Hello Jaime,

You can try working on Mapman and Pageman software. They have inbuilt A.thaliana mappings and will generate good graphics for your data

http://mapman.gabipd.org/

Bon Research..!!

Hello Sourabh, 

Thanks for your answer, I'm working with Mapman and graphics generated were good, but not really what I'm looking for. I'll keep trying. 

I found this tool that do exactly what I want... but only for human genes, here for an example; http://actin.pharm.mssm.edu/genes2networks

Bests

Please see the article Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics, by Ana Conesa* and Stefan Götz (doi: 10.1155/2008/619832) in the link http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375974/

In this paper, they describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary.

It may be helpful to you to find a solution to your problems.

Another software I came to notice is KaPPA-View.  It is a web-based tool for integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps

Please the following book also.

R. Tamassia, Handbook of Graph Drawing and Visualization,  Chapman and Hall/CRC, 2013.

Dear Sudev,

I used to work with Blast2GO, is a good tool for annotation, GO analysis and others approaches, but doesn't graph what I'm looking for.

I'll try KaPPA, thanks.

Hello Jaime,

I think WGCNA package in R will be able to do so.., As suggested by Sudev, kappa view is also a good tool for thi spurpose. But if you are familiar with R, then I will suggest to use WGCNA for this.

Jaime, most of your replies contained "[the software] doesn't graph what I'm looking for", so please be more specific and descriptive on what are you looking for exactly and that way we will be able to point you one direction or another.

There are plenty of ways to construct and visualize networks (by co-regulation, protein-protein interaction, using many kinds of correlation, metabolic pathways, signalling pathways etc) so please give us a hint here and tell us what exactly you want, in particular, what would you like to use as nodes and linkers.

Hi Gustavo and partners, I found GeneMania (http://www.genemania.org/) that have A.thaliana between other species and let me choose what kinds of interactions use for the networks. I didn't specify cause I was interesting in every connection at the first view of my data. Then I choose one or more of the interactions. 

and yes, this one "graphs exactly what I'm looking for"

Thanks everyone