[Biopython] Retrieving miRNA target data from TargetScan

[Sean Davis]

On Tue, Feb 23, 2010 at 6:00 PM, Nizar Ghneim <abumustafa3 at gmail.com> wrote:
> Thank you for the speedy reply, Sean.
>
> For a 100 MB file, this seems to have everything I need!
> Just a few questions about the file
> 1 - What does the "CHR" column represent
> 2 - When was the data compiled? (I understand the method used was miRanda.)

Hi, Nizar.  You'll probably want to look at the website that hosts the
data for the details:

http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/

Sean

> On Tue, Feb 23, 2010 at 4:31 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>> 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
>> > _______________________________________________
>> > Biopython mailing list  -  Biopython at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython
>> >
>
>