Error while installing domain graph plugin

[Rajasimha, Harsha (NIH/NEI) [C]]

I am trying Altanalyze and Domaingraph for the first time.
I got AltAnalyze running OK. I installed Cytoscape and now when I try to install DomainGraph plugin on CYtoscape, I get the following error:
Please help (also attaching screen shot of error)

cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin: Unable to read plugin jar: java.util.zip.ZipException: invalid CEN header (bad signature) Caused by: Unable to read plugin jar: java.util.zip.ZipException: invalid CEN header (bad signature) at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:734) at cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.java:70) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(Unknown Source) at javax.swing.JMenuItem.fireMenuDragMouseReleased(Unknown Source) at javax.swing.JMenuItem.processMenuDragMouseEvent(Unknown Source) at javax.swing.JMenuItem.processMouseEvent(Unknown Source) at javax.swing.MenuSelectionManager.processMouseEvent(Unknown Source) at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(Unknown Source) at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Unknown Source) at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Unknown Source) at java.awt.Toolkit.notifyAWTEventListeners(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.util.zip.ZipException: invalid CEN header (bad signature) at cytoscape.plugin.JarUtil.getPluginClass(JarUtil.java:131) at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:704) at cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.java:70) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(Unknown Source) at javax.swing.JMenuItem.fireMenuDragMouseReleased(Unknown Source) at javax.swing.JMenuItem.processMenuDragMouseEvent(Unknown Source) at javax.swing.JMenuItem.processMouseEvent(Unknown Source) at javax.swing.MenuSelectionManager.processMouseEvent(Unknown Source) at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(Unknown Source) at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Unknown Source) at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Unknown Source) at java.awt.Toolkit.notifyAWTEventListeners(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Thanks,
Harsha

[Nathan Salomonis]

Hi Harsha,

There is an embedded version of Cytoscape with the plugins DomainGraph and GPML that are downloaded and extracted to the AltAnalyze program directory to avoid any version incompatibilities (Cytoscape or dependent plugins). Have you tried using this? You will only need to be install the species database for DomainGraph once opened. You can open this program from within AltAnalyze after an analysis or directly from this folder.

An issue that is known to us, is when two instances of the plugins are installed and called from different Cytoscape folders. This is simply fixed by deleting the hidden directory .Cytoscape in your Windows user directory (Documents and Settings/account name).

Which version of Cytoscape are you using?

Best,
Nathan

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[Rajasimha, Harsha (NIH/NEI) [C]]

Thanks Nathan! I went a bit too fast - I installed Cytoscape and Altanalyze both separately and 2 versions of Altanalyze - creating confusion.
I later realized I needed to upgrade Java on the machine.
Now, I have uninstalled Cytoscape and there is Cytoscape_v2.6.1 within the altanalyze dir.
How do I start / open Cytoscpae/DomainGraph without rerunning AltAnalyze analysis?
How do I upgrade to the latest version of Cytoscape?

Thanks for your help!
Harsha

________________________________________
From: Nathan Salomonis [nsalo...@gmail.com]
Sent: Thursday, March 24, 2011 9:15 PM
To: Rajasimha, Harsha (NIH/NEI) [C]
Cc: alt_pre...@googlegroups.com
Subject: Re: Error while installing domain graph plugin

[Nathan Salomonis]

Hi Harsha,

Looking into this further, in Windows it does appear that there is a problem with the Cytoscape folder extracted by AltAnalyze. This used to not be an issue, since the Cytoscape folder was included with the program directly, instead of downloaded upon first use. While the actual Cytocape download itself seems to work fine when manually extracted, when AltAnalyze performs the unzip process, the Cytoscape files appear to be corrupted due to some Python related extraction error.

As an interim fix, delete the AltAnalyze Cytoscape folder and then download the Cytoscape archive directly from:
http://altanalyze.org/archiveDBs/Cytoscape/cytoscape.zip

and extract this to the AltAnalyze folder. The exe should work fine. Please tell me if this doesn't work. Sorry for the problems, I will try to come up with a long term solution soon.

Best,
Nathan

On Fri, Mar 25, 2011 at 12:00 PM, Rajasimha, Harsha (NIH/NEI) [C] <rajas...@nei.nih.gov> wrote:

Thanks Nathan - I tried on a total different computer from scratch - altanalyze runs just fine - but I cannot start Cytoscape from the packaged folder (I tried both cytoscape.exe and .bat and also tried to instantiate from AltAnalyze).
Nothing happens - no error - no cytoscape. I am very eager to visualize these results as I believe there is no other tool that can do this job.  It will be fun once I can get this going.

How can I overcome this?

Thank you!

HARSHA K RAJASIMHA, Ph.D.
Digicon Contractor, ITMB/NNRL/NEI
Bioinformatics Programmer / Analyst
National Institutes of Health
6 CENTER DR RM 303 MSC 0610
BETHESDA MD 20892-0610
Tel:  301-402-5734
Fax:  301-480-1769
Email: rajas...@nei.nih.gov

-----Original Message-----
From: Nathan Salomonis [mailto:nsalo...@gmail.com]
Sent: Friday, March 25, 2011 1:08 PM
To: Rajasimha, Harsha (NIH/NEI) [C]

Subject: Re: Error while installing domain graph plugin

Hi Harsha,

I would stick with the version of Cytoscape that comes with AltAnalyze. To begin your analysis, simply double click the Cytoscape.exe file in the Cytoscape program directory (in the AltAnalyze program directory) and follow the example directions from the DomainGraph website. The three main steps will be to register, select species database for download and select the AltAnalyze DomainGraph input file.

