A network propagation based method for inferring the perturbed microRNA regulatory networks from gene expression data


This network propagation based method (NP-method), which takes advantage of the global network differential information, carries out a integrated random walk plus forward searching algorithm to infer the perturbed miRNAs as well as their leading-edge target genes.

Get NP-method

The lastest release is programmed with R language.

Scripts can be downloaded here.

Supporting and test data can be downloaded here.

How to use

See details in README.

Simple usage:

Step 1: precalculate M matrix using precalculate_M.R

Step 2: get foreground NPESs for miRNAs using NP.fg.R

Step 3: get background NPES distributions for miRNAs using NP.bg.R

Step 4: normalize NPESs and get p-values for miRNAs using NP.pvalue.R


Please feel free to contact us when you have questions.

Ting Wang (wang9ting@gmail.com) or Jin Gu (wellgoo@gmail.com)