolute values
• Generate network modules
• Set module filter
  • size
  • average correlation
• Generate subnetwork

Query FI source

• retrieve annotation for network edge

Fetch FIs for node

• retrieve annotated FIs for selected node

Show pathway diagram

• retrieve a pathway diagram (node genes in KEGG pathway shown in red)

Load cancer gene index annotations

• Load NCI disease terms tree
  • select disease which will show nodes with an annotation for that disease
• View detailed annotations for selected node

Survival analysis

• Network must have already been created
• Load file
  • 3 columns (headers: Samples, OSDURATION, OSEVENT)
• Choose survival analysis model
  • coxph
  • Kaplan-Meyer
    • choose module