Question: Gene network comparison
gravatar for giuseppe.minardi95
6 months ago by
giuseppe.minardi9510 wrote:

For an University project I have two networks from A. Thaliana and V. Vinifera both regarding the ERF superfamily, my goal is to extract information from both of them. I have little knowledge of graph theory and I know absolute nothing about biological networks. Which analysis can I perform in order to compare them?

rna-seq gene • 261 views
ADD COMMENTlink written 6 months ago by giuseppe.minardi9510

What is the question you want to address ?

ADD REPLYlink written 6 months ago by Jean-Karim Heriche20k

Mainly infer putative function in Vitis given omologus genes from arabidopsis

ADD REPLYlink written 6 months ago by giuseppe.minardi9510

You don't have to use graphs for this. This is usually addressed by transferring functional annotations by orthology, i.e. an unannotated gene inherits functional annotations from its orthologs in other species. Staying at the simple level of sequence homology is less precise. However, if you need to use graphs for this, I think what you're looking for are subgraphs or modules that are common to both networks such that you can transfer the function from one annotated subgraph/module to its equivalent in the other graph. There is a whole litterature on subgraph mining. If most of the nodes in the two graphs can be matched one to one, you could try co-clustering the two graphs using tensor factorization.

ADD REPLYlink written 6 months ago by Jean-Karim Heriche20k

If you’ve asked your question like this:

gene network analysis by cytoscape

you would find some useful posts, for example:

Clustering Analysis In Gene Coexpression Network

network with cytoscape

Cytoscape network of upregulate and downregulate transcription factors: how to draw?

How To Visualize Network Comparatively Via Cytoscape Or Other Tools

See the right panel, there are a lot of

other useful posts as well.

ADD REPLYlink modified 6 months ago • written 6 months ago by natasha.sernova3.5k
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