[rat-forum] Batch Query - gene search

[Smith, Jennifer]

Anbarasu,

 

I'm afraid our keyword search does not currently include a way to do
bulk searches except for queries on gene families where the gene symbols
all start with the same letters, e.g. searches for "Defb" or "defb*"
will return all of the members of the beta-defensin family of genes.
For other types of bulk queries, you have several options.  The first
option is to use our BioMart tool (http://biomart.mcw.edu:9999/) which
allows you to either paste a list of identifiers into the search box, or
upload a file containing the identifiers.  I'm including some
instructions below to help you get started if you would like to try this
option.

 

The second possibility would be to download the GENES_RAT file from our
ftp site and extract the information about the genes that you are
interested in from there.

 

The third option would be to email me personally at jrsmith at mcw.edu with
the genes that you are interested in and the data that you need and I
would be happy to run queries against our database for you.  Anything
that you sent would, of course, be kept confidential as would my
response.

 

Sincerely,

 

Jennifer Smith

Scientific Curator

RGD

 

 

Instructions for using BioMart:

 

Go to the BioMart home page at http://biomart.mcw.edu:9999/

 

Click "Start MartView Session" at the bottom of the page

 

Under "CHOOSE DATABASE", select "RGD Mart" from the dropdown list

 

Several links will appear in the list on the left of the window,
including "Filters" and "Attributes"

 

Click "Filters"

 

This page gives you several options of types of data and identifiers
that you can "search on".  For instance, if you have a list of gene
symbols, click the plus sign by "Gene Information", check the box beside
"Gene Symbol" and enter a comma-separated list of gene symbols into the
box.  If you have a list of RGD IDs, UniProt IDs, Genbank Accession
numbers, Entrez Gene IDs, etc., select "External database Identifiers",
check "Limit to Genes with...", select the appropriate type of ID and
paste your list (either comma-separated or with a single ID per line)
into the box.

 

Once you have selected which genes you want to search for, click
"Attributes" to choose what data you want to get back about those genes.

 

On this page, you have the choice of "Gene and Function" which includes
map positions and functional annotations like disease, phenotype and
gene ontology annotations, or "Database Accessions".  In either case,
you will always want to include at least RGD ID and/or Symbol from the
"Gene Data" section as well as whatever other information you are
looking for.

 

Once you have selected your desired output, click "Results" at the top
left of the page.

 

On the results page, you can see that the RGD ID for each object links
to its RGD report page.  Also, the results can be viewed in the browser
window or downloaded as an HTML, TSV, CSV or Excel format file.

 

 

 

 

Jennifer R. Smith

Scientific Curator

Rat Genome Database

Medical College of Wisconsin

8701 Watertown Plank Rd

Milwaukee, WI  53226

(414) 456-8871 (Phone)

(414) 456-6595 (Fax)

jrsmith at mcw.edu

http://rgd.mcw.edu <http://rgd.mcw.edu/> 

 

________________________________

From: rat-forum-bounces at mcw.edu [mailto:rat-forum-bounces at mcw.edu] On
Behalf Of Anbarasu L A
Sent: Friday, February 13, 2009 11:51 AM
To: rat-forum at mcw.edu
Subject: [rat-forum] Batch Query - gene search

 

Hi,

Can I use RGD for searching multiple genes together? I have tried using
comma but doesn't work in that way, I guess. 

Thanks.

Kind regards,
Anbarasu

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