Should be straight forward.

Best,
Nathan

[Rajasimha, Harsha (NIH/NEI) [C]]

Thanks Nathan – this solved my problem and I was able to open DomainGraph.  I used version 2.6.1 zip archive from cytoscape website.

Where can I find more information on all the altsplice output directory structure and column label annotations of all files?

I found an excel sheet with column label annotations on the website but it does not cover all the columns and not in the same order or label strings.

Could you tell me which files will give me the following? I see several files that contain this information that confuses me.

1.       A final list of highly significantly alternatively spliced genes (which column tells me the significance, does less mean more?)

2.       The microRNA binding to alternatively spliced exons: I find a file with this info but the columns are not intuitive – where can I find this file type description?

3.       The protein domain info file

 

If I look only at the files in the dir DomainGraph that are imported into that Cytoscape plugin – what will I miss (if any)?

Thank you very much!

 

HARSHA K RAJASIMHA, Ph.D.

Digicon Contractor, ITMB/NNRL/NEI

Bioinformatics Programmer / Analyst

National Institutes of Health

6 CENTER DR RM 303 MSC 0610

BETHESDA MD 20892-0610

Tel:  301-402-5734

Fax:  301-480-1769

Email: rajas...@nei.nih.gov

 

[Nathan Salomonis]

 Hi Harsha,

I'm glad that worked. Sorry about the issue for Windows. I have fixed it for the next version which I hope to release in the next two weeks. As for your questions, see below:

On Sun, Mar 27, 2011 at 7:45 PM, Rajasimha, Harsha (NIH/NEI) [C] <rajas...@nei.nih.gov> wrote:

Thanks Nathan – this solved my problem and I was able to open DomainGraph.  I used version 2.6.1 zip archive from cytoscape website.

Where can I find more information on all the altsplice output directory structure and column label annotations of all files?

The directory structure is illustrated on our tutorial pages, for example:
http://code.google.com/p/altanalyze/wiki/Tutorial_AltExpressionAnalysis (half way down the page)

Detailed column label descriptions can be found here:
http://www.altanalyze.org/help_main.htm
http://code.google.com/p/altanalyze/wiki/AnalyzingASResults
http://code.google.com/p/altanalyze/wiki/ProteinDirectionIndicator
 

I found an excel sheet with column label annotations on the website but it does not cover all the columns and not in the same order or label strings.

If you are referring to this file:
http://altanalyze.org/image/SI_examples.xls

This only gives columns for the exon-level results file (e.g., Hs_RNASeq_NP_vs_hESC-splicing-index-exon-inclusion-results.txt). The gene-level version of this file has near identical column headers, but reports the most highly changed exon score and all exons regulated for that gene.

Could you tell me which files will give me the following? I see several files that contain this information that confuses me.

1.       A final list of highly significantly alternatively spliced genes (which column tells me the significance, does less mean more?)

I would focus on exons rather than genes, since exons are ultimately what are tested (or junctions for RNASeq experiments). In this case, you would focus on the above example file, ending in "splicing-index-exon-inclusion-results.txt". From this file, I look primarily at the columns:

Splicing-Index (2nd column) - this is effectively the alternative exon fold change between the two conditions.
midas p-value (10th column) - this is the MiDAS test p-value for the exon relative to gene expression
SI_p-value (21st column) - this is the t-test p-value of the normalized intensities used to calculate the Splicing-Index for all samples

These columns differ for reciprocal junction comparison analyses (e.g., RNA-seq).

2.       The microRNA binding to alternatively spliced exons: I find a file with this info but the columns are not intuitive – where can I find this file type description?

I would filter this data from the "splicing-index-exon-inclusion-results.txt", column "functional_prediction" (column 15), using the search term "microRNA-target". The file with the suffix, "splicing-index-microRNA-zscores.txt" provides over-representation statistics, so I recommend focusing on the previous file. I realize this is not the most intuitive way to specifically get this data, which requires you to currently filter the spreadsheet in Excel.

3.       The protein domain info file

Again, I would get this from the "splicing-index-exon-inclusion-results.txt", column "uniprot-ens_feature_predictions" (column 16) and "ens_overlapping_domains" (column 18). The first gives you domains (InterPro) and motifs (UniProt) that differ between the two isoforms from column 15. Column 18 lists domains that directly overlap with the alternative exon as opposed to those that differ between the two associated isoforms. Hence, this column is more analogous to DomainGraph. More on this can be found here:
http://code.google.com/p/altanalyze/wiki/ProteinDirectionIndicator
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000553
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896198/?tool=pubmed

If I look only at the files in the dir DomainGraph that are imported into that Cytoscape plugin – what will I miss (if any)?

You will only be able to obtain the probesets, genes, scores and p-values but none of the domain, splice-event, protein, microRNA targeting annotations in addition to over-representation statistics for pathways, GO-terms, domains and microRNA binding sites. The microRNA and splice-event level annotations are provided from within DomainGraph though. Please note, for non-exon array analyses, DomainGraph uses the overlapping exon array probeset IDs as it is currently only compatible with these arrays.

If you have any other questions, please don't hesitate.

Best,
Nathan