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With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form:

  entry1="46" entry2="41" type="PPrel"
  subtype name="inhibition" value="--|"/
  subtype name="phosphorylation" value="+p"/   

In some entries, the reaction "subtype" entries are 2 in number while in some, it is one, as for the above-mentioned interaction. Another entry is as follows:

   entry1="47" entry2="46" type="PPrel"
      subtype name="phosphorylation"
    value="+p"/   relation

Why do some of the entries have 2 interaction types while some have one? What does this signify biologically?

There is an interaction type called "compound". What does a compound interaction signify biologically?

  <relation entry1="17" entry2="16" type="PPrel">
    <subtype name="compound" value="4"/>
    </relation>
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  • $\begingroup$ have you looked at this description? $\endgroup$ – De Novo Jun 27 '18 at 5:27
  • $\begingroup$ @DanHall yes but they have not explained why one entry can have 2 subtypes or how 2 genes are contributing to the formation of a compound... $\endgroup$ – girl101 Jun 27 '18 at 5:35
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See the manual:

PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother.

For the first and second example, the subtype(s) give more information about the interaction. They aren't necessarily mutually exclusive. For example, phosphorylation can result in activation, inhibition, something else, or unknown. For the first one, there is phosphorylation and the effect is inhibition. For the second one, the interaction is phosphorylation but the effect is not characterized.

When compound is under subtype for a PPrel relation, the value is the entry element ID for the compound (so go look for entry element 4), and it refers to an intermediate of two interacting proteins.

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  • $\begingroup$ Why can't the first one be " it is inhibition and the effect is phosphorylation"? $\endgroup$ – girl101 Jun 27 '18 at 6:03
  • $\begingroup$ @girl101 that just happens to be the causal pathway -- phosphorylation of a protein causes inhibition (in some cases... in other cases it is activation). $\endgroup$ – De Novo Jun 27 '18 at 6:05

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