gene network analysis

Question

[nitishd.dave]

Hello, I have been asked to do network analysis of a gene with a set of other genes (co-expression network) but I am new to this, so can anyone help me out or can give step by step guidance I tried GENEMANIA online tool AND learned the basics, however, there is still certain query regarding which algorithm to use in co-expression network analysis and how to interpret the resultant network.

Thank you.......

[arta]

Have you tried WGCNA package from R. You can also read their paper if you would like to gain more theoretical information.

[Kevin Blighe]

For one, I put a tutorial here: Network plot from expression data in R using igraph

Also look at these:

• how to get genes and their interactions from RNA-Seq data?
• Which method do you use to build adjacency matrix of a genes co-expression network?
• How to define regulatory role by gene A upon B
• Network analysis software

[nitishd.dave]

thank you kevin actually my work include to find out a set of genes which are co-expressing with SOS1 gene which is found in Arabidopsis thaliana and then to find out orthologs of that co-expressed gene in Populus tree species. so, can you please tell me how it is done. thanks again.

[Kevin Blighe]

There is a way to make a particular gene the focus of a network and to check it's interactions as first neighbours. We (well, my colleague) did this recently for the TTN gene using Cytoscape. Take a look at Figure 6 of our pre-print:

• New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks