GlueGo- network simplification
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Ivy Ngai
Apr 10, 2016, 10:06:01 PM4/10/16
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Hi there,
I am trying to include only nodes relate to "binding" after processing my network according to biological process, please kindly let me know I to process.
Also, I am bit confused by the function of "use GO term fusion", how to used it after the network generated?
Thank you so much for your kind help!
Best,
Ivy
Ivy Ngai
Apr 10, 2016, 10:07:15 PM4/10/16
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PS, I am using Version 2.2.5
piet molenaar
Apr 11, 2016, 4:09:45 AM4/11/16
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Hi, this is specific to the ClueGo app so I'll forward it to one of the authors of the app.
Cheers,
Piet
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Piet Molenaar
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Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
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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
Bernhard
Apr 11, 2016, 9:33:18 AM4/11/16
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Hi Ivy, first, the GO term fusion has to be clicked/checked before you start ClueGO. There is a (?) next to where you can read what exactly the fusion is doing.
CluePedia will always show the nodes from your input list (red label). If you want to see more or all Genes from the found GO terms you have to increase the number of Genes shown (CluePedia options ins the left panel in read).
To show only genes that have a binding interaction follow the steps on the attached image here.
First you make the network (with or without fusion).
Then show the initial genes (1.).
Now select STRING v10 and binding.
Then click (2.) show genes that are not from the input list but have a binding to one of the initial genes.
(if you want to show also the binding links between all genes deselect the button between (2.) and (3.) )
Then click (3.) to hide all genes that are not linked with any binding (even the gene from the input list).
Now you should have a network with only genes with binding interactions.
(You can now also show/hide the GO terms with the first option in that toolbar)
Best
CluePedia will always show the nodes from your input list (red label). If you want to see more or all Genes from the found GO terms you have to increase the number of Genes shown (CluePedia options ins the left panel in read).
To show only genes that have a binding interaction follow the steps on the attached image here.
First you make the network (with or without fusion).
Then show the initial genes (1.).
Now select STRING v10 and binding.
Then click (2.) show genes that are not from the input list but have a binding to one of the initial genes.
(if you want to show also the binding links between all genes deselect the button between (2.) and (3.) )
Then click (3.) to hide all genes that are not linked with any binding (even the gene from the input list).
Now you should have a network with only genes with binding interactions.
(You can now also show/hide the GO terms with the first option in that toolbar)
Best
Ivy Ngai
Apr 12, 2016, 5:07:46 AM4/12/16
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Hi, thank you so much for your reply and kind help!
I processed my data according to your instruction, however I have one question, do I need to click "update" after select STRING v10 and binding?
Than you so much!
Best,
Ivy
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Bernhard
Apr 12, 2016, 6:45:13 AM4/12/16
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Hi Ivy, yes you are right, you have to click on update after selecting the e.g. binding to apply it to the network. I forgot this in my explanation.
Best
Best
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Ivy Ngai
Apr 15, 2016, 4:35:49 AM4/15/16
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Thank you so much for the explaination!
Have a nice day!
Ivy
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Ivy Ngai
Apr 15, 2016, 11:27:48 PM4/15/16
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Hi, sorry to bother you again!
Now I have a five-group-comparison result like below, could you kindly show me how to make the graph more clusted and organized, as I try all the layout, non of the works. If I used apps like clustermaker, then somehow the result lost its color.
Also, can I change the color of the go terms or the background in the app, currently they are both white.
Thank you so much for your help!! Ivy
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Bernhard
Apr 18, 2016, 11:40:03 AM4/18/16
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Hi Ivy, here I cannot really help you. The layout-algorithms are based on how the genes/terms are linked to each other. You could try to reduce the number of links (using evidence codes like experimental) to get a more clean view or reduce the number of terms to the most significant/interesting ones.
On the left side image you see an example to change the background. Follow steps 1-4.
On the right side image you see how to change the colour of a Group. You can only change the colour of groups. Follow steps 1-5.
Best
On the left side image you see an example to change the background. Follow steps 1-4.
