gene network analysis
0
0
Entering edit mode
3.1 years ago
nitishd.dave ▴ 20

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.......

network analysis • 1.0k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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:

ADD REPLY

Login before adding your answer.

Traffic: 2597 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6