Recent changes to RSEM-barplot

RSEM-barplot modified by Keith Ching

Keith Ching — Sat, 29 Oct 2016 18:38:57 -0000

RSEM-barplot modified by Keith Ching

Keith Ching — Sat, 29 Oct 2016 18:36:48 -0000

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 21 Sep 2016 19:47:02 -0000

--- v15
+++ v16
@@ -6,6 +6,7 @@

 *HUGO* : enter a gene symbol to plot. (required)  eg. kras
          (optional) add a gene with -c to change the plot to a scatter plot of exp vs. cnv. eg. kras kras-c [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras+kras-c&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+         (optional) if two gene symbols, the first will be used for the barplot and the second will be used to generate scatter plots for each dataset.

 [[img src=kras_exp_cnv.png alt=cnvplot width=700px]]
 x-axis: expression level of KRAS. y-axis: log2 CNV of KRAS (red >=1 )

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 22:39:56 -0000

--- v14
+++ v15
@@ -14,7 +14,7 @@
 Plot the mutation load across TCGA datasets. Enter 'MUT-COUNT' as the HUGO symbol. [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=MUT-COUNT&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

 **Plotting Meta values**
-Plot numeric meta-data values across categorical meta values.  Enter 'META-NNNN' as the HUGO symbol for the numerical meta value where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a categorical metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the categorical metavalue. 
+Plot numeric meta-data values across categorical meta values.  Enter 'META-NNNN' as the HUGO symbol for the numerical meta value where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a categorical metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the categorical metavalue. To find meta value ids, see [meta_search]

 Boxpot of meta value by categorical dataset meta value
 [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=META-15331+META-14456&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 22:36:27 -0000

--- v13
+++ v14
@@ -13,9 +13,11 @@

 Plot the mutation load across TCGA datasets. Enter 'MUT-COUNT' as the HUGO symbol. [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=MUT-COUNT&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

-Plot numeric meta-data values across datasets.  Enter 'META-NNNN' as the HUGO symbol where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a dataset metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the dataset metavalue. 
+**Plotting Meta values**
+Plot numeric meta-data values across categorical meta values.  Enter 'META-NNNN' as the HUGO symbol for the numerical meta value where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a categorical metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the categorical metavalue. 

-Boxpot of meta value by categorical dataset value
+Boxpot of meta value by categorical dataset meta value
 [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=META-15331+META-14456&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

+Boxplot of meta value by categorical subtype meta value.
 [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 22:33:18 -0000

--- v12
+++ v13
@@ -15,4 +15,7 @@

 Plot numeric meta-data values across datasets.  Enter 'META-NNNN' as the HUGO symbol where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a dataset metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the dataset metavalue. 

-[Example](http://54.149.52.246/cgi-bin/RPPA/cellxbeta.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)
+Boxpot of meta value by categorical dataset value
+[Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=META-15331+META-14456&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+
+[Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 22:19:04 -0000

--- v11
+++ v12
@@ -15,4 +15,4 @@

 Plot numeric meta-data values across datasets.  Enter 'META-NNNN' as the HUGO symbol where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a dataset metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the dataset metavalue. 

-[Example](http://cellx.pfizer.com/cgi-bin/RPPA/cellxbeta.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)
+[Example](http://54.149.52.246/cgi-bin/RPPA/cellxbeta.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 22:18:27 -0000

--- v10
+++ v11
@@ -14,3 +14,5 @@
 Plot the mutation load across TCGA datasets. Enter 'MUT-COUNT' as the HUGO symbol. [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=MUT-COUNT&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

