Constructing Pathway With List Of Gene Using Cytoscape

Question

[williamjohn360]

We have around list of 10 nucleotide sequence sequenced from new plant organism that does not exist in available KEGG pathways. Can I do blast against Arabidopsis and get 10 closest homologue gene name. I am beginner in using Cytoscape. Can I construct pathway using Cytoscape these homologue gene name, how can I do that?. After constructing pathway, if want to study particular gene of interest, how can I do that?. Can one help my giving workflow for this?

[williamjohn360]

Anybody can help by giving the work flow?. If question is not clear, please let me know.

Answer 1

[B. Arman Aksoy]

You might also find GeneMania useful in this context, especially to get a sense about the functions of genes of interest to you. I suggest having a look at the paper to have a sense of the functionality: http://nar.oxfordjournals.org/content/38/suppl_2/W214.short

The website uses CytoscapeWeb to visualize the networks and there is also a Cytoscape plug-in if you want to work within Cytoscape environment.

Answer 2

[miquelduranfrigola]

Hi William,

In general, at least as a starting point, you can BLAST your sequences and translate your problem to Arabidopsis. Cytoscape is mostly a network visualization tool (it will be useful eventually, but first you need to define your "network" or "pathway").

For this, go to this link: http://www.arabidopsis.org/portals/proteome/proteinInteract.jsp

Here, you will find several arabidopsis protein interaction resources. This should be useful to reconstruct small networks around your genes of interest.

Answer 3

[Sudeep]

Since you mentioned KEGG pathways, you can also take a look at KEGG Automatic Annotation Server to get functional annotations