Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.
|Author||Junwei Han, Zeguo Sun|
|Date of publication||2016-05-16 14:45:44|
|Maintainer||Junwei Han <firstname.lastname@example.org>|
|License||GPL (>= 2)|
drawAHeatMap: Draw a heatmap for the genes of a pathway
findSigGenes: Find genes significantly differentially expressed between two...
geneSetDetail: Gain insight into the detail of the genes in a certain...
getExampleData: Get the example data
getNet: Get the background lncRNA-mRNA interaction network
lncPath: Identify pathways synergisticly regulated by lncRNA sets.
lncPath2Table: Simplify the lncPath object into table
LncPathEnvir: The variables in the environment variable 'LncPathEnvir' of...
LncPath-internal: LncPath internal functions
plotRunningES: Visualize the Kolmogorov-Smirnov running score of pathway
printSignifResult: Output the details of significant pathways