query

[rashi parihar]

I am new to EGAN.I want to ask two questions.First that is egan is
accessible through cytoscape?I mean that there is any way to see the
output of EGAN through cytoscape? Second question is that can egan is
used to do analysis of any organism or it can be used for selected
organism?

[ucsf egan]

Hi Rashi,

Thanks for posting.  Here are the answers to your questions:

1) No, at this point EGAN is not accessible through Cytoscape, and the
semantic graphs in EGAN cannot currently be exported to Cytoscape.

However, EGAN uses the graph visualization library of Cytoscape to lay
out and visualize its graphs - therefore the EGAN visualization of a
network is effectively the same as seeing the output of EGAN via
Cytoscape.  Also, EGAN readily accepts files in the .SIF format which
is extensively used in Cytoscape.

2) EGAN can be used to do analysis of any organism:

a) Using the default files that EGAN provides (currently 10 organisms)
b) Using your own files that contain gene sets and gene-gene
interaction data for your organism.  If you have questions about this
one, please post them because this functionality is rather under-
documented.
c) Using a homology bridge - experiment data for organisms that are
poorly annotated (few gene sets, few protein-protein interactions) can
be mapped to better-annotated organisms by using a homology mapping
file (e.g. one that maps the Entrez Gene ID for a gene in rice to the
Entrez Gene ID for its homolog in Arabidopsis - then you can use EGAN
Arabidopsis to view your rice data). You can also map gene sets and/
or gene-gene interaction data in the other direction.  For example,
you can map the Arabidopsis gene sets into EGAN Rice by using the
homology mapping file (i.e. a file that maps Arabidopsis Entrez Gene
IDs to rice Entrez Gene IDs).

Please post again if you have any more questions.

Regards,


Jesse

[rashi parihar]

Thanx Jesse for your information See I have to see the gene interaction in one of the bacteia.I do not have gene intaerction data avilable for that organism .How can I proceed?.For example i have to serach a gene"ERG1" in one of bacteria.how to do that?
PLz help me out as i am new to EGAN.Waiting for your reply.

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“Many Smiles Begin Because Of Another Smile . . . ."
 
Regards,
Rashi

[ucsf egan]

Hi Rashi,

I'm not sure EGAN can easily provide what you need.  Unfortunately there aren't any pre-collated bacterial gene set/interaction collections automatically available at our website or at a third-party site.

You can create your own collections and then specify them using the Launch EGAN Wizard (let me know and I'll guide you through the process), but it will take quite a bit of work just for you to acquire gene sets/interactions.  It will require scripting/programming.  This site (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/) is a good source of gene sets.  For protein-protein interactions, I suggest BioGRID (http://thebiogrid.org/) and/or IntAct (http://www.ebi.ac.uk/intact/).

I suggest you take a look at BioCyc (http://biocyc.org/) and see if that can help you with your single-gene search.

Best of luck,

Jesse

[rashi parihar]

Thanx dear!!! you have said that "You can create your own collections and then specify them using the Launch EGAN Wizard".How to do that?plz guide me.Thanx once again!!! 

 

You can create your own collections and then specify them using the Launch EGAN Wizard

[rashi parihar]

Thanx once again!!as u have told that Using a homology bridge - experiment data for organisms that are

poorly annotated (few gene sets, few protein-protein interactions) can
be mapped to better-annotated organisms by using a homology mapping
file (e.g. one that maps the Entrez Gene ID for a gene in rice to the
Entrez Gene ID for its homolog in Arabidopsis - then you can use EGAN
Arabidopsis to view your rice data).  You can also map gene sets and/
or gene-gene interaction data in the other direction.  For example,
you can map the Arabidopsis gene sets into EGAN Rice by using the
homology mapping file (i.e. a file that maps Arabidopsis Entrez Gene

IDs to rice Entrez Gene IDs).how to do this.I Mean which steps I have to follow for performing this task?plz tell me in detail.

 

 

 

“Many Smiles Begin Because Of Another Smile . . . ."
 
Regards,
Rashi