Kegg pathway --> gene network
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Gavai, Anand ▴ 40
@gavai-anand-2004
Last seen 10.3 years ago
Hi Everyone, I had been searching over google but to no avail. Actually I had been searching on the net for any equivalent package in bioconductor which would help the community to construct an equivalent gene network from available pathway database like KEGG. For e.g. To find all genes available in Glycolysis pathway and depending on the direction of arcs between metabolites, to construct an equivalent gene regulatory network from the same. off course doing this manually and construct a graphNel object is possible, but to do this for more pathways would be cumbersome, so was wondering if there are any tools available in this regard or any pointers .? Any information would be of great help. Thanks in advance, Anand [[alternative HTML version deleted]]
Pathways Network Pathways Network • 2.0k views
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Sim, Fraser ▴ 350
@sim-fraser-2871
Last seen 10.3 years ago
Hi Anand- I searched for a similar package in the archives but I think the KEGG database is not available in a format that describes the 'edges' in a manner which can be easily parsed into a graph object. Biocarta on the otherhand does have this information available as an xml file. I have written some code to parse Biocarta and plot pathways accordingly using graphviz. I was thinking about making this available as a package but haven't gotten around to it yet. Cheers, Fraser -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Anand Gavai Sent: Thursday, December 11, 2008 7:46 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Kegg pathway --> gene network Hi Everyone, I had been searching over google but to no avail. Actually I had been searching on the net for any equivalent package in bioconductor which would help the community to construct an equivalent gene network from available pathway database like KEGG. For e.g. To find all genes available in Glycolysis pathway and depending on the direction of arcs between metabolites, to construct an equivalent gene regulatory network from the same. off course doing this manually and construct a graphNel object is possible, but to do this for more pathways would be cumbersome, so was wondering if there are any tools available in this regard or any pointers .? Any information would be of great help. Thanks in advance, Anand [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Before anyone runs off to write a new package, a new package is being added to bioconductor right now that looks like it might do some of what you are looking for: Package: KEGGgraph Type: Package Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor Version: 0.8.6 Date: 2008-12-11 Author: Jitao David Zhang and Stefan Wiemann Maintainer: Jitao David Zhang <j.zhang at="" dkfz.de=""> Description: KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. License: GPL (>=2) LazyLoad: yes Depends: methods, XML (>= 1.96-0), graph Suggests: RBGL, Rgraphviz (>= 1.18.0), KEGG.db Collate: kegg2graph-functions.R parse.R graph.R kgmlfile.R misc.R vis.R URL: http://www.dkfz.de/en/mga/index.html biocViews: Pathways This should show up in the devel branch in the next couple of days. I am just a messenger here so if it helps you, be sure to thank the maintainer. Marc Sim, Fraser wrote: > Hi Anand- > > I searched for a similar package in the archives but I think the KEGG > database is not available in a format that describes the 'edges' in a > manner which can be easily parsed into a graph object. > > Biocarta on the otherhand does have this information available as an xml > file. > > I have written some code to parse Biocarta and plot pathways accordingly > using graphviz. I was thinking about making this available as a package > but haven't gotten around to it yet. > > Cheers, > Fraser > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Anand Gavai > Sent: Thursday, December 11, 2008 7:46 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Kegg pathway --> gene network > > Hi Everyone, > > I had been searching over google but to no avail. Actually I had been > searching on the net for any equivalent package in bioconductor which > would > help the community to construct an equivalent gene network from > available > pathway database like KEGG. > > For e.g. To find all genes available in Glycolysis pathway and depending > on > the direction of arcs between metabolites, to construct an equivalent > gene > regulatory network from the same. > > > > off course doing this manually and construct a graphNel object is > possible, > but to do this for more pathways would be cumbersome, so was wondering > if > there are any tools available in this regard or any pointers .? > > > > Any information would be of great help. > > > > Thanks in advance, > > Anand > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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@jitao-david-zhang-3188
Last seen 7.9 years ago
Hi Anand, The package 'KEGGgraph' does exactly the task you need. It is added to bioc-devel these days and I assume it will be available from bioc- devel before holidays. I am the maintainer of this package and am ready to answer your questions around it. Best wishes, David > Hi Everyone, > > I had been searching over google but to no avail. Actually I had been > searching on the net for any equivalent package in bioconductor which would > help the community to construct an equivalent gene network from available > pathway database like KEGG. > > For e.g. To find all genes available in Glycolysis pathway and depending on > the direction of arcs between metabolites, to construct an equivalent gene > regulatory network from the same. > > > > off course doing this manually and construct a graphNel object is possible, > but to do this for more pathways would be cumbersome, so was wondering if > there are any tools available in this regard or any pointers .? > > > > Any information would be of great help. > > > > Thanks in advance, > > Anand > > -- Cheers, David [[alternative HTML version deleted]]
