Setting

[yasemin ekinci]

Hi there, I am so new to using cytoscape and am starting to analyse my daya using cluego. 

I have questions about that. 

1:  When  I ran my protein list using gProfiller and clue go cytoscape , they gave a different list for me, even though the statistical filter is the same. What is the reason for that? 

2: I have different size of protein lists, and their protein numbers are different :  for example : 47, 65, 120 , 500. So I am confused about the advanced trm/pathway selections setting. If I choose a small number, it gives a huge connection, and if I choose a high number , it gives a lower BP pathway. So , for consistency and to visualize, I decided to use cytoscpae, but i need help. 

Thanks 

[Scooter Morris]

Greetings,

I'll try to help if I can...

On Wednesday, June 26, 2024 at 10:00:05 AM UTC-7 ek.yase...@gmail.com wrote:

Hi there, I am so new to using cytoscape and am starting to analyse my daya using cluego. 

I have questions about that. 

1:  When  I ran my protein list using gProfiller and clue go cytoscape , they gave a different list for me, even though the statistical filter is the same. What is the reason for that? 

That's difficult to answer in the abstract.  g:Profiler allows you to give both ordered and unordered gene lists.  ClueGO is strictly unordered.  That might impact your results.

 

2: I have different size of protein lists, and their protein numbers are different :  for example : 47, 65, 120 , 500. So I am confused about the advanced trm/pathway selections setting. If I choose a small number, it gives a huge connection, and if I choose a high number , it gives a lower BP pathway. So , for consistency and to visualize, I decided to use cytoscpae, but i need help. 

I guess I would need more information.  There are three settings under Advanced Term/Pathway Selection Options.  Which one are you referring to?

Thanks 

I would also suggest you read through the  ClueGO tutorial at: http://www.ici.upmc.fr/cluego/cluegoDocumentation.shtml

-- scooter

[yasemin ekinci]

Hi Scooter, 

Thank you for your quick response. I am referring to the second one: the min # genes and % genes section. How do I set this section for 150 and 350 proteins?

Thanks 

Scooter Morris <ssbsm...@gmail.com>, 27 Haz 2024 Per, 00:32 tarihinde şunu yazdı:

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