Can'T See Green Node In Kgml (Xml) File

Question

[charly.blanche.t]

Hello all,

I recently ran a pathway analysis with Kegg and results can be found at this link or at this one.

My goal is to extract the "green" nodes - "Nodes in green represent biological entities that occur in the current organism" - for some differential analysis. Unfortunately, the KGML I downloaded from the link do not contain any information on the green nodes even though those are present on the maps.

Could somebody pls tell me how I can to extract the names of only the green nodes.

Thank you.

[Pierre Lindenbaum]

where is the kgml ? I cannot find it in your links. (POST-method/cookie problem ?)

Answer 1

[Sudeep]

I just checked the kgml file for Pentose phosphate pathway in your results, and I could see the "green" nodes. It could be that you were trying to find EC number node ids as you see in the figure, but you have to look for Kegg ortholog ids (ko:K....). For nodes: 3.1.1.17 (K01053) and 1.1.1.49 (K00036), see the entries

<entry id="64" name="ko:K01053" type="ortholog" reaction="rn:R01519" link="&lt;a href=" http:="" www.kegg.jp="" dbget-bin="" www_bget?K01053"="" rel="nofollow">http://www.kegg.jp/dbget-bin/www_bget?K01053">
    <graphics name="K01053" fgcolor="#000000" bgcolor="#BFBFFF" type="rectangle" x="421" y="156" width="46" height="17"/>
</entry>

and

<entry id="58" name="ko:K00036" type="ortholog" reaction="rn:R02736" link="&lt;a href=" http:="" www.kegg.jp="" dbget-bin="" www_bget?K00036"="" rel="nofollow">http://www.kegg.jp/dbget-bin/www_bget?K00036">
    <graphics name="K00036" fgcolor="#000000" bgcolor="#BFBFFF" type="rectangle" x="280" y="320" width="46" height="17"/>
</entry>

in the kgml file.

[charly.blanche.t]

These are purple and this color is given to a lot of KO number. These purple nodes are almost for all "orthologs". Green is #BFFFBF and it is definitely not present in the kgml

[Sudeep]

Did you cross check the KO ids of your "green" nodes with KO ids that you find in kgml file ? you will end up with these kgml nodes for the green nodes I took as an example.