Identifying the Pathways Regulated by LncRNA Sets of Interest
Draw a heatmap for the genes of a pathway
Find genes significantly differentially expressed between two conditio...
Gain insight into the detail of the genes in a certain pathway
Get the example data
Get the background lncRNA-mRNA interaction network
LncPath internal functions
Identify pathways synergisticly regulated by lncRNA sets.
Simplify the lncPath object into table
Visualize the Kolmogorov-Smirnov running score of pathway
Output the details of significant pathways
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.