Finding a way to comparison man-made cells and real tissue by Cytoscape!

[falsafi...@gmail.com]

Hi,
I have some gene expression data from induced cells by some small molecule in vitro (different kind of small molecules in different data sets) that convert to a kind of tissue and of course the real tissue expression from part of body (for instance DEGs of converted cell to brain and DEGs of a real brain) to show how similar are this conversion to real tissue and how successful is in the aspect of gene expression and their Gene Regulatory Networks? .Then to construct a gene-TF interaction network for this data, deferentially expressed genes with a typical filters were used and TFs with highest probability interactions were found, finally these interaction were given to the Cytoscape. my final goal is to find modules for both induced cells gene-TF interactions and that of tissue and compare these to kind of networks to show similarities and differences.

So my questions are, 1- Is finding modules a good way?
2-what is the best plugin to find module base on DEGs and TFs interaction for my gene regulatory network?
3-Is it possible to use JActivemadule plugin to find modules?since I have read in some papers that JActivemodule is used for finding modules of genes with their p.value and fold change not for gene-TF interactions.

any suggestion would be helpful

many thanks

[Gary Bader]

Hi - one way to do this is to use pathway enrichment analysis.  We have a good workflow for this at https://www.biorxiv.org/content/early/2017/12/12/232835  In terms of finding modules from a gene list, you can try http://apps.cytoscape.org/apps/reactomefiplugin

http://apps.cytoscape.org/apps/iregulon is useful for identifying regulators of genes in your list.

There are many ways to do differential analysis, but hopefully these provide a useful starting point.

Best,

Gary

[falsafi.raziuni]

Thanks Gary

It is so helpful.

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از: Gary Bader <gary.ba...@gmail.com>

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موضوع: [cytoscape-helpdesk] Re: Finding a way to comparison man-made cells and real tissue by Cytoscape!

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[Nafiseh Falsafi]

Hi again Gary,

would you please give me supplementary tables? I can't achieve them by this page :https://www.biorxiv.org/content/early/2017/12/12/232835.article-metrics  

best regards

Nafiseh Falsafi

[Ruth Isserlin]

Hi Nafiseh, 

Sorry about that.  I have added the supplementary files to our protocol website here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/index.html

all the supplementary files can be downloaded together here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/SupplementaryData_EM_Protocol.tar.gz

Thanks, 

Ruth 

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[falsafi.raziuni]

Dear Ruth,

I appreciate you and your group member all. You are the best.

Hope success and acheivment.

I wish I could be part of your team.

Thanks a million.

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موضوع: Re: [cytoscape-helpdesk] Finding a way to comparison man-made cells and real tissue by Cytoscape!

[Nafiseh Falsafi]

Dear Dr. Bader

I really have no word to express my gratitude from you and your group. I found your workflow on pathway enrichment analysis really helpful And I have done the protocol for GSEA step by step. first, I could do it with your supplementary very well, but unfortunately, when I have done the protocol with my own data, I have encountered the error in GSEA app (the file was attached). I can not understand what is the mistake.

I also attached my rnk file for your information.

would you please help me to find the mistake?

Many thanks in advance.

Nafiseh Falsafi

--

[Ruth Isserlin]

Hi Nafiseh,

The issue is that none of the ids that are in your rank file are matching your geneset file.  The error in the log file is:

"xtools.api.param.BadParamException: After pruning, none of the gene sets passed size thresholds."

Where did you get your gmt file?  According to the log message that you sent it is EM_Genesets.Mouse.GOBP.AllPathways.symbol.gmt.txt but I am not sure where that file is from.  (I was able to run your rank file with file I downloaded from here:http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/ and it worked ok.)

Thanks, 

Ruth 

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<Application Messege.txt><22292.rnk>

[Nafiseh Falsafi]

Hi Ruth,

Thanks for your response.

Yes I have downloaded the gmt file from  "http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/". entiteled "Mouse_GOBP_AllPathways_no_GO_iea_April_01_2019_symbol.gmt" 

is it wrong file? DO I need another gmt file from the Baderlab?

Nafiseh Falsafi

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[Ruth Weinberger]

Hi Nafiseh,

That is the right file.  In the error log it was listed with a slightly different name.  Did you open the file and re-save it using Excel or any other program?  It might have done something to the file (like adding quotes around gene names) that is confusing GSEA.

Thanks, 

Ruth 

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[Nafiseh Falsafi]

Hi Ruth,

No, I have just save it with shorter name also when I have wanted to save it the system add txt to end of the file name! Maybe it did not work because of this!

در تاریخ سه‌شنبه ۱۴ مهٔ ۲۰۱۹،‏ ۳:۴۹ Ruth Weinberger <rr.wei...@gmail.com> نوشت:

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[Ruth Isserlin]

Hi Nafiseh, 

The .txt at the end of the file name shouldn't matter.  I ran it with the same ending and it worked fine.  What operating system are you on?  I am not sure what is happening because you said the files from the protocol work fine.

Thanks, 

Ruth 

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[Nafiseh Falsafi]

Hi again,

My system is a 7-core laptop with 12G Ram.

By the way, Thanks for the time.

در تاریخ سه‌شنبه ۱۴ مهٔ ۲۰۱۹،‏ ۱۷:۵۳ Ruth Isserlin <ruth.i...@utoronto.ca> نوشت:

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