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I am doing a Protein protein interaction network clustering project. For testing the result I downloaded the data set from DIP database. It is having DIP-id for each protein and I want to compare the cluster(DIP-id as protein name) with the golden data set CYC2008 which has common name/ORF name as protein name in complex definition. Can anyone help me in converting DIP-id to gene name. For example DIP-839N to Taf1p .

deepthi vr
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1 Answers1

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The obvious and easiest way is to get a database management person to do it for you. A contractor could do this for very cheap, but if the database is an SQL database it is just a matter of using

SELECT * FROM protein WHERE DIP-id='DIP-839N'

After that you would want to 

UPDATE table_name
SET column1=value1,column2=value2,...
WHERE some_column=some_value;

You can put that together with something like

update
    Table
set
    Table.example = a.value
from
    TableExample a
where
    Table.field = "key value"

If you send me the database I might be able to work up an exact query.

Also with certain database tools you might be able to just insert this into Access, Excel, Google Docs, or something like that. I am unfamiliar with this database though.

Goddard
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  • Thank you for your help. From the DIP database I am getting protein protein interactions with their DIP-id as a tab delimited file , I'm afraid , we cann't directly query on their database. – deepthi vr Feb 02 '15 at 08:54
  • Then my advice would change into getting that file imported into a modern database rather then a file. – Goddard Feb 02 '15 at 16:35