[BioC] How does pathview deal with enzyme with several coding genes?

[Luo Weijun]

As described in Page 7 of pathview vignette:
“..Note in native KEGG view, a gene node may represent multiple genes/proteins with similar or redundant functional role. The number of member genes range from 1 up to several tens. They are intentionally put together as a single node on pathway graphs for better clarity and readability. Therefore, we do not split node and mark each member genes separately by default. But rather we visualize the node-wise data by summarize gene-wise data, users may specify the summarization method using node.sum arguement.” 
Native KEGG graph use the most informative name to label multiple-gene nodes. When Graphviz view or 2-layer graph is specified, we choose to use the most common gene symbol (among multiple ones).

Check the function documentation of pathview:
?pathview
node.sum argument, character, the method name to calculate node summary given that multiple genes
or compounds are mapped to it. Potential options include "sum","mean", "median","max", "max.abs" and "random". Default node.sum="sum".

Below are the data you provided. You may want to check whether the fold change sum of your 3 genes is about 0.299 or 0.4.
> Gene    Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB;
> Log2fc  -1.22;-0.118;1.645;

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On Mon, 2/17/14, 刘鹏飞 <liupfskygre at gmail.com> wrote:

 Subject: Re: How does pathview deal with enzyme with several coding genes?
 To: "bioconductor at r-project.org list" <Bioconductor at r-project.org>

 Date: Monday, February 17, 2014, 2:33 AM

 Hi,I found in the
 mol.data that pathview just do some add calculation, for
 example, acs-1=-1.7283407; acs-2=-4.1076455, in the
 mol.data, just acs-1 was chosen, and data was set as
 acs-1=-5.835986205; but, for Gene   
 Mtc_1383/aroF;
 Mtc_2501/fbaA;
 Mtc_0384/fbaB;
 Log2fc  -1.22;-0.118;1.645;
 in mol.data, fbaB=0.299; but
 aroF+fbaB=0.4, which is not equal to 0.299;
 So, I am confused on this issue
 now!and more, if several genes
 encoding for different subunits of a enzyme,  all get a log2
 fold was less than 1, but add all them up would exceed 1,
 and give us a wrong information. or like the case above,
 which also give us some wrong information. 
 why the data in the mol.data is
 not the average of several genes encoding for different
 subunit of the same enzyme? And for iso-functional enzyme,
 could we display them separately(like fbaB and aroF)?


 Thanks! 


 2014-02-17 14:37 GMT+08:00 刘鹏飞 <liupfskygre at gmail.com>:

 Dear all, Now I am using
 pathview to map my RNAseq expression data to the keggmap of
 my organism ‘mez’. I want to know how pathview
 deal with the colour of enzyme with several conding genes,
 for example:

 In pathway: Glycolysis / Gluconeogenesis, mez00010, the
 gene node (enzyme 4.1.2.13) has 3 genes related to it.
 Gene   
 Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB;

 Log2fc 
 -1.22;-0.118;1.645; aroF
 and fbaB all significantly regulated and has a |log2 fold
 change| >1.  Another example
 is that one enzyme has several subunits, each has a encoding
 gene, but with different expression level(here I mean the
 log2 fold change of treat/ck).

  I found pathview just choose to plot
 one data onto the map(eg, fbaB and aroF, it just choose
 fbaB, due to it appear first in the gene.names?). which one
 will pathview choose to plot? How could I display all
 information on one plot, like aroF and fbaB, separate and
 display them on the map? what about genes encoding for
 different subunits of a gene?

  Thanks!
 -- 
 Pengfei Liu, PhD Candidate

 Lab of Molecular Ecology -
 Max Planck Partner Group

 College of Resources and Environmental Sciences
 China Agricultural University
 No.2 Yuanmingyuanxilu, Beijing, 100193
 P.R. China

 Tel: +86-10-62731358
 Fax: +86-10-62731016
  
 E-mail: liupfskygre at gmail.com








 -- 
 Pengfei Liu, PhD Candidate
 Lab of Molecular Ecology -
 Max Planck Partner Group

 College of Resources and Environmental Sciences
 China Agricultural University
 No.2 Yuanmingyuanxilu, Beijing, 100193
 P.R. China

 Tel: +86-10-62731358
 Fax: +86-10-62731016
  
 E-mail: liupfskygre at gmail.com