Question: gene network analysis
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gravatar for nitishd.dave
2.6 years ago by
nitishd.dave20
India
nitishd.dave20 wrote:

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 • 844 views
ADD COMMENTlink written 2.6 years ago by nitishd.dave20

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

ADD REPLYlink written 2.6 years ago by arta600

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

Also look at these:

ADD REPLYlink written 2.6 years ago by Kevin Blighe66k

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 REPLYlink written 2.6 years ago by nitishd.dave20

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 REPLYlink written 2.6 years ago by Kevin Blighe66k
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