Bingo- Selecting only genes in specific GO term, pathway, biological function in network

[Bonnie Blalock]

Hello,

Does anyone know how to only select/highlight genes within a given biological function (e.g. cell cycle, kinase signalling cascade) on your protein network?

I have been working on creating a network of my differentially expressed genes (DEG) from a microarray experiment.  I uploaded my DEG into string and saved the output then uploaded to cytoscape so I could have an network of interacting genes.  I have been able to overlay my expression data onto the network and visualize the fold levels with different colors.  I ran bingo and received an output of different GO categories of my DEG protein interaction network but I have not been able to figure out how to only select these genes on my network?  My network is somewhat large and I would like to examine some specific pathways.

Does anyone have any ideas?  Thank you very much for the help.  I appreciate it greatly.

Bonnie    

[piet molenaar]

Hi Bonnie,

From the docs: http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html and my experience, if you have run a Bingo analysis you can select nodes in the original network by selecting the appropriate categeories in the Bingo output panel and clicking 'select nodes'.

Hope this helps,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[Bonnie Blalock]

Thank you very much!  I still had some trouble getting this to work but I saved the output Bingo file and was able to copy and paste the genes within a given GO category when separated by commas.  Thank you, I appreciate the help!

On Monday, November 28, 2016 at 4:56:16 AM UTC-5, Piet wrote:

Hi Bonnie,

From the docs: http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html and my experience, if you have run a Bingo analysis you can select nodes in the original network by selecting the appropriate categeories in the Bingo output panel and clicking 'select nodes'.

Hope this helps,

Piet

On Sat, Nov 26, 2016 at 2:46 AM, Bonnie Blalock <bonnie....@gmail.com> wrote:

Hello,

Does anyone know how to only select/highlight genes within a given biological function (e.g. cell cycle, kinase signalling cascade) on your protein network?

I have been working on creating a network of my differentially expressed genes (DEG) from a microarray experiment.  I uploaded my DEG into string and saved the output then uploaded to cytoscape so I could have an network of interacting genes.  I have been able to overlay my expression data onto the network and visualize the fold levels with different colors.  I ran bingo and received an output of different GO categories of my DEG protein interaction network but I have not been able to figure out how to only select these genes on my network?  My network is somewhat large and I would like to examine some specific pathways.

Does anyone have any ideas?  Thank you very much for the help.  I appreciate it greatly.

Bonnie    

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[anandp...@gmail.com]

Hello Bonnie,
I am a beginner in computational biology and am also in the process of constructing a protein-protein interaction network using DEGs obtained from microarray analysis. I used LIMMA in R to obtain the list of DEGs. I uploaded them in STRING and downloaded the network. I uploaded the network into cytoscape. After this I m struck and searching for tutorials to proceed next step.

You have mentioned that " you overlaid your expression data onto the network and visualize the fold levels with different colors". Can you explain me how you did this ? Or Can you send me any tutorial links to do this.

Please help me. Thanks.

[Barry Demchak]

Have you considered using filters (i.e., the Select tab on the far left panel) to select nodes based in the GO category value of interest? 

Barry Demchak -- from my mobile phone

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[Barry Demchak]

And to color nodes based on GO term, use a descrete mapping for the node color attribute in the Style tab.

Does this help?

Barry Demchak -- from my mobile phone

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[Premanand Adaikalasamy]

Hello Barry, 

Thanks a lot for your kind information. I believe this will help me a lot. 

2017-09-28 18:18 GMT+05:30 Barry Demchak <idekerlab...@gmail.com>:

And to color nodes based on GO term, use a descrete mapping for the node color attribute in the Style tab.

Does this help?

Barry Demchak -- from my mobile phone

On Sep 28, 2017 5:43 AM, <anandp...@gmail.com> wrote:

On Saturday, November 26, 2016 at 7:16:13 AM UTC+5:30, Bonnie Blalock wrote:
> Hello,
>
>
> Does anyone know how to only select/highlight genes within a given biological function (e.g. cell cycle, kinase signalling cascade) on your protein network?
>
>
> I have been working on creating a network of my differentially expressed genes (DEG) from a microarray experiment.  I uploaded my DEG into string and saved the output then uploaded to cytoscape so I could have an network of interacting genes.  I have been able to overlay my expression data onto the network and visualize the fold levels with different colors.  I ran bingo and received an output of different GO categories of my DEG protein interaction network but I have not been able to figure out how to only select these genes on my network?  My network is somewhat large and I would like to examine some specific pathways.
>
>
> Does anyone have any ideas?  Thank you very much for the help.  I appreciate it greatly.
>
>
> Bonnie    

Hello Bonnie,
I am a beginner in computational biology and am also in the process of constructing a protein-protein interaction network using DEGs obtained from microarray analysis. I used LIMMA in R to obtain the list of DEGs. I uploaded them in STRING and downloaded the network. I uploaded the network into cytoscape. After this I m struck and searching for tutorials to proceed next step.

You have mentioned that " you overlaid your expression data onto the network and visualize the fold levels with different colors". Can you explain me how you did this ? Or Can you send me any  tutorial links to do this.

Please help me. Thanks.

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Regards..

Premanand A, M.Sc Biotech.,

Junior Research Fellow (CSIR),

Ph.D. Research Scholar,

School of Bio Sciences and Technology,

VIT University, Vellore -632014.