loading excel data
Gema
dataset because i only have a protein list from a 2D-PAGE experiment
and i´d like cytoscape to show a network with my proteins list. I don
´t have previous knowledge about how interact my proteins among them
so I cant select source colum and target colum in the input dataset
window on cytoscape. How can I get a network with my dataset??
Thank you!
allan_k...@agilent.com
Example #1: Retrieving Protein-Protein Interaction Networks from IntAct
Select: File → Import → Network from web services...
From the pull-down menu, select the IntAct Web Service Client.
Enter one or more search terms, such as BRCA1
Click the Search button.
You can cut and paste multiple search terms into the query window. So, if you have a column in your data which has protein names in the format of gene symbols, you can cut and paste names from that column into the query window.
AllanK
Allan Kuchinsky
Principal Project Scientist
Molecular Tools
Agilent Laboratories
Agilent Technologies, Inc.
Santa Clara, CA, USA
408.553.2423
allan_k...@agilent.com
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Gema Sanz
Hello Allan,
First of all, thank you very much for your attention.
I´ve tried to do what you said to me, but I don’t have the InAct web service client, I paste you a print-screen:
I still don´t know what to do with my data set… I only want to get a network with my proteins and see how interact among them.
allan_k...@agilent.com
Gema, you can also use the PathwayCommons web service to get networks for your protein data.
But maybe I misunderstood your question. Do you want to get a network that contains only proteins in your data set and interactions between them? That is, do you want your network’s nodes to be only those in your dataset? Also, how many proteins are in your dataset?
AllanK
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Allan Kuchinsky |
Principal Project Scientist |
Molecular Tools |
Agilent Laboratories |
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Agilent Technologies, Inc. |
Santa Clara, CA, USA |
From: Gema Sanz
[mailto:ge2s...@uco.es]
Sent: Monday, November 30, 2009 7:38 AM
To: cytoscape...@googlegroups.com
Subject: RE: [cytoscape-helpdesk] loading excel data
Hello Allan,
First of all, thank you very much for your attention.
Ive tried to do what you said to me, but I dont have the InAct web service client, I paste you a print-screen:
I still dont know what to do with my data set I only want to get a network with my proteins and see how interact among them.
Gema Sanz
Yes, it is what I exactly want to do. I want my network´s nodes were molecules from my dataset, but I don’t mind if other related molecules appear, but mainly all the possible molecules from my dataset. I don´t know if there is any plugin to do that.
When dataset is from proteomic approach, I usually have 30-50 proteins in my list, if is a microarray approach I have about 500-800 genes.
Gema
allan_k...@agilent.com
Gema, good news. There is indeed a plugin that does exactly what you want. This is the MiMI plugin from University of Michigan. It’s latest version will enable you to restrict to direct interactions between your genes or proteins. On the MiMI plugin input dialog box, first enter your gene list (you can also load a gene file). There is "what to retrieve" drop down menu, choose option 2, you will get direct interactions only among input genes. You can get the MiMI plugin via Cytoscape’s plugin manager.
I hope that this is helpful.
