[BioC] pathview puzzle
Luo Weijun
luo_weijun at yahoo.com
Sat Aug 24 03:53:18 CEST 2013
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
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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