[Biopython] Fwd: Retrieving miRNA target data from TargetScan

[Sean Davis]

---------- Forwarded message ----------
From: Nizar Ghneim <abumustafa3 at gmail.com>
Date: Tue, Feb 23, 2010 at 8:53 PM
Subject: Re: [Biopython] Retrieving miRNA target data from TargetScan
To: "Davis, Sean (NIH/NCI) [E]" <sdavis2 at mail.nih.gov>

Although you solved my problem without Biopython, this utility has
been invaluable to me. I would also like to thank everyone involved in
the development of Biopython. Keep up the great work guys!

Nizar

On Tue, Feb 23, 2010 at 6:17 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
> 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
> >> >
> >
> >