Asking opinion on the right way in gene network construction

[hani sarah]

Hi all,

I would like to ask your opinion on the project that I am currently doing on gene network construction. 

Previously, I had constructed a gene network from Arabidopsis thaliana using several co-expression tools (GeneMANIA, ATTED, AraNet v2). These three tools provide co-expression data for several model organism. 

Next, I intend to build a gene network on Carica papaya using the same query as been used in Arabidopsis thaliana. As there is not much co-expression data that can be achieved in Carica papaya, can I do sequence similarity on the gene network from Arabidopsis and compare it with the Carica papaya genome?

Can the results retrieved from sequence similarity on Carica papaya be named as Carica papaya gene network? Hopefully I can have some insights from you. Thanks so much 

[piet molenaar]

Well, this is actually more of a biological question, of course you can use a sequence similarity network but the expression values tend to be more organism specific, at least that's the case for mammalian gene networks...

Probably you can ask folks at the plantgdb resource for comparative plant genomics for the scientific merits of this comparison: http://www.plantgdb.org/site/

Hope this helps,

Piet

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Piet Molenaar
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Department of Oncogenomics, M1-131
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[Ankush Sharma]

Dear Hani Sarah

Is there any available dataset of gene expression on array express or GEO e.g. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38105.  Then you can use R packages for weighted gene co expression network analysis or Aracne to make coexpression networks, and then import it on Cytoscape.

Hope this helps

Best Regards,

​Ankush Sharma,PhD 

Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7)

​

​I​

​nstitute of Clinical Physiology

​- National Research Council, ​

 Siena (IT)
LISM, Institute of Clinical Physiology, Siena (Italy)
Faculty of Information Technology, United Arab Emirates University, Al-Ain (UAE)

[hani sarah]

Thanks piet and Ankush..

Well, there are certainly gene expression data that are available at those databases. However, I am not that familiar with the R packages. Is there any online material that I can refer to? Thanks 

[piet molenaar]

Hi,

There is an app for that: http://apps.cytoscape.org/apps/aracne

Hope this helps,

Piet

[hani sarah]

thanks piet! of course it helps

[Rizwan Akram]

Hi Dear Sara have you solved your problem regarding the gene co-expression network? 

 I am also facing that problem, I have  transcriptome expression data of two plant varieties in different tissues , so now i want to do gene co-expression network analysis using whole transcriptome expression and intersection with my known target genes, 

 so how can do?

[Scooter Morris]

Hi Rizwan,

Sara's post was from 6 years ago, can you be more specific about what species you want to compare?  There are certainly more tools available these days (eggNog, aracne, etc.) to map genes from one species to another using orthology, but more information about what you are trying to achieve in detail would be helpful...

-- scooter