How does pathview deal with enzyme with several coding genes?
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刘鹏飞 ▴ 80
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Dear all, Now I am using pathview to map my RNAseq expression data to the keggmap of my organism 'mez'. I want to know how pathview deal with the colour of enzyme with several conding genes, for example: In pathway: Glycolysis / Gluconeogenesis, mez00010, the gene node (enzyme 4.1.2.13) has 3 genes related to it. Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; Log2fc -1.22;-0.118;1.645; aroF and fbaB all significantly regulated and has a |log2 fold change| >1. Another example is that one enzyme has several subunits, each has a encoding gene, but with different expression level(here I mean the log2 fold change of treat/ck). I found pathview just choose to plot one data onto the map(eg, fbaB and aroF, it just choose fbaB, due to it appear first in the gene.names?). which one will pathview choose to plot? How could I display all information on one plot, like aroF and fbaB, separate and display them on the map? what about genes encoding for different subunits of a gene? Thanks! -- Pengfei Liu, PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 E-mail: liupfskygre@gmail.com [[alternative HTML version deleted]]
RNASeq Organism pathview RNASeq Organism pathview • 1.9k views
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刘鹏飞 ▴ 80
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Hi, I found in the mol.data that pathview just do some add calculation, for example, acs-1=-1.7283407; acs-2=-4.1076455, in the mol.data, just acs-1 was chosen, and data was set as acs-1=-5.835986205; but, for Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; Log2fc -1.22;-0.118;1.645; in mol.data, fbaB=0.299; but aroF+fbaB=0.4, which is not equal to 0.299; So, I am confused on this issue now! and more, if several genes encoding for different subunits of a enzyme, all get a log2 fold was less than 1, but add all them up would exceed 1, and give us a wrong information. or like the case above, which also give us some wrong information. why the data in the mol.data is not the average of several genes encoding for different subunit of the same enzyme? And for iso-functional enzyme, could we display them separately(like fbaB and aroF)? Thanks! 2014-02-17 14:37 GMT+08:00 ÁõÅô·É <liupfskygre@gmail.com>: > Dear all, > > Now I am using pathview to map my RNAseq expression data to the keggmap of my organism ¡®mez¡¯. I want to know how pathview deal with the colour of enzyme with several conding genes, for example: > > In pathway: Glycolysis / Gluconeogenesis, mez00010, the gene node (enzyme 4.1.2.13) has 3 genes related to it. > > Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > > Log2fc -1.22;-0.118;1.645; > > > > aroF and fbaB all significantly regulated and has a |log2 fold change| >1. > > > > Another example is that one enzyme has several subunits, each has a encoding gene, but with different expression level(here I mean the log2 fold change of treat/ck). > > > > I found pathview just choose to plot one data onto the map(eg, fbaB and aroF, it just choose fbaB, due to it appear first in the gene.names?). which one will pathview choose to plot? How could I display all information on one plot, like aroF and fbaB, separate and display them on the map? what about genes encoding for different subunits of a gene? > > > > Thanks! > > > -- > Pengfei Liu, PhD Candidate > Lab of Molecular Ecology - Max Planck Partner Group > College of Resources and Environmental Sciences > China Agricultural University > No.2 Yuanmingyuanxilu, Beijing, 100193 > P.R. China > > Tel: +86-10-62731358 > Fax: +86-10-62731016 > > E-mail: liupfskygre@gmail.com > > -- Pengfei Liu, PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 E-mail: liupfskygre@gmail.com [[alternative HTML version deleted]]
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As described in Page 7 of pathview vignette: ?..Note in native KEGG view, a gene node may represent multiple genes/proteins with similar or redundant functional role. The number of member genes range from 1 up to several tens. They are intentionally put together as a single node on pathway graphs for better clarity and readability. Therefore, we do not split node and mark each member genes separately by default. But rather we visualize the node-wise data by summarize gene-wise data, users may specify the summarization method using node.sum arguement.? Native KEGG graph use the most informative name to label multiple-gene nodes. When Graphviz view or 2-layer graph is specified, we choose to use the most common gene symbol (among multiple ones). Check the