incorrect direction in compound-gene interactions
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AR3513 • 0
@ar3513-11025
Last seen 2.1 years ago

Hello, 

I noticed that quite often the gene-compound interactions from the KEGG maps are not retrieved with the right direction when using the function "KEGGpathway2Graph". For example, in  "hsa04930" the D-glucose ("cpd:C00031") interacts with "hsa:5581". This is the direction reported in both the .png image and the corresponding xml file. In particular, in the "hsa04930.xml" file it says: 

<relation type="PCrel" entry2="15" entry1="18"> </relation>

, where "15" is "cpd:C00031" and "18" is "hsa:5581"

However, when I use  "KEGGpathway2Graph", the interaction is retrieved in the opposite direction: i.e. "hsa:5581" interacts with "cpd:C00031". See details below.

I have observed this same problem other times, always between compound and gene interactions. Any chance this can be fixed?

Thanks very much, 

Andrea

 

library(KEGGgraph)

library(RCurl)

path <- "hsa04930"
file <- paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "")
pathway <- getURL(file)
path_parsed <- parseKGML(pathway)
path_network <- KEGGpathway2Graph(path_parsed, genesOnly = FALSE,
                                 expandGenes = TRUE)
adj_matrix <- as(path_network, "matrix")

adj_matrix[c("cpd:C00031", "hsa:5581"), c("hsa:5581", "cpd:C00031")]

#           hsa:5581 cpd:C00031
# cpd:C00031        0          0
# hsa:5581             0          1

 

kegggraph • 629 views
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@zhang-jitao-david-5737
Last seen 2.6 years ago
Switzerland
Dear Andrea, Thanks for the report of the interesting observation. I think in the KGML definition, an interaction should be of the direction from 'entry1' to 'entry2' <http: www.kegg.jp="" kegg="" xml="" docs=""/>, which would translate into "hsa:5581"--> "cpd:C00031". But indeed as I read the PNG figure, it's clear that the direction is reversed. That means unfortunately there's an inconsistency between the KGML specification and the implementation. I will try to consult KEGG people. Before I get a clear answer, please understand that I cannot change the code of the package. Best wishes and thanks again for reporting the issue, David On Tue, Jul 11, 2017 at 2:49 PM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User AR3513 <https: support.bioconductor.org="" u="" 11025=""/> wrote Question: > incorrect direction in compound-gene interactions > <https: support.bioconductor.org="" p="" 97952=""/>: > > Hello, > > I noticed that quite often the gene-compound interactions from the KEGG > maps are not retrieved with the right direction when using the function > "KEGGpathway2Graph". For example, in "hsa04930" the D-glucose > ("cpd:C00031") interacts with "hsa:5581". This is the direction reported in > both the .png image and the corresponding xml file. In particular, in the > "hsa04930.xml" file it says: > > <relation type="PCrel" entry2="15" entry1="18"> </relation> > > , where "15" is "cpd:C00031" and "18" is "hsa:5581" > > However, when I use "KEGGpathway2Graph", the interaction is retrieved in > the opposite direction: i.e. "hsa:5581" interacts with "cpd:C00031". See > details below. > > I have observed this same problem other times, always between compound and > gene interactions. Any chance this can be fixed? > > Thanks very much, > > Andrea > > > > *library(KEGGgraph)* > > *library(RCurl)* > > > > > > > > *path <- "hsa04930" file <- paste("http://rest.kegg.jp/get/ > <http: rest.kegg.jp="" get=""/>", path, "/kgml", sep = "") pathway <- > getURL(file) path_parsed <- parseKGML(pathway) path_network <- > KEGGpathway2Graph(path_parsed, genesOnly = FALSE, > expandGenes = TRUE) adj_matrix <- as(path_network, "matrix")* > > *adj_matrix[c("cpd:C00031", "hsa:5581"), c("hsa:5581", "cpd:C00031")]* > > > > *# hsa:5581 cpd:C00031 # cpd:C00031 0 0 # > hsa:5581 0 1* > > > > ------------------------------ > > Post tags: kegggraph > > You may reply via email or visit incorrect direction in compound-gene interactions > -- *Dr. Jitao David Zhang | 张继涛 | Computational Biology and Bioinformatics* *Roche Pharmaceutical Research and Early Development (pRED) | Pharmaceutical Sciences, Translational Technologies and Bioinformatics (PS-TTB) | Roche Innovation Center Basel | F. Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland* *Building 93/3.34* *Tel +41 61 688 62 51* Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. *Please inform me immediately in case attached documents are missing!*
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AR3513 • 0
@ar3513-11025
Last seen 2.1 years ago

Hi, 

Thanks very much for your reply. Of course, I understand. 

Best wishes, 

Andrea

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