Question: Constructing Pathway With List Of Gene Using Cytoscape
gravatar for williamjohn360
6.8 years ago by
williamjohn36090 wrote:

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?

nucleotide cytoscape • 5.6k views
ADD COMMENTlink modified 6.6 years ago by Biostar ♦♦ 20 • written 6.8 years ago by williamjohn36090

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

ADD REPLYlink written 6.8 years ago by williamjohn36090
gravatar for B. Arman Aksoy
6.8 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

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:

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

ADD COMMENTlink written 6.8 years ago by B. Arman Aksoy1.2k
gravatar for miquelduranfrigola
6.8 years ago by
miquelduranfrigola760 wrote:

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:

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

ADD COMMENTlink written 6.8 years ago by miquelduranfrigola760
gravatar for Sudeep
6.8 years ago by
Sudeep1.6k wrote:

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

ADD COMMENTlink written 6.8 years ago by Sudeep1.6k
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