function documentation of pathview: ?pathview node.sum argument, character, the method name to calculate node summary given that multiple genes or compounds are mapped to it. Potential options include "sum","mean", "median","max", "max.abs" and "random". Default node.sum="sum". Below are the data you provided. You may want to check whether the fold change sum of your 3 genes is about 0.299 or 0.4. > Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > Log2fc -1.22;-0.118;1.645; -------------------------------------------- On Mon, 2/17/14, ??? <liupfskygre at="" gmail.com=""> wrote: Subject: Re: How does pathview deal with enzyme with several coding genes? To: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Date: Monday, February 17, 2014, 2:33 AM Hi,I found in the mol.data that pathview just do some add calculation, for example, acs-1=-1.7283407; acs-2=-4.1076455, in the mol.data, just acs-1 was chosen, and data was set as acs-1=-5.835986205; but, for?Gene??? Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; Log2fc? -1.22;-0.118;1.645; in mol.data, fbaB=0.299; but aroF+fbaB=0.4, which is not equal to 0.299; So, I am confused on this issue now!and more, if several genes encoding for different subunits of a enzyme, all get a log2 fold was less than 1, but add all them up would exceed 1, and give us a wrong information. or like the case above, which also give us some wrong information. why the data in the mol.data is not the average of several genes encoding for different subunit of the same enzyme? And for iso-functional enzyme, could we display them separately(like fbaB and aroF)? Thanks! 2014-02-17 14:37 GMT+08:00 ??? <liupfskygre at="" gmail.com="">: Dear all, Now I am using pathview to map my RNAseq expression data to the keggmap of my organism ?mez?. I want to know how pathview deal with the colour of enzyme with several conding genes, for example: In pathway: Glycolysis / Gluconeogenesis, mez00010, the gene node (enzyme 4.1.2.13) has 3 genes related to it. Gene??? Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; Log2fc? -1.22;-0.118;1.645;?aroF and fbaB all significantly regulated and has a |log2 fold change| >1. ?Another example is that one enzyme has several subunits, each has a encoding gene, but with different expression level(here I mean the log2 fold change of treat/ck). ?I found pathview just choose to plot one data onto the map(eg, fbaB and aroF, it just choose fbaB, due to it appear first in the gene.names?). which one will pathview choose to plot? How could I display all information on one plot, like aroF and fbaB, separate and display them on the map? what about genes encoding for different subunits of a gene? ?Thanks! -- Pengfei Liu,?PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 ? E-mail: liupfskygre at gmail.com -- Pengfei Liu,?PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 ? E-mail: liupfskygre at gmail.com
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Thank you for your comprehensive explanation£¬I read some parts of the vignette in details as you mentioned, realized several ways to visualize my data. Pathview is really a nice tools£¡ I also found a little problem, although it does not affect my use. when the list of expression data has only one gene, the pathview would not map the data to the kegg map and send error message: No of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong. Working in directory C:/Users/microbe/Documents Writing image file pth00480.pthmeanGID.png I do not whether other user has similar problem. Regards! 2014-02-18 11:21 GMT+08:00 Luo Weijun <luo_weijun@yahoo.com>: > As described in Page 7 of pathview vignette: > ¡°..Note in native KEGG view, a gene node may represent multiple > genes/proteins with similar or redundant functional role. The number of > member genes range from 1 up to several tens. They are intentionally put > together as a single node on pathway graphs for better clarity and > readability. Therefore, we do not split node and mark each member genes > separately by default. But rather we visualize the node-wise data by > summarize gene-wise data, users may specify the summarization method using > node.sum arguement.