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Hi David- I am still unable to install KEGGgraph using biocLite. > source("http://www.bioconductor.org/biocLite.R") > biocLite("KEGGgraph") Running biocinstall version 2.3.9 with R version 2.8.0 Your version of R requires version 2.3 of Bioconductor. Warning message: package 'KEGGgraph' is not available > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.0 > Any idea when this package might be ready? Cheers, Fraser -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jitao David Zhang Sent: Friday, December 12, 2008 6:29 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Kegg pathway --> gene network Hi Anand, The package 'KEGGgraph' does exactly the task you need. It is added to bioc-devel these days and I assume it will be available from bioc- devel before holidays. I am the maintainer of this package and am ready to answer your questions around it. Best wishes, David > Hi Everyone, > > I had been searching over google but to no avail. Actually I had been > searching on the net for any equivalent package in bioconductor which would > help the community to construct an equivalent gene network from available > pathway database like KEGG. > > For e.g. To find all genes available in Glycolysis pathway and depending on > the direction of arcs between metabolites, to construct an equivalent gene > regulatory network from the same. > > > > off course doing this manually and construct a graphNel object is possible, > but to do this for more pathways would be cumbersome, so was wondering if > there are any tools available in this regard or any pointers .? > > > > Any information would be of great help. > > > > Thanks in advance, > > Anand > > -- Cheers, David [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Fraser -- New packages are added to the 'devel' branch of Biocondcutor. 'devel' packages require the 'devel' version of R. You're using the 'release' version of R. http://cran.fhcrc.org/bin/windows/base/rdevel.html Martin Sim, Fraser wrote: > Hi David- > > I am still unable to install KEGGgraph using biocLite. > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("KEGGgraph") > Running biocinstall version 2.3.9 with R version 2.8.0 > Your version of R requires version 2.3 of Bioconductor. > Warning message: > package 'KEGGgraph' is not available >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > loaded via a namespace (and not attached): > [1] tools_2.8.0 > > Any idea when this package might be ready? > > Cheers, > Fraser > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jitao David > Zhang > Sent: Friday, December 12, 2008 6:29 AM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Kegg pathway --> gene network > > Hi Anand, > > The package 'KEGGgraph' does exactly the task you need. It is added to > bioc-devel these days and I assume it will be available from bioc- devel > before holidays. > > I am the maintainer of this package and am ready to answer your > questions > around it. > > Best wishes, > David > >> Hi Everyone, >> >> I had been searching over google but to no avail. Actually I had been >> searching on the net for any equivalent package in bioconductor which > would >> help the community to construct an equivalent gene network from > available >> pathway database like KEGG. >> >> For e.g. To find all genes available in Glycolysis pathway and > depending on >> the direction of arcs between metabolites, to construct an equivalent > gene >> regulatory network from the same. >> >> >> >> off course doing this manually and construct a graphNel object is > possible, >> but to do this for more pathways would be cumbersome, so was wondering > if >> there are any tools available in this regard or any pointers .? >> >> >> >> Any information would be of great help. >> >> >> >> Thanks in advance, >> >> Anand >> >>
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@elliot-kleiman-2565
Last seen 10.3 years ago
Hi Fraser, Although KEGGgraph has not yet been formally released, you may still manually install it. First, download it to your local machine * [ http://www.bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html ] For example, I am [still] running R version 2.7.2 and I have installed KEGGgraph, by doing, ... # must be su (or root) or have sudo permissions % R CMD INSTALL KEGGgraph_0.8.7.tar.gz # print-out sessionInfo() > sessionInfo() R version 2.7.2 (2008-08-25) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;L C_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] RBGL_1.18.0 biomaRt_1.14.1 RCurl_0.92-0 Rgraphviz_1.18.1 [5] KEGGgraph_0.8.7 graph_1.20.0 XML_1.98-1 loaded via a namespace (and not attached): [1] cluster_1.11.11 tools_2.7.2 Hope that helps, ... Elliot -- MS graduate student Computational Science Program San Diego State University http://www.csrc.sdsu.edu/ http://www.sdsu.edu/
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@martin-morgan-1513
Last seen 5 months ago
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Elliot Kleiman <kleiman at="" rohan.sdsu.edu=""> writes: > Hi Fraser, > > Although KEGGgraph has not yet been > formally released, you may still manually > install it. This sounds like a very dangerous solution -- packages have complicated and often implicit dependencies. This will, sooner or later, lead to grief -- an obscure error caused by incompatibilities between packages from different release versions. A non-negligible fraction of the mail on this list is from exactly this situation. The 'what is your sessionInfo()' / 'update your packages' solution that most often addresses the problem takes time away from more meaningful work, for all parties. Might as well just 'do it right' in the first place. Martin > First, download it to your local machine > * [ http://www.bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html ] > > For example, I am [still] running R version 2.7.2 and I have installed > KEGGgraph, by doing, ... > > # must be su (or root) or have sudo permissions > % R CMD INSTALL KEGGgraph_0.8.7.tar.gz > > # print-out sessionInfo() > > sessionInfo() > R version 2.7.2 (2008-08-25) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C ;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE= C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] RBGL_1.18.0 biomaRt_1.14.1 RCurl_0.92-0 Rgraphviz_1.18.1 > [5] KEGGgraph_0.8.7 graph_1.20.0 XML_1.98-1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 tools_2.7.2 > > Hope that helps, > > ... Elliot > > -- > MS graduate student Computational Science Program San Diego State > University > http://www.csrc.sdsu.edu/ http://www.sdsu.edu/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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