[Biopython] Retrieving miRNA target data from TargetScan

[Sean Davis]

On Tue, Feb 23, 2010 at 4:25 PM, Nizar Ghneim <abumustafa3 at gmail.com> wrote:
> Hello All,
>
> I have been using BioPython for a while now; this is my first time to post
> on here. I currently have a list of ~150 miRNAs (that I obtained from a
> microarray) that I would like analyze. My approach is to use TargetScan.org
> (or miRanda, PicTar, etc.) to retrieve a list of target genes for each miRNA
> in the list.

Hi, Nizar.

You might just download the data from here:

ftp://ftp.ebi.ac.uk/pub/databases/microcosm/v5/arch.v5.txt.homo_sapiens.zip

Sean


> Calling this website directly:
>>>
> http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100
> Will give me a list of gene targets for the miRNA hsa-mir-100
>
> Using the Bio.Entrez.efetch() method as I guide, I wrote the following code:
>
> import urllib
> f = urllib.urlopen(
> http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&mirg=hsa-mir-100
> )
>
> I get the following error message:
>
>  File "c:\Python26\lib\urllib.py", line 87, in urlopen
>    return opener.open(url)
>  File "c:\Python26\lib\urllib.py", line 206, in open
>    return getattr(self, name)(url)
>  File "c:\Python26\lib\urllib.py", line 345, in open_http
>    h.endheaders()
>  File "c:\Python26\lib\httplib.py", line 892, in endheaders
>    self._send_output()
>  File "c:\Python26\lib\httplib.py", line 764, in _send_output
>    self.send(msg)
>  File "c:\Python26\lib\httplib.py", line 723, in send
>    self.connect()
>  File "c:\Python26\lib\httplib.py", line 704, in connect
>    self.timeout)
>  File "c:\Python26\lib\socket.py", line 514, in create_connection
>    raise error, msg
> IOError: [Errno socket error] [Errno 10061] No connection could be made
> because the target machine actively refused it
>
> I have little to no experience with cgi (or any web-based programming for
> that matter). Any help would be greatly appreciated.
>
> Thank you and regards,
> Abu Mustafa
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