Gaggle Components
Geese
Data Standards
Boss

Firegoose target websites

A target is a web site with which the Firegoose can exchange data.

DAVID

The DAVID database provides functional annotations given a list of genes.

  • DAVID doesn't work well with VNG numbers. Use GI instead, via the translator.
  • You can broadcast genes back from DAVID by holding down the control (or command) key and selecting with the mouse, which allows you to select a single row or column in an HTML table. Then use the Capture Selection feature (in the right-click menu).

EMBL STRING

STRING is a database of protein interactions. Broadcasting a list of gene names to String will result in an interaction network based on several kinds of evidence. The toolbar can retrieve the network or a list of participants.

  • A long pause will happen when broadcasting a large list of genes to STRING. Be patient. Wait until it says, "Done" in the lower left corner of the browser window. Then press the button marked Continue->.
  • When broadcasting a network back from STRING, there is another long pause during which it looks like the browser is doing nothing. Be patient. It takes up to 15-20 seconds to download and parse the XML representation of the network.

Entrez Gene

The Firegoose can search the Entrez gene database at NCBI for a list of genes. There is a shortcut this feature in the right-click context menu, which will search for whatever text is highlighted in the browser window.

As search criteria, Entrez Gene accepts GeneIDs, locus tags, gene names, COG ids, and many other properties. See the docs for more information.

Entrez Protein

The Firegoose can also search the Entrez protein database at NCBI.

Halo Annotations

The Firegoose exchanges data with the Annotated Proteome database for Halobacterium. A list of VNG gene names can be used to query the database or to broadcast the results of a query back to the Gaggle.

KEGG Pathway

KEGG is the Kyoto Encyclopedia of Genes and Genomes. The Firegoose can broadcast a list of gene names to the KEGG pathways database, retrieving a set of pathways in which the genes are known to participate. Lists of Genes in a particular pathway can be broadcast back to the Gaggle or the pathway itself can be broadcast back as a network (to a limited extent).

More...

The More... option in the target menu allows more targets to be enabled, such as t1DBase, Metlin, Page Goose, and a few others. These are not shown by default because they are experimental or specific to in-house applications. It won't hurt anything to try them out, but they may or may not work.

© 2006, Institute for Systems Biology, All Rights Reserved
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