converting Flybase identifiers into gene names

[F Casares]

This is a question from a fly person: Does anyone know how to convert
Flybase identifiers into gene symbols (once the node attributes have
been imported from DroID) in a Cytoscape network (if there were such a
possibility?)
thanks a lot
Fernando Casares
fca...@upo.es
CABD (CSIC, UPO), Seville, SPAIN

[Jianjiong Gao]

Hi Fernando,

You could try CyThesaurus (ID mapping) plugins. It is available from
the plugin manager in the category "Network and Attribute I/O". After
installing the plugin, I would suggest the following steps to map from
Flybase identifiers to gene symbols

* Open your session file
* From menu: Plugin => CyThesaurus plugin
* Click "ID Mapping Resources Configuration" at bottom left size of
the dialog.
* Click on the node "Web Services"
* Choose web service type as "BioMart web service"
* Choose a mart/database as "ENSEMBL 58 GENES (SANGER UK)"
* Choose a dataset as "Drosophila melanogaster genes (BDGP5.13)"
* click "OK" and wait.
* Select "flybase_gene_id" as the source ID type for the node
attribute that containing flybase ids.
* Select a target ID type, e.g., "flybasename_gene"
* Click "OK" and wait, close the dialog
* In the Data Panel, display the new attribute "flybasename_gene"
which was just created.

Please let me know if you have any problem trying out the plugin.

-JJ

On Jun 14, 9:51 am, F Casares <seminarios.c...@gmail.com> wrote:
> This is a question from a fly person: Does anyone know how to convert
> Flybase identifiers into gene symbols (once the node attributes have
> been imported from DroID) in a Cytoscape network (if there were such a
> possibility?)
> thanks a lot
> Fernando Casares

> fcas...@upo.es

[Fernando Casares]

thanks a lot, JJ

best

Fer

On 17/06/2010, at 3:52, Jianjiong Gao wrote:

Hi Fernando,

You could try CyThesaurus (ID mapping) plugins. It is available from

the plugin manager in the category "Network and Attribute I/O". After

installing the plugin, I would suggest the following steps to map from

Flybase identifiers to gen e symbol -top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; ">

* Open your session file

* From menu: Plugin => CyThesaurus plugin

* Click "ID Mapping Resources Configuration" at bottom left size of

the dialog.

* Click on the node "Web Services"

* Choose web service type as "BioMart web service"

* Choose a mart/da ES (SANGER UK)"

* Choose a dataset as "Drosophila melanogaster genes (BDGP5.13)"

* click "OK" and wait.

* Select "flybase_gene_id" as the source ID type for the node

attribute that containing flybase ids.

* Select a target ID type, e.g., "flybasename_gene"

* Click "OK" and wait, close the dialog

* In the Data Panel, display the new attri bute "fl style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">which was just created.

Please let me know if you have any problem trying out the plugin.

-JJ

On Jun 14, 9:51 am, F Casares <seminarios.c...@gmail.com> wrote:

Flybase identifiers into gene symbols (once the node attributes have

been imported from DroID) in a Cytoscape network (if there were such a

possibility?)

thanks a lot

Fernando Casares

fcas...@upo.es

CABD (CSIC, UPO), Seville, SPAIN

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Fernando Casares

CABD-Centro Andaluz de Biologia del Desarrollo

Univ. Pablo de Olavide-CSIC

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