[BioC] pathview puzzle

[Luo Weijun]

Oleg,
I am glad that it works for you. thanks for all the feedback!
Weijun

--------------------------------------------
On Tue, 9/3/13, Oleg Moskvin <moskvin at wisc.edu> wrote:

 Subject: Re: [BioC] pathview puzzle

 Cc: Bioconductor at r-project.org
 Date: Tuesday, September 3, 2013, 10:26 AM

 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
 > 
 > --------------------------------------------

 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
 > 
 > --------------------------------------------

 > 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,

 > 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