Microarray data for Cytoscape: how to generate network, or how to annotate with gene expression

[Allie Ong]

Hi guys,

I'm a complete amateur to cytoscape, so any help is very appreciated. So my project started off with microarray data with Entrez number (and gene name), and expression data (fold change), with genes in rows and samples in columns.

That brings me to the first question: Would I be able to create a network based on this excel file? 

I've read a few papers that recommends cPath (not available in the newer Cytoscape), MiML amongst other programs, but it didn't work for me. I tried so many things from so many websites on the internet until I can't even remember all that i've tried.

Any advice for me to go ahead with this??

As I'm stuck with that (troubleshooting this), I decided to just try and obtain a network from innatedb, since my project has basis in that field. Gotten a sif file from that, and managed to have a network.

That brings me to the second question: How do I annotate the network with the fold change values from my microarray experiment? 

I've formatted the file according to the reference paper (Cline et al., 2007 Nat Prot), but it doesn't read!

I then thought it could be that the gene ID is somehow changed by innatedb, hence i attempted mapping the identifiers using Cythesaurus but i can't get what was shown in the tutorial pages.

Youtube, google, pubmed I have tried them all. I've even searched through this page and at the discussion's page but to no avail. I could really use some help, and perhaps someone out there faces the same problem.

Thanks in advance for anyone who could give a guidance or two!

x

Allie

[Scooter Morris]

Hi Allie,

On 3/22/15 1:52 PM, Allie Ong wrote:

Hi guys,

I'm a complete amateur to cytoscape, so any help is very appreciated. So my project started off with microarray data with Entrez number (and gene name), and expression data (fold change), with genes in rows and samples in columns.

That brings me to the first question: Would I be able to create a network based on this excel file?

What kind of network are you looking for?  You can use this data to generate a Protein-protein interaction network or a coexpression network, but you sort of need to decide what you want.

I've read a few papers that recommends cPath (not available in the newer Cytoscape), MiML amongst other programs, but it didn't work for me. I tried so many things from so many websites on the internet until I can't even remember all that i've tried.

Any advice for me to go ahead with this??

As I'm stuck with that (troubleshooting this), I decided to just try and obtain a network from innatedb, since my project has basis in that field. Gotten a sif file from that, and managed to have a network.

That brings me to the second question: How do I annotate the network with the fold change values from my microarray experiment?

Well, you essentially are going to read your excel file in twice.  First, you'll read it in as a network (File-Import->Network->File) and only select your Entrez gene numbers or gene names as the "Source".  Don't select a target or an interaction.  This will essentially create a bunch of nodes.  Next, you can read in all of the other data as attribute on those nodes (File-Import->Table->File) and import the rest of the data, selecting the same column you used to import the nodes as the "Key".

I've formatted the file according to the reference paper (Cline et al., 2007 Nat Prot), but it doesn't read!

I then thought it could be that the gene ID is somehow changed by innatedb, hence i attempted mapping the identifiers using Cythesaurus but i can't get what was shown in the tutorial pages.

Youtube, google, pubmed I have tried them all. I've even searched through this page and at the discussion's page but to no avail. I could really use some help, and perhaps someone out there faces the same problem.

Thanks in advance for anyone who could give a guidance or two!

x

Allie

-- scooter

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[Karim Mezhoud]

Hi,

1- Be sure and use Gene Symbol (HUGO).

2- How to import table to Cytoscape.

3- How to predict network from gene symbol list: recommended App: ReactmeFI

4- walk through example to attribute fold change to node color:

  4-1 you need to do some statistics before Node attributes (see example).

5- Enrichment Analysis: recommended App: ClueGO

Karim