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@gmail.com

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