about the input for jactivemodules

[Tongjun Gu]

Hi, I am working on discovering enriched submodules from the public available yeast network using jActivemodules. Could anyone point me where the manual is about using jActivemodules? What is the input, the whole set of P values or selected P values for the differential expressed genes? If we don't have the P values for all the genes in the reference network, how will the missing values affect the analysis? Thank you!

[Barry Demchak]

Tongjun –

 

Does this help?? http://apps.cytoscape.org/apps/jactivemodules

 

There are links to a few documents that should help.

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Monday, January 16, 2017 6:34 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi, I am working on discovering enriched submodules from the public available yeast network using jActivemodules. Could anyone point me where the manual about using jActivemodules? What is the input, the whole set of gene expression or selected differential expressed genes? Thank you!

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[Tongjun Gu]

Hi Barry, Thanks for sending me the link but I can't find statement about the inputs. The problem I have is that I only have expression values for part of the reference network genes and look for the submodules that enriched significantly differential expressed genes in my datasets. I am not sure how the missing value will affect the analysis results.

Anyway, thank you very much.

Tongjun

On Tuesday, January 17, 2017 at 11:14:15 AM UTC-5, Barry Demchak wrote:

Tongjun –

 

Does this help?? http://apps.cytoscape.org/apps/jactivemodules

 

There are links to a few documents that should help.

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Monday, January 16, 2017 6:34 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi, I am working on discovering enriched submodules from the public available yeast network using jActivemodules. Could anyone point me where the manual about using jActivemodules? What is the input, the whole set of gene expression or selected differential expressed genes? Thank you!

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[Barry Demchak]

Hi, Tongjun –

 

I gather that you found step 2 of the instructions in the Help document. Your question appears to be regarding what happens if not all of the nodes have expression values.

 

I’m not sure, myself. It should be possible to figure this out, though, by going back to the original 2002 paper (attached) and inspecting the source (https://github.com/idekerlab/jActiveModules/tree/master/src/main/java/csplugins/jActiveModules). It looks like most of the action is in the ActivePathsFinder.java module.

 

As an alternative, there are other clustering algorithms to look at … consider ClusterMaker2 … newer and with lots of different approaches.

 

 

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Tuesday, January 17, 2017 12:29 PM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi Barry, Thanks for sending me the link but I can't find statement about the inputs. The problem I have is that I only have expression values for part of the reference network genes and look for the submodules that enriched significantly differential expressed genes in my datasets. I am not sure how the missing value will affect the analysis results.

Anyway, thank you very much.

Tongjun

On Tuesday, January 17, 2017 at 11:14:15 AM UTC-5, Barry Demchak wrote:

Tongjun –

 

Does this help?? http://apps.cytoscape.org/apps/jactivemodules

 

There are links to a few documents that should help.

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Monday, January 16, 2017 6:34 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi, I am working on discovering enriched submodules from the public available yeast network using jActivemodules. Could anyone point me where the manual about using jActivemodules? What is the input, the whole set of gene expression or selected differential expressed genes? Thank you!

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[Tongjun Gu]

Hi Berry,

Thank you for the useful resources and suggestions! Will try clustermaker2 and look at their method in detail.

Tongjun

On Tuesday, January 17, 2017 at 4:54:35 PM UTC-5, Barry Demchak wrote:

Hi, Tongjun –

 

I gather that you found step 2 of the instructions in the Help document. Your question appears to be regarding what happens if not all of the nodes have expression values.

 

I’m not sure, myself. It should be possible to figure this out, though, by going back to the original 2002 paper (attached) and inspecting the source (https://github.com/idekerlab/jActiveModules/tree/master/src/main/java/csplugins/jActiveModules). It looks like most of the action is in the ActivePathsFinder.java module.

 

As an alternative, there are other clustering algorithms to look at … consider ClusterMaker2 … newer and with lots of different approaches.

 

 

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Tuesday, January 17, 2017 12:29 PM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi Barry, Thanks for sending me the link but I can't find statement about the inputs. The problem I have is that I only have expression values for part of the reference network genes and look for the submodules that enriched significantly differential expressed genes in my datasets. I am not sure how the missing value will affect the analysis results.

Anyway, thank you very much.

Tongjun

On Tuesday, January 17, 2017 at 11:14:15 AM UTC-5, Barry Demchak wrote:

Tongjun –

 

Does this help?? http://apps.cytoscape.org/apps/jactivemodules

 

There are links to a few documents that should help.

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tongjun Gu
Sent: Monday, January 16, 2017 6:34 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] about the input for jactivemodules

 

Hi, I am working on discovering enriched submodules from the public available yeast network using jActivemodules. Could anyone point me where the manual about using jActivemodules? What is the input, the whole set of gene expression or selected differential expressed genes? Thank you!

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