¡± > Native KEGG graph use the most informative name to label multiple- gene > nodes. When Graphviz view or 2-layer graph is specified, we choose to use > the most common gene symbol (among multiple ones). > > Check the function documentation of pathview: > ?pathview > node.sum argument, character, the method name to calculate node summary > given that multiple genes > or compounds are mapped to it. Potential options include "sum","mean", > "median","max", "max.abs" and "random". Default node.sum="sum". > > Below are the data you provided. You may want to check whether the fold > change sum of your 3 genes is about 0.299 or 0.4. > > Gene Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > > Log2fc -1.22;-0.118;1.645; > > -------------------------------------------- > On Mon, 2/17/14, ÁõÅô·É <liupfskygre@gmail.com> wrote: > > Subject: Re: How does pathview deal with enzyme with several coding genes? > To: "bioconductor@r-project.org list" <bioconductor@r-project.org> > Cc: luo_weijun@yahoo.com > Date: Monday, February 17, 2014, 2:33 AM > > Hi,I found in the > mol.data that pathview just do some add calculation, for > example, acs-1=-1.7283407; acs-2=-4.1076455, in the > mol.data, just acs-1 was chosen, and data was set as > acs-1=-5.835986205; but, for Gene > Mtc_1383/aroF; > Mtc_2501/fbaA; > Mtc_0384/fbaB; > Log2fc -1.22;-0.118;1.645; > in mol.data, fbaB=0.299; but > aroF+fbaB=0.4, which is not equal to 0.299; > So, I am confused on this issue > now!and more, if several genes > encoding for different subunits of a enzyme, all get a log2 > fold was less than 1, but add all them up would exceed 1, > and give us a wrong information. or like the case above, > which also give us some wrong information. > why the data in the mol.data is > not the average of several genes encoding for different > subunit of the same enzyme? And for iso-functional enzyme, > could we display them separately(like fbaB and aroF)? > > > Thanks! > > > 2014-02-17 14:37 GMT+08:00 ÁõÅô·É <liupfskygre@gmail.com>: > > Dear all, Now I am using > pathview to map my RNAseq expression data to the keggmap of > my organism ¡®mez¡¯. I want to know how pathview > deal with the colour of enzyme with several conding genes, > for example: > > In pathway: Glycolysis / Gluconeogenesis, mez00010, the > gene node (enzyme 4.1.2.13) has 3 genes related to it. > Gene > Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > > Log2fc > -1.22;-0.118;1.645; aroF > and fbaB all significantly regulated and has a |log2 fold > change| >1. Another example > is that one enzyme has several subunits, each has a encoding > gene, but with different expression level(here I mean the > log2 fold change of treat/ck). > > I found pathview just choose to plot > one data onto the map(eg, fbaB and aroF, it just choose > fbaB, due to it appear first in the gene.names?). which one > will pathview choose to plot? How could I display all > information on one plot, like aroF and fbaB, separate and > display them on the map? what about genes encoding for > different subunits of a gene? > > Thanks! > -- > Pengfei Liu, PhD Candidate > > Lab of Molecular Ecology - > Max Planck Partner Group > > College of Resources and Environmental Sciences > China Agricultural University > No.2 Yuanmingyuanxilu, Beijing, 100193 > P.R. China > > Tel: +86-10-62731358 > Fax: +86-10-62731016 > > E-mail: liupfskygre@gmail.com > > > > > > > > > -- > Pengfei Liu, PhD Candidate > Lab of Molecular Ecology - > Max Planck Partner Group > > College of Resources and Environmental Sciences > China Agricultural University > No.2 Yuanmingyuanxilu, Beijing, 100193 > P.R. China > > Tel: +86-10-62731358 > Fax: +86-10-62731016 > > E-mail: liupfskygre@gmail.com > > > > > > -- Pengfei Liu, PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 E-mail: liupfskygre@gmail.com [[alternative HTML version deleted]]
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This is not an error message. Just a friendly reminder that nothing (genes or compounds) can be mapped to the specified pathway. In your case, this is because there is only 1 gene in your data. -------------------------------------------- On Tue, 2/18/14, ??? <liupfskygre at="" gmail.com=""> wrote: Subject: Re: How does pathview deal with enzyme with several coding genes? Cc: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Date: Tuesday, February 18, 2014, 7:52 AM Thank you for your comprehensive explanation?I read some parts of the vignette in details as you mentioned, realized several ways to visualize my data.?Pathview is really a nice tools?? I also found a little problem, although it does not affect my use.when the list of expression data has?only?one gene, the pathview would not map the data to the kegg map and send error message: No of the genes or compounds mapped to the pathway!Argument gene.idtype or cpd.idtype may be wrong.Working in directory C:/Users/microbe/DocumentsWriting image file pth00480.pthmeanGID.png I do not whether other user has similar problem.? Regards! As described in Page 7 of pathview vignette: ?..Note in native KEGG view, a gene node may represent multiple genes/proteins with similar or redundant functional role. The number of member genes range from 1 up to several