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netboxr (version 1.6.0)

Gene list:

A newline-delimited text file that contains a list of genes of interest

P-Value Cut-Off:

The corrected p-value (or q-value) cut-off to apply for the graph output. Default: 0.05

Community detection method:

Community detection methods include edge betweenness score (EBC), leading eigenvector method (LEC), Louvain method (LOUV), or Leiden method (LEID). Default: EBC

Global network null model:

Perform global network null model analysis. The global network null model calculates the empirical p-value as the number of times (over a set of iterations) the size of the largest connected component (the giant component) in the network coming from the same number of randomly selected genes equals or exceeds the size of the largest connected component in the observed network. Default: Yes

Global network null model iterations:

Global network null model iterations. Recommended: 1000

Global network model number of genes:

Global network null model number of genes.

Local network null model:

Perform local network null model analysis. The local network null model evaluates the deviation of modularity in the observed network from modularity distribution in the random network. Default: Yes

Local network null model iterations:

Local network null model iterations. Recommended: 1000

Network plot:

Output the annotated graph of netboxr output. Default: Yes

Network plot width:

Plot width. Recommended: 9

Network in SIF format:

Output the network in SIF format. Default: Yes

Neighbor list:

Output a table containing the information of all neighbor nodes. Default: Yes

Module membership:

Output a table containing the identified pathway module numbers. Default: Yes

Node type:

Output a table containing the information of node types. Default: Yes

NetBox is a network-based approach that combines prior knowledge with a network clustering algorithm. The algorithm allows for the identification of functional modules and allows for combining multiple data types, such as mutations and copy number alterations. NetBox performs network analysis on human interaction networks, and comes pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.

INPUTS

Gene list A newline-delimited text file that contains a list of genes of interest is required.

Example of text file contents:

EGFR TP53 ACTB GAPDH

Cutoff value The corrected p-value (or q-value) cut-off to apply for the graph output. The default p-value is 0.05.

OUTPUTS

A PDF with a plot of the edge annotated graph (optional)
A text file with tabular data containing information of all neighbor nodes (optional)