Identify and overlap number of publications to each gene and functional nodes in ClueGO

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BIOMICS

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Nov 2, 2017, 6:18:50 AM11/2/17
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Dear All,
I wish to identify and list down all publications associated with each gene associated with a functional node in a ClueGO analysis  in cytoscape.
I also wish to show the number of publications corresponding to each node as a bar chart. I request your help in this regard. 
Thanks in advance. 
Nara


Scooter Morris

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Nov 2, 2017, 12:10:16 PM11/2/17
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Hi Nara,
   Sorry, but I'm not aware of any Cytoscape apps that will do what you want.

-- scooter

Bernhard

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Nov 6, 2017, 1:00:36 PM11/6/17
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Hi Nara, you could try this. See down. Click on the extract pubmed info for each selected gene (1). Then select a file name to extract the info to. Then set the number of abstracts to one (2) this is to reduce waiting time. Then click on start. You will get a file with all information for the selected genes with pubmed info and citing articles. There is also a column with number of citing articles for each gene. If you format the data and upload to cytoscape and then use the Enhanced Graphics plugin you could display this information for each gene. I never did this before but it could work. Just don't do this for more then 100 genes it could take very long. The function uses efech utils from NCBI so for each gene there will be several queries to be done and this takes time.
Best


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