tens. They are intentionally put together as a single node on pathway graphs for better clarity and readability. Therefore, we do not split node and mark each member genes separately by default. But rather we visualize the node-wise data by summarize gene-wise data, users may specify the summarization method using node.sum arguement.? Native KEGG graph use the most informative name to label multiple-gene nodes. When Graphviz view or 2-layer graph is specified, we choose to use the most common gene symbol (among multiple ones). Check the function documentation of pathview: ?pathview node.sum argument, character, the method name to calculate node summary given that multiple genes or compounds are mapped to it. Potential options include "sum","mean", "median","max", "max.abs" and "random". Default node.sum="sum". Below are the data you provided. You may want to check whether the fold change sum of your 3 genes is about 0.299 or 0.4. > Gene ? ?Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > Log2fc ?-1.22;-0.118;1.645; -------------------------------------------- On Mon, 2/17/14, ??? <liupfskygre at="" gmail.com=""> wrote: ?Subject: Re: How does pathview deal with enzyme with several coding genes? ?To: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> ?Date: Monday, February 17, 2014, 2:33 AM ?Hi,I found in the ?mol.data that pathview just do some add calculation, for ?example, acs-1=-1.7283407; acs-2=-4.1076455, in the ?mol.data, just acs-1 was chosen, and data was set as ?acs-1=-5.835986205; but, for?Gene??? ?Mtc_1383/aroF; ?Mtc_2501/fbaA; ?Mtc_0384/fbaB; ?Log2fc? -1.22;-0.118;1.645; ?in mol.data, fbaB=0.299; but ?aroF+fbaB=0.4, which is not equal to 0.299; ?So, I am confused on this issue ?now!and more, if several genes ?encoding for different subunits of a enzyme, ?all get a log2 ?fold was less than 1, but add all them up would exceed 1, ?and give us a wrong information. or like the case above, ?which also give us some wrong information. ?why the data in the mol.data is ?not the average of several genes encoding for different ?subunit of the same enzyme? And for iso-functional enzyme, ?could we display them separately(like fbaB and aroF)? ?Thanks! ?2014-02-17 14:37 GMT+08:00 ??? <liupfskygre at="" gmail.com="">: ?Dear all, Now I am using ?pathview to map my RNAseq expression data to the keggmap of ?my organism ?mez?. I want to know how pathview ?deal with the colour of enzyme with several conding genes, ?for example: ?In pathway: Glycolysis / Gluconeogenesis, mez00010, the ?gene node (enzyme 4.1.2.13) has 3 genes related to it. ?Gene??? ?Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; ?Log2fc? ?-1.22;-0.118;1.645;?aroF ?and fbaB all significantly regulated and has a |log2 fold ?change| >1. ?Another example ?is that one enzyme has several subunits, each has a encoding ?gene, but with different expression level(here I mean the ?log2 fold change of treat/ck). ??I found pathview just choose to plot ?one data onto the map(eg, fbaB and aroF, it just choose ?fbaB, due to it appear first in the gene.names?). which one ?will pathview choose to plot? How could I display all ?information on one plot, like aroF and fbaB, separate and ?display them on the map? what about genes encoding for ?different subunits of a gene? ??Thanks! ?-- ?Pengfei Liu,?PhD Candidate ?Lab of Molecular Ecology - ?Max Planck Partner Group ?College of Resources and Environmental Sciences ?China Agricultural University ?No.2 Yuanmingyuanxilu, Beijing, 100193 ?P.R. China ?Tel: +86-10-62731358 ?Fax: +86-10-62731016 ?? ?E-mail: liupfskygre at gmail.com ?-- ?Pengfei Liu,?PhD Candidate ?Lab of Molecular Ecology - ?Max Planck Partner Group ?College of Resources and Environmental Sciences ?China Agricultural University ?No.2 Yuanmingyuanxilu, Beijing, 100193 ?P.R. China ?Tel: +86-10-62731358 ?Fax: +86-10-62731016 ?? ?E-mail: liupfskygre at gmail.com -- Pengfei Liu,?PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 ? E-mail: liupfskygre at gmail.com
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This is not an error message. Just a friendly reminder that nothing (genes or compounds) can be mapped to the specified pathway. In your case, this is because there is only 1 gene in your data. -------------------------------------------- On Tue, 2/18/14, ??? <liupfskygre at="" gmail.com=""> wrote: Subject: Re: How does pathview deal with enzyme with several coding genes? Cc: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> Date: Tuesday, February 18, 2014, 7:52 AM Thank you for your comprehensive explanation?I read some parts of the vignette in details as you mentioned, realized several ways to visualize my data.?Pathview is really a nice tools?? I also