PAGnetMRAInterface: PAGnet: Pseudomonas aeruginosa genomic integrated regulatory...

In huanghalone/PAGnet: PAGnet: Pseudomonas aeruginosa genomic integrated regulatory network.

Description

Master Regulator Analysis (MRA) for identification of key transcription factors mediating a biological process or pathway. First, the user can choose to use the default PAVIRnet or to upload their own regulatory network in a predefined format. Second, the user needs to specify a gene signature associated with a biological function or pathway of interest, either by selecting a gene set from public databases or uploading a user-customized gene list. In the current version, the platform provides gene sets in Gene Ontology (GO) and KEGG databases obtained from Pseudomonas Genome DB. Having completed master regulator analysis, a table will be returned with information about each transcription factor<e2><80><99>s corresponding gene ID, gene name, number of target genes, total number of hits (all signature genes in the network), observed hits (signature genes in the TF<e2><80><99>s regulon), and a p-value calculated based on a hypergeometric test. The table is sorted according to the statistical significance indicated by the p-values, and the top significant TFs can be prioritized as master regulators.

Usage

  pagnet.mra.interface()

Examples

  library(PAGnet)

  #To start interface, call pagnet.mra.interface
  pagnet.mra.interface()

huanghalone/PAGnet documentation built on May 28, 2019, 9 p.m.