Importing data from GEO database
Edmund Tsui
Barry Demchak
I'm trying to import data from GEO database (either .soft, .txt files), but it does not import correctly with Cytoscape v3.3 (the columns are empty after importing), is there something I have to change in the file or settings to adjust in Cytoscape?Thanks!
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: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
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Edmund Tsui
On Saturday, January 30, 2016 at 12:31:31 PM UTC-5, Barry Demchak wrote:
Hi --It sounds like you have a network already loaded into Cytoscape and now you're trying to add the GEO data.Cytoscape will create the columns you identify, and then it will go row by row through the file. For each row, it'll take the node name in the row and search for it in the network. If it finds a match, it'll take the values in the row and apply them to the column values for the node.It sounds like there's a mismatch between the node names in the network and the node names in our import file.Could that be??Feel free to send us file so we can take a look ourselves.
On Sat, Jan 30, 2016 at 9:26 AM, Edmund wrote:
I'm trying to import data from GEO database (either .soft, .txt files), but it does not import correctly with Cytoscape v3.3 (the columns are empty after importing), is there something I have to change in the file or settings to adjust in Cytoscape?Thanks!
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Barry Demchak
Thanks, Edmund … sorry for the delay … we had some excitement with the App Store this morning. I’ll look at this right now.
From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Edmund Tsui
Sent: Monday, February 01, 2016 11:19 AM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] Importing data from GEO database
Hi Barry,
I was wondering if you had a chance to take a look at the data file. I am not sure if it had sent in my last message. Thank you.
On Saturday, January 30, 2016 at 12:31:31 PM UTC-5, Barry Demchak wrote:
Hi --
It sounds like you have a network already loaded into Cytoscape and now you're trying to add the GEO data.
Cytoscape will create the columns you identify, and then it will go row by row through the file. For each row, it'll take the node name in the row and search for it in the network. If it finds a match, it'll take the values in the row and apply them to the column values for the node.
It sounds like there's a mismatch between the node names in the network and the node names in our import file.
Could that be??
Feel free to send us file so we can take a look ourselves.
On Sat, Jan 30, 2016 at 9:26 AM, Edmund wrote:
I'm trying to import data from GEO database (either .soft, .txt files), but it does not import correctly with Cytoscape v3.3 (the columns are empty after importing), is there something I have to change in the file or settings to adjust in Cytoscape?
Thanks!
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: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
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Barry Demchak
Hi, Edmund –
OK … I have had a look at this and I think I understand the issues.
The GEO database page you sent me presents its observation data in a format that Cytoscape can’t handle directly. You can see this if you open either the SOFT or TXT file in an editor (though, the files are very large).
Cytoscape needs to see two things … a header row containing value names, and then a series of rows where each row contains a gene name and a list of values … just like an Excel spreadsheet, though it can be in Excel, CSV, TSV, TXT or a number of other formats.
GEO isn’t this. So, you’d need to get the data into that format somehow. In looking through the App Store and HelpDesk posts, I see that GSE integration has been attempted, but mostly in the distant past. There was an app (called DvD) that ran with a combination of Cytoscape v2.x and R, but it’s very old and might take some work to get going.
In looking at other solutions (e.g., reading in R and piping to Cytoscape), I see that questions came up about this before 2010. I don’t know the current situation with R reading GEO.
I don’t think we have a ready solution for you … can you get the GEO results into a tabular format?
If you can, that’s most of the work. The other part is getting the IDs matching. The Human network contains IDs using the Entrez ID convention. The GEO dataset uses a different naming convention, and you might do well with this site for renaming: https://david.ncifcrf.gov/home.jsp ... Or the Cytoscape BridgeDB app.
Sorry to say, not so easy … can I help more?
From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Edmund Tsui
Sent: Monday, February 01, 2016 11:19 AM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] Importing data from GEO database
Hi Barry,
I was wondering if you had a chance to take a look at the data file. I am not sure if it had sent in my last message. Thank you.
On Saturday, January 30, 2016 at 12:31:31 PM UTC-5, Barry Demchak wrote:
Hi --
It sounds like you have a network already loaded into Cytoscape and now you're trying to add the GEO data.
Cytoscape will create the columns you identify, and then it will go row by row through the file. For each row, it'll take the node name in the row and search for it in the network. If it finds a match, it'll take the values in the row and apply them to the column values for the node.
It sounds like there's a mismatch between the node names in the network and the node names in our import file.
Could that be??
Feel free to send us file so we can take a look ourselves.
On Sat, Jan 30, 2016 at 9:26 AM, Edmund wrote:
I'm trying to import data from GEO database (either .soft, .txt files), but it does not import correctly with Cytoscape v3.3 (the columns are empty after importing), is there something I have to change in the file or settings to adjust in Cytoscape?
Thanks!
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: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
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Dubay, Christopher J
Edmund,
One nice tool that can pull GEO data, and get it into tabular format is BRBarray. (It does a lot more too with gene expression and other data sets).
It runs as an Excel add-on under a Windows OS that talks to R to run Bioconductor (and other) packages.
It is free, and can be found here:
http://brb.nci.nih.gov/BRB-ArrayTools/
Christopher
Christopher Dubay, PhD
Biomedical Informatics Program Manager
Laboratory of Molecular and Tumor Immunology
Earle A. Chiles Research Institute
Providence Cancer Center
4805 NE Glisan St.- 2N57
Portland, OR 97213 USA
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Barry Demchak
Very cool, Christopher … glad to know about this!