found a little problem, although it does not affect my use.when the list of expression data has?only?one gene, the pathview would not map the data to the kegg map and send error message: No of the genes or compounds mapped to the pathway!Argument gene.idtype or cpd.idtype may be wrong.Working in directory C:/Users/microbe/DocumentsWriting image file pth00480.pthmeanGID.png I do not whether other user has similar problem.? Regards! As described in Page 7 of pathview vignette: ?..Note in native KEGG view, a gene node may represent multiple genes/proteins with similar or redundant functional role. The number of member genes range from 1 up to several tens. They are intentionally put together as a single node on pathway graphs for better clarity and readability. Therefore, we do not split node and mark each member genes separately by default. But rather we visualize the node-wise data by summarize gene-wise data, users may specify the summarization method using node.sum arguement.? Native KEGG graph use the most informative name to label multiple-gene nodes. When Graphviz view or 2-layer graph is specified, we choose to use the most common gene symbol (among multiple ones). Check the function documentation of pathview: ?pathview node.sum argument, character, the method name to calculate node summary given that multiple genes or compounds are mapped to it. Potential options include "sum","mean", "median","max", "max.abs" and "random". Default node.sum="sum". Below are the data you provided. You may want to check whether the fold change sum of your 3 genes is about 0.299 or 0.4. > Gene ? ?Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; > Log2fc ?-1.22;-0.118;1.645; -------------------------------------------- On Mon, 2/17/14, ??? <liupfskygre at="" gmail.com=""> wrote: ?Subject: Re: How does pathview deal with enzyme with several coding genes? ?To: "bioconductor at r-project.org list" <bioconductor at="" r-project.org=""> ?Date: Monday, February 17, 2014, 2:33 AM ?Hi,I found in the ?mol.data that pathview just do some add calculation, for ?example, acs-1=-1.7283407; acs-2=-4.1076455, in the ?mol.data, just acs-1 was chosen, and data was set as ?acs-1=-5.835986205; but, for?Gene??? ?Mtc_1383/aroF; ?Mtc_2501/fbaA; ?Mtc_0384/fbaB; ?Log2fc? -1.22;-0.118;1.645; ?in mol.data, fbaB=0.299; but ?aroF+fbaB=0.4, which is not equal to 0.299; ?So, I am confused on this issue ?now!and more, if several genes ?encoding for different subunits of a enzyme, ?all get a log2 ?fold was less than 1, but add all them up would exceed 1, ?and give us a wrong information. or like the case above, ?which also give us some wrong information. ?why the data in the mol.data is ?not the average of several genes encoding for different ?subunit of the same enzyme? And for iso-functional enzyme, ?could we display them separately(like fbaB and aroF)? ?Thanks! ?2014-02-17 14:37 GMT+08:00 ??? <liupfskygre at="" gmail.com="">: ?Dear all, Now I am using ?pathview to map my RNAseq expression data to the keggmap of ?my organism ?mez?. I want to know how pathview ?deal with the colour of enzyme with several conding genes, ?for example: ?In pathway: Glycolysis / Gluconeogenesis, mez00010, the ?gene node (enzyme 4.1.2.13) has 3 genes related to it. ?Gene??? ?Mtc_1383/aroF; Mtc_2501/fbaA; Mtc_0384/fbaB; ?Log2fc? ?-1.22;-0.118;1.645;?aroF ?and fbaB all significantly regulated and has a |log2 fold ?change| >1. ?Another example ?is that one enzyme has several subunits, each has a encoding ?gene, but with different expression level(here I mean the ?log2 fold change of treat/ck). ??I found pathview just choose to plot ?one data onto the map(eg, fbaB and aroF, it just choose ?fbaB, due to it appear first in the gene.names?). which one ?will pathview choose to plot? How could I display all ?information on one plot, like aroF and fbaB, separate and ?display them on the map? what about genes encoding for ?different subunits of a gene? ??Thanks! ?-- ?Pengfei Liu,?PhD Candidate ?Lab of Molecular Ecology - ?Max Planck Partner Group ?College of Resources and Environmental Sciences ?China Agricultural University ?No.2 Yuanmingyuanxilu, Beijing, 100193 ?P.R. China ?Tel: +86-10-62731358 ?Fax: +86-10-62731016 ?? ?E-mail: liupfskygre at gmail.com ?-- ?Pengfei Liu,?PhD Candidate ?Lab of Molecular Ecology - ?Max Planck Partner Group ?College of Resources and Environmental Sciences ?China Agricultural University ?No.2 Yuanmingyuanxilu, Beijing, 100193 ?P.R. China ?Tel: +86-10-62731358 ?Fax: +86-10-62731016 ?? ?E-mail: liupfskygre at gmail.com -- Pengfei Liu,?PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 ? E-mail: liupfskygre at gmail.com
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