[BioC] pathview puzzle
Luo Weijun
luo_weijun at yahoo.com
Fri Aug 30 16:26:59 CEST 2013
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
--------------------------------------------
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>
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