Kegg pathways overlay with log fold change values

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Amit Kumar Kashyap ▴ 50

@amit-kumar-kashyap-5166

Last seen 10.3 years ago

Hello all, does anyone knows how we can overlay expression data { coloring with up and down genes } in pathways using R package or any other script. Especially the results from SPIA package , we get the kegg link like this ... http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915+36 73+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+9063+ 1029+355+650+5743+596+7188+1612+2113+4254 Now I would like to color up and down regulated genes according to differentially expressed genes from limma package results. Thanks in advance. Kind Regards -Amit Kumar [[alternative HTML version deleted]]

Pathways limma SPIA Pathways limma SPIA • 2.9k views

ADD COMMENT • link updated 12.5 years ago by alessandro brozzi ▴ 120 • written 12.5 years ago by Amit Kumar Kashyap ▴ 50

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alessandro brozzi ▴ 120

@alessandro-brozzi-5276

Last seen 10.0 years ago

European Union

hi, you might try this: http://bioinformatics.oxfordjournals.org/content/25/11/1470.short http://bioc.ism.ac.jp/2.8/bioc/html/KEGGgraph.html Alex On Mon, Jun 11, 2012 at 2:18 PM, Amit Kumar Kashyap <amitonbiochem@gmail.com> wrote: > Hello all, > > does anyone knows how we can overlay expression data { coloring with up > and down genes } in pathways using R package or any other script. > > Especially the results from SPIA package , we get the kegg link like this > ... > > > http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915+ 3673+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+906 3+1029+355+650+5743+596+7188+1612+2113+4254 > > > Now I would like to color up and down regulated genes according to > differentially expressed genes from limma package results. > > > Thanks in advance. > > Kind Regards > -Amit Kumar > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD COMMENT • link 12.5 years ago alessandro brozzi ▴ 120

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With RCytoscape http://bioconductor.org/packages/2.10/bioc/html/RCytoscape.html http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/curr ent/index.html it is straightforward to 1) Display a KEGG network retrieved by Jitao David Zhang's KEGGgraph package 2) control all visual attributes of the graph, using simple 'vizmap' rules and data (e.g., from limma and SPIA) For instance, to control node color: cw <- new.CytoscapeWindow ('setNodeColorRule.test', graph=makeSimpleGraph()) displayGraph (cw) layoutNetwork (cw, 'jgraph-spring') control.points <- c (-3.0, 0.0, 3.0) # typical range of log-fold- change ratio values # paint negative values shades of green, positive values shades of # red, out-of-range low values are dark green; out-of-range high # values are dark red node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000") setNodeColorRule (cw, node.attribute.name='lfc', control.points, node.colors, mode='interpolate') redraw (cw) # applies all current vizmap rules Reproducing the original KEGG layout can be a bit of work. In principle, we could obtain the coordinates from the kgml file, and apply them with repeated calls to RCytoscape's setNodePosition method. In practice, I usually use a combination of automatic layout, and manual layout, saving the result via a call to the saveLayout method. For a fully worked up example, see http://rcytoscape.systemsbiology.net/versions/current/gallery/fendtY east/ - Paul On Jun 11, 2012, at 5:24 AM, alessandro brozzi wrote: > hi, > you might try this: > > http://bioinformatics.oxfordjournals.org/content/25/11/1470.short > http://bioc.ism.ac.jp/2.8/bioc/html/KEGGgraph.html > > Alex > On Mon, Jun 11, 2012 at 2:18 PM, Amit Kumar Kashyap <amitonbiochem at="" gmail.com="">> wrote: > >> Hello all, >> >> does anyone knows how we can overlay expression data { coloring with up >> and down genes } in pathways using R package or any other script. >> >> Especially the results from SPIA package , we get the kegg link like this >> ... >> >> >> http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915 +3673+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+90 63+1029+355+650+5743+596+7188+1612+2113+4254 >> >> >> Now I would like to color up and down regulated genes according to >> differentially expressed genes from limma package results. >> >> >> Thanks in advance. >> >> Kind Regards >> -Amit Kumar >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 12.5 years ago Paul Shannon ▴ 750

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Hello , Thank you very much , I will look in these links . Kind Regards -Amit Kumar On Mon, Jun 11, 2012 at 2:42 PM, Paul Shannon <pshannon@fhcrc.org> wrote: > With RCytoscape > > http://bioconductor.org/packages/2.10/bioc/html/RCytoscape.html > > http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/curr ent/index.html > > it is straightforward to > > 1) Display a KEGG network retrieved by Jitao David Zhang's KEGGgraph > package > 2) control all visual attributes of the graph, using simple 'vizmap' > rules and data (e.g., from limma and SPIA) > > For instance, to control node color: > > cw <- new.CytoscapeWindow ('setNodeColorRule.test', > graph=makeSimpleGraph()) > displayGraph (cw) > layoutNetwork (cw, 'jgraph-spring') > control.points <- c (-3.0, 0.0, 3.0) # typical range of log-fold- change > ratio values > # paint negative values shades of green, positive values shades of > # red, out-of-range low values are dark green; out-of-range high > # values are dark red > node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000") > setNodeColorRule (cw, node.attribute.name='lfc', control.points, > node.colors, mode='interpolate') > redraw (cw) # applies all current vizmap rules > > Reproducing the original KEGG layout can be a bit of work. In principle, > we could obtain the coordinates from the kgml file, and apply them with > repeated calls to RCytoscape's setNodePosition method. In practice, I > usually use a combination of automatic layout, and manual layout, saving > the result via a call to the saveLayout method. > > For a fully worked up example, see > > http://rcytoscape.systemsbiology.net/versions/current/gallery/fendt Yeast/ > > - Paul > > On Jun 11, 2012, at 5:24 AM, alessandro brozzi wrote: > > > hi, > > you might try this: > > > > http://bioinformatics.oxfordjournals.org/content/25/11/1470.short > > http://bioc.ism.ac.jp/2.8/bioc/html/KEGGgraph.html > > > > Alex > > On Mon, Jun 11, 2012 at 2:18 PM, Amit Kumar Kashyap < > amitonbiochem@gmail.com > >> wrote: > > > >> Hello all, > >> > >> does anyone knows how we can overlay expression data { coloring with up > >> and down genes } in pathways using R package or any other script. > >> > >> Especially the results from SPIA package , we get the kegg link like > this > >> ... > >> > >> > >> > http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915+ 3673+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+906 3+1029+355+650+5743+596+7188+1612+2113+4254 > >> > >> > >> Now I would like to color up and down regulated genes according to > >> differentially expressed genes from limma package results. > >> > >> > >> Thanks in advance. > >> > >> Kind Regards > >> -Amit Kumar > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]

ADD REPLY • link 12.5 years ago Amit Kumar Kashyap ▴ 50

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