Gene Regulation Network

Information

To predict a gene regulation network to identify similarity among gene expression across different experiments using a R package called BUS. The gene network will be displayed using CytoscapeJS

BUS: Jin Y, Peng H, Wang L, Fronza R, Liu Y and Nardini C (2010). BUS: Gene network reconstruction. R package version 1.28.0.
CytoscapeJS: Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003 Nov; 13(11):2498-504

Network Prediction

The BUS package allows computation of two similarities, correlation and mutual information
Mutual information is a quantification of dependency between random variables based on the difference between conditional and unconditional entropies. It captures nonlinear dependence.
Steps:
gene.similarity() calculate adjacency matrix using mutual information metric for gene-gene interaction.
gene.pvalue() calculates p-value for gene-gene interaction. The null hypothesis is that there is no gene-gene interaction.
pred.network() To predict the gene network, based on the similarity matrix and filtered according to a corrected p-value matrix.

Instructions

Steps to follow

Click on Select experiments and select the experiments to be considered for gene network prediction
Below the label Filter by expression value
- Select the experiment from the dropdown menu
- Select the operand (less than and equal to or more than and equal to) from the dropdown menu
- Enter the integer value for the cutoff
Step 1: Click on Count to get the count of gene ids that are considered for the network analysis.
NOTE: Please make sure the number of genes is less than 100.
Step 2: Click on Network to generate the network using Cytoscape.
Wait for the page to load the gene network
Feel free to zoom in, zoom out and move around. Click on the nodes to get gene id and gene description in the box below

Select Experiments

ear and tassel development series [select all]

ramosa series [unselect all]

fasciated ear4 (fea4) experiment [unselect all]

knotted1 [unselect all]

nod (in RPM) [select all]