[BioC] pathview puzzle

Tue Sep 3 16:26:44 CEST 2013

Hi Weijun, 

This works perfectly as expected! Thank you for the fast update. This option is indeed destined to be very useful for many researchers. 

Best,

Oleg

On 08/30/13, Luo Weijun  wrote:
> The updated pathview (version 1.1.5) is now available through BioC devel version:
> http://bioconductor.org/packages/2.13/bioc/html/pathview.html
> R-forge version failed to build because they haven’t installed some dependency package with their new R 3.0.1. I’ve contact their admin, but not sure when this can be solved.
> Weijun
> 
> --------------------------------------------
> On Wed, 8/28/13, Luo Weijun <luo_weijun at yahoo.com> wrote:
> 
> Subject: Re: [BioC] pathview puzzle
> To: "Oleg Moskvin" <moskvin at wisc.edu>
> Cc: Bioconductor at r-project.org
> Date: Wednesday, August 28, 2013, 2:44 PM
> 
> Hi Oleg,
> I just update pathview package so it can process and analyze
> data labeled with KEGG gene IDs other than Entrez Gene. It
> turns out that this issue affects many other species too. So
> with this update, you can literaully work with all ~2300
> (and more forth-coming) KEGG species data with pathview now.
> I’ve also added new content with working examples on KEGG
> species and Gene ID usage in page 14-16 of the vignette.
> Notice that you need to specified gene.idtype="KEGG" when
> calling pathview.
> I’ve posted the new package to R-forge. You should be able
> to access it in the next few hours at http://r-forge.r-project.org/R/?group_id=1619. Just
> install it follow the instruction there. The Bioc version
> will also be updated in the next 1-2 days: http://bioconductor.org/packages/devel/bioc/html/pathview.html.
> Let me know how that works or if you have questions. HTH.
> Weijun
> 
> --------------------------------------------
> On Fri, 8/23/13, Luo Weijun <luo_weijun at yahoo.com>
> wrote:
> 
> Subject: Re: [BioC] pathview puzzle
> To: Bioconductor at r-project.org,
> "Oleg Moskvin" <moskvin at wisc.edu>
> Date: Friday, August 23, 2013, 9:53 PM
> 
> Hi Oleg,
> Thanks for the note. This is indeed a problem I didn’t
> realize previously! KEGG uses Entrez Gene ID for all other
> model organisms I’ve checked.
> I am working on a generic fix (not only for E coli but
> other
> species with similar situation) and will incorporate that
> into the development version of pathview soon. Will keep
> you
> posted.
> Thanks for pointing this out.
> Weijun
> 
> 
> --------------------------------------------
> On Fri, 8/23/13, Oleg Moskvin <moskvin at wisc.edu>
> wrote:
> 
> Subject: Re: [BioC] pathview puzzle
> To: Bioconductor at r-project.org,
> luo_weijun at yahoo.com
> Date: Friday, August 23, 2013, 12:19 PM
> 
> Hi Weijun,
> 
> Thank you for the response. 
> 
> The problem seems to be deeper than that and is
> connected
> to
> special handling of a particular species - E.coli -
> by
> KEGG.
> 
> 
> I looked into the pathview() code and here is what I
> see: 
> 
> 1) gene.data is remapped internally via mol.sum() to
> have
> ENTREZ IDs;
> 2) remapped gene.data is used by node.map() to map
> onto
> KEGG
> nodes using node.data
> 3) the node.data used in (2) was originally extracted
> from
> the KEGG XML by node.info()
> 
> The above route implies that the "name" entries in
> the
> KEGG
> XML of type="gene" have "speciesID:ENTREZ" format...
> 
> And in the case of E.coli this doesn't hold true! See
> the
> examples of XML entries for H.sapience and E.coli
> from my
> yesterday's message (below). 
> 
> In fact, in KEGG XML for E.coli "gene" records
> b-numbers
> are
> used as IDs! 
> 
> So, for the cases like that, when KEGG fails to be
> consistent in the supplied XML structure, one may
> suggest
> introducing an "id.bypass" option to pathview() which
> will
> take the gene.data as is (with the IDs supplied by
> user
> that
> match KEGG XML ids; for example, b-numbers), and pass
> this
> directly to the step 3 (node matching).
> 
> Thanks!
> 
> Oleg
> 
> 
> 
> On 08/22/13, Luo Weijun wrote:
> > Hi Oleg,
> > You are right, the problem is due to ID type
> inconsistency.
> > You have to specify gene.idtype when calling
> pathview
> function, if your gene id type is not Entrez Gene. I
> don’t
> think b-numbers are recognized for sure. For your
> gene
> name
> example, if you mean official gene symbols by
> “gene
> name”, you should specify gene.idtype="SYMBOL"
> (lower
> case
> is fine):
> > eco2.out <- pathview(gene.data =
> T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id =
> "02010",
> gene.idtype="SYMBOL", out.suffix = "T2ACSH", species
> =
> "eco", kegg.native=TRUE)
> 
> 
> On 08/22/13, Oleg Moskvin wrote:
> 
> > 
> > <entry id="2" name="hsa:51343" type="gene"
> > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343">
> > <graphics name="FZR1, CDC20C, CDH1, FZR,
> FZR2,
> HCDH,
> HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"
> > type="rectangle" x="919" y="536" width="46"
> height="17"/>
> > </entry>
> > 
> > 
> > <entry id="4" name="eco:b1513" type="gene"
> > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513">
> > <graphics name="lsrA" fgcolor="#000000"
> bgcolor="#BFFFBF"
> > type="rectangle" x="339" y="1882" width="46"
> height="17"/>
> > </entry>

--
---------------------------------------------------------
Oleg Moskvin, PhD 
Associate Scientist (Computational Biology)
Great Lakes Bioenergy Research Center
University of Wisconsin-Madison
1552 University Ave Room 4241 
Madison, Wisconsin 53706
Phone: (608) 890-2361
Email: moskvin at wisc.edu