Question: extracting interactions between members of the KEGG pathways
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gravatar for Jane Fridlyand
13.7 years ago by
Jane Fridlyand90 wrote:
Hello, I was wondering whether there is an infrastructure in one of the BioC packages to extract connections between members of the KEGG pathways. As far as I can tell KEGG package allows to get the identifiers of the members very easily, however I do not see a way of going one step further so to be able to produce a graph (where presence of each edge indicates known interaction or same compound ) Thank you. Any help /suggestion is greatly appreciated. Jane ********************************************************************** ********** Jane Fridlyand, Assistant Professor Department of Epidemiology and Biostatistics Center for Bioinformatics and Molecular Biostatistics UCSF Comprehensive Cancer Center, Box 0128 San Francisco, CA 94143-0128 Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179
ADD COMMENTlink modified 13.7 years ago by rgentleman5.5k • written 13.7 years ago by Jane Fridlyand90
Answer: extracting interactions between members of the KEGG pathways
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gravatar for Wolfgang Huber
13.7 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Hi Jane, here's what Imre Vastrik from Reactome said regarding your question: "We probably can't help with KEGG ;-). Reactome content is projected into pair-wise interaction space (see http://www.reactome.org/download/interactions.README.txt). The data (human only) is available at: http://www.reactome.org/download/current/homo_sapiens.interactions.txt .gz I imagine that another bit of useful information would be the association of sequence identifiers with pathways (not contained in the file above) so that one can go from a pathway to identifiers and for an indentifier to pathways." ---- There are a number of additional datasets in different file formats to download http://www.reactome.org/download/ Cheers Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber ------------------------------------- Jane Fridlyand wrote: > Hello, > > I was wondering whether there is an infrastructure in one of the BioC > packages to extract connections between members of the KEGG pathways. As > far as I can tell KEGG package allows to get the identifiers of the > members very easily, however I do not see a way of going one step further > so to be able to produce a graph (where presence of each edge indicates > known interaction or same compound ) > > Thank you. Any help /suggestion is greatly appreciated. > > Jane > >
ADD COMMENTlink written 13.7 years ago by Wolfgang Huber13k
> Hello, > > I was wondering whether there is an infrastructure in one of the BioC > packages to extract connections between members of the KEGG pathways. As > far as I can tell KEGG package allows to get the identifiers of the > members very easily, however I do not see a way of going one step further > so to be able to produce a graph (where presence of each edge indicates > known interaction or same compound ) > > Thank you. Any help /suggestion is greatly appreciated. > > Jane Have you looked at the Rgraphviz package? "HowTo layout a pathway", focuses on drawing genetic networks using a KEGG pathway as an example: http://www.bioconductor.org/repository/devel/vignette/layingOutPathway s.pdf Installation: ------------- Install graphviz from www.graphviz.org and then within R simply do: source("http://www.bioconductor.org/biocLite.R") biocLite("Ruuid") biocLite("graph") biocLite("Rgraphviz") General Documentation: ---------------------- HowTo Render A Graph Using Rgraphviz: http://www.bioconductor.org/repository/devel/vignette/Rgraphviz.pdf Peter
ADD REPLYlink written 13.7 years ago by Peter170
Peter (BioConductor List) wrote: >> Hello, >> >> I was wondering whether there is an infrastructure in one of the BioC >> packages to extract connections between members of the KEGG pathways. As >> far as I can tell KEGG package allows to get the identifiers of the >> members very easily, however I do not see a way of going one step further >> so to be able to produce a graph (where presence of each edge indicates >> known interaction or same compound ) >> >> Thank you. Any help /suggestion is greatly appreciated. >> >> Jane > > > Have you looked at the Rgraphviz package? > > "HowTo layout a pathway", focuses on drawing genetic networks using a > KEGG pathway as an example: > > http://www.bioconductor.org/repository/devel/vignette/layingOutPathw ays.pdf Having said that, re-reading this document (Jeff Gentry, May 17, 2005) it probably won't help you very much: > At this time, there is no automated way to extract the appropriate information > from KEGG (or other sites) and construct a graph. If one wishes to layout their > own pathways, it requires manual construction of a graph, creating each node > and then recording the edges. Likewise, for any basic attributes ..., they too > must be collected by hand. :(
ADD REPLYlink written 13.7 years ago by Peter170
Answer: extracting interactions between members of the KEGG pathways
0
gravatar for rgentleman
13.7 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
There is some stuff done in the cMAP and pathRender packages, but this has not progressed that far, mostly due to a lack of resources cMAP is a meta-data package which has information from both KEGG and BioCarta (original data from the NCI) pathRender is in the development archive best wishes Robert Jane Fridlyand wrote: > Hello, > > I was wondering whether there is an infrastructure in one of the BioC > packages to extract connections between members of the KEGG pathways. As > far as I can tell KEGG package allows to get the identifiers of the > members very easily, however I do not see a way of going one step further > so to be able to produce a graph (where presence of each edge indicates > known interaction or same compound ) > > Thank you. Any help /suggestion is greatly appreciated. > > Jane > > > > > > ******************************************************************** ************ > Jane Fridlyand, Assistant Professor > Department of Epidemiology and Biostatistics > Center for Bioinformatics and Molecular Biostatistics > UCSF Comprehensive Cancer Center, > Box 0128 San Francisco, CA 94143-0128 > Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD COMMENTlink written 13.7 years ago by rgentleman5.5k
Another issue is availability of cMAP data: data for download is very different from that driving cMAP online querries. The downloadable data is only a small subset of online data, and there are quite some discrepencies between the two. The downloadable data is unchanged since early 2005. Li > There is some stuff done in the cMAP and pathRender packages, but this > has not progressed that far, mostly due to a lack of resources > > cMAP is a meta-data package which has information from both KEGG and > BioCarta (original data from the NCI) > > pathRender is in the development archive > > best wishes > Robert > > > Jane Fridlyand wrote: >> Hello, >> >> I was wondering whether there is an infrastructure in one of the BioC >> packages to extract connections between members of the KEGG pathways. As >> far as I can tell KEGG package allows to get the identifiers of the >> members very easily, however I do not see a way of going one step >> further >> so to be able to produce a graph (where presence of each edge indicates >> known interaction or same compound ) >> >> Thank you. Any help /suggestion is greatly appreciated. >> >> Jane >> >> >> >> >> >> ******************************************************************* ************* >> Jane Fridlyand, Assistant Professor >> Department of Epidemiology and Biostatistics >> Center for Bioinformatics and Molecular Biostatistics >> UCSF Comprehensive Cancer Center, >> Box 0128 San Francisco, CA 94143-0128 >> Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 13.7 years ago by Li Long120
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