 Plot numeric meta-data values across datasets.  Enter 'META-NNNN' as the HUGO symbol where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a dataset metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the dataset metavalue. 
+
+[Example](http://cellx.pfizer.com/cgi-bin/RPPA/cellxbeta.cgi?source=ALL_HG18&expstat_low=4&expstat_numresults=25&tabledump_table=cells&METACOLORS=green+blue&mean=2&rnai_source=NONE&exp_ic50_low=100&venn_segment=none&ic50low=100&SUBMIT=SUBMIT&vennexpgene5=%3e10&venncnvgene1=%3e1&mut_expression_method=t-test&ic50high=500&activehtab=1&kcluster=2&expstat_high=10&venncnvgene5=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&fisher_mutation_high=10&venncnvgene2=%3e1&tissues=ALL&PLOTCUTOFFAXIS=Z&venncnvgene4=%3e1&percentile=5&mirna_source=NONE&expmirna_numresults=25&expcnv_colors=red+blue+green+violet+orange+yellow+black&expcore_datasets=10&expmirna_high=1&combo_cnv_cutoff=1&compound_source=NONE&tsvtable=RSEM-barplot&expstat_direction=both&expcor_numresults=25&combo_low=100&mutation_source=NONE&expcore_direction=both&expcnv_numresults=25&cnvamp=2&expcnv_minsize=10&vennexpgene6=%3e10&vennexpgene1=%3e10&expmirna_low=1&combo_high=500&expcnv_maxsize=10&combination_datatype=ALL&venncnvgene3=%3e1&combination_id=ALL&fisher_mutation_low=4&PLOTPOS=bottomright&vennexpgene3=%3e10&expmirna_colors=red+blue+green+violet+orange+yellow+black&maxsize=10&minsize=100&affy_source=NONE&rppa_source=NONE&sort=mean&expcore_method=correlation&combination_id2=NONE&target=EGFR&cnvdel=-2&venncnvgene7=%3e1&expcnv_high=1&cnvminsnp=10&exp_ic50_high=500&vennexpgene2=%3e10&cnvminbp=10000&expcnv_low=1&vennexpgene4=%3e10&expmut_numresults=25&venncnvgene6=%3e1&vennexpgene7=%3e10&metadata_source=NONE&expcore_scale=none&searchtype=co-occur&expcore_top=100&genes=META-19014+META-3899&active_Expression=1&compound_sourcename=ALL)

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 20:31:52 -0000

--- v9
+++ v10
@@ -11,6 +11,6 @@
 x-axis: expression level of KRAS. y-axis: log2 CNV of KRAS (red >=1 )

-Plot the mutation load across TCGA datasets. Enter 'MUT-COUNT' as the HUGO symbol.
+Plot the mutation load across TCGA datasets. Enter 'MUT-COUNT' as the HUGO symbol. [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=MUT-COUNT&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

 Plot numeric meta-data values across datasets.  Enter 'META-NNNN' as the HUGO symbol where NNNN is the primary key listed in the meta-pull down menu.  Additionally, a dataset metavalue must be defined to assign the meta-values to groups to plot. The final HUGO entry will look like META-NNNN META-MMMM where MMMM is the primary key of the dataset metavalue.

RSEM-barplot modified by Keith Ching

Keith Ching — Wed, 02 Mar 2016 20:29:48 -0000

--- v8
+++ v9
@@ -2,7 +2,7 @@
 [[img src=kras_barplot.png alt=barplot width=700px]]

-RSEM-barplot : generates a barchart of expression values for all RSEM datasets with normal samples plotted separately.  Also generates a strip chart and generates histograms for each dataset.  Alternatively, it can generate expression vs. CNV plots for all RSEM datasets.
+RSEM-barplot : generates a barchart of expression values for all RSEM datasets with normal samples plotted separately.  [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10) Also generates a strip chart and generates histograms for each dataset.  Alternatively, it can generate expression vs. CNV plots for all RSEM datasets.

 *HUGO* : enter a gene symbol to plot. (required)  eg. kras
          (optional) add a gene with -c to change the plot to a scatter plot of exp vs. cnv. eg. kras kras-c [Example](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&combination_id2=NONE&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=ALL_HG18&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&exp_ic50_high=500&tsvtable=RSEM-barplot&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=1&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=NONE&vennexpgene1=%3e10&expmut_numresults=25&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&rnai_source=NONE&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&tabledump_table=cells&mirna_source=NONE&metadata_source=NONE&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=kras+kras-c&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)