On the right side image you see how to change the colour of a Group. You can only change the colour of groups. Follow steps 1-5.
Best
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Ivy Ngai
Apr 19, 2016, 11:41:03 PM4/19/16
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Morning, thank you so much for your reply and explanation. However, I still have two small questions regarding Gluego:
Firstly, I reading from the documentation that there is a function called cluster comparison, but I failed to find it in the app.
Also, if I want to exclude gene names in the final results, how should I do that? I have turned off the gene visualization, nut there are still some, please find the below pics.
Thank you so much!! Best, Ivy
(biological process-Ellipse/ pathway- triangle)
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Ivy Ngai
Apr 20, 2016, 4:36:56 AM4/20/16
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Also, the last part of the tutorial, it set the false and true value of the node label to only keep the leading terms, however I failed to set the value,
probably because I failed to do the group comparison?
Ps, I attached my data for your reference. Thank you so much!!!!!!
Bernhard
Apr 20, 2016, 4:49:41 AM4/20/16
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Hi Ivy,
first, the documentation is not on its latest state. So the comparison of "cluster" was extended to multiple cluster so the result panel now shows now a tab for each "cluster" with terms specific for it and a tab for unspecific terms, so all terms that are common among the "cluster".
Regarding the second point,
to hide gene labels you can use the cytoscape bypass function. This one allows you to temporarily overwrite the current settings. To do this in combination with ClueGO follow the steps from 1-7 on the attached figure.
1. Uncheck the show terms button
2. Select all gene (you should only see the genes now, no terms)
3-4. Click on Style and then Node tab
5. Click on the bypass button
6-7. Enter nothing (empty string to overwrite labels from all selected genes) and click OK.
8. Click to show again the terms with the genes
(You can at any time remove the bypass again you just set to show the initial gene labels)
You can also hide names from terms that are no group leading terms. To do this follow steps 8-10.
If you want to remove all labels you can remove the pass through mapping (click on the trash icon close to step 5 on the fig, you will see it if you scroll a bit on the right).
I hope this helps
Best
first, the documentation is not on its latest state. So the comparison of "cluster" was extended to multiple cluster so the result panel now shows now a tab for each "cluster" with terms specific for it and a tab for unspecific terms, so all terms that are common among the "cluster".
Regarding the second point,
to hide gene labels you can use the cytoscape bypass function. This one allows you to temporarily overwrite the current settings. To do this in combination with ClueGO follow the steps from 1-7 on the attached figure.
1. Uncheck the show terms button
2. Select all gene (you should only see the genes now, no terms)
3-4. Click on Style and then Node tab
5. Click on the bypass button
6-7. Enter nothing (empty string to overwrite labels from all selected genes) and click OK.
8. Click to show again the terms with the genes
(You can at any time remove the bypass again you just set to show the initial gene labels)
You can also hide names from terms that are no group leading terms. To do this follow steps 8-10.
If you want to remove all labels you can remove the pass through mapping (click on the trash icon close to step 5 on the fig, you will see it if you scroll a bit on the right).
I hope this helps
Best
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Bernhard
Apr 20, 2016, 4:59:04 AM4/20/16
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Hi Ivy, as I said in my last post, this part of the tutorial has to be updated (it is still showing Cytoscape 2.8).
Now I see the problem with the labels. To hide the labels of not leading terms was just meant to work with showing "Groups", but if you select" Cluster" you can select all nodes from which you want to hide the label and apply steps 1-7 from my previous post to bypass the node labels with an empty string. This should work.
Best
Now I see the problem with the labels. To hide the labels of not leading terms was just meant to work with showing "Groups", but if you select" Cluster" you can select all nodes from which you want to hide the label and apply steps 1-7 from my previous post to bypass the node labels with an empty string. This should work.
Best
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Ivy Ngai
Apr 22, 2016, 2:32:35 AM4/22/16
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Hi, thank you so much for the detailed explanation! They are extremely helpful!!!
Have a nice day!
Best regards,
Ivy
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