Recent changes to matrix

matrix modified by Keith Ching

Keith Ching — Mon, 17 Apr 2017 16:15:38 -0000

--- v10
+++ v11
@@ -35,7 +35,7 @@

 For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.

-Example [query](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&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=ALL&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=CCLE&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=matrix&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&active_Other=5&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=breast&affy_source=CCLE&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=erbb2+cdkn2a+rb1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+Example [query](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=ALL&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&mirna_numresults=25&methylation_source=NONE&expmirna_low=1&activehtab=3&cnvminbp=10000&compound_source=NONE&source=CCLE&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=matrix&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&active_Other=5&expcnv_low=1&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&venncnvgene1=%3e1&cnvamp=2&tissues=breast&affy_source=CCLE&expmut_numresults=25&vennexpgene1=%3e10&vennexpgene4=%3e10&venncnvgene2=%3e1&expcore_colors=red+blue+green+violet+orange+yellow+black&mut_expression_method=t-test&venncnvgene5=%3e1&mut_meth_method=t-test&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&mut_mirna_method=t-test&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expressionbarplot_type=none&expcnv_minsize=10&methmut_numresults=25&expcnv_high=1&genes=erbb2+cdkn2a+rb1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

 Codes for summary Table:
 F = focal cnv size <= 10 MB

matrix modified by Keith Ching

Keith Ching — Mon, 17 Apr 2017 16:09:47 -0000

--- v9
+++ v10
@@ -26,11 +26,12 @@
 HT29,1000

-Note: Expression values are median centered.  If there are few samples, there will appear to be extremes in expression which may be misleading.
+Note: 
+(gene_e) Expression values are median centered.  If there are few samples, there will appear to be extremes in expression which may be misleading.

-CNV values are the mean log2R of the highest absolute value segment which overlaps the gene's coding region.  The 'F' indicates a focal segment of <= 10MB in size.
+(gene_c) CNV values are the mean log2R of the highest absolute value segment which overlaps the gene's coding region.  The 'F' indicates a focal segment of <= 10MB in size.

-MUT indicates any mutation of any type annotated for the gene in question.
+(gene_m) MUT indicates any mutation of any type annotated for the gene in question.

 For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.

matrix modified by Keith Ching

Keith Ching — Fri, 04 Mar 2016 20:58:50 -0000

--- v8
+++ v9
@@ -35,3 +35,13 @@
 For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.

 Example [query](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&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=ALL&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=CCLE&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=matrix&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&active_Other=5&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=breast&affy_source=CCLE&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=erbb2+cdkn2a+rb1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+
+Codes for summary Table:
+F = focal cnv size <= 10 MB
+A = amplified  cnv >= 1
+D = deleted cnv <= -1
+O = overexpressed median exp >= 1
+U = underexpressed  median exp <= -1
+M = mutation
+S = STOP mutation
+P = splice site mutation

matrix modified by Keith Ching

Keith Ching — Wed, 25 Nov 2015 01:42:01 -0000

--- v7
+++ v8
@@ -33,3 +33,5 @@
 MUT indicates any mutation of any type annotated for the gene in question.

 For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.
+
+Example [query](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&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=ALL&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=CCLE&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=matrix&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&active_Other=5&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=breast&affy_source=CCLE&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&genes=erbb2+cdkn2a+rb1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

matrix modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 22:28:11 -0000

--- v6
+++ v7
@@ -32,4 +32,4 @@

 MUT indicates any mutation of any type annotated for the gene in question.

-For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file.
+For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.

matrix modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 13:56:13 -0000

--- v5
+++ v6
@@ -1,3 +1,4 @@
+[[img src=matrix.png alt=matrix]]
 [Instructions]
 **matrix** : Output expression, CNV, and mutations in table format.

matrix modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 09:41:56 -0000

--- v4
+++ v5
@@ -30,3 +30,5 @@
 CNV values are the mean log2R of the highest absolute value segment which overlaps the gene's coding region.  The 'F' indicates a focal segment of <= 10MB in size.

 MUT indicates any mutation of any type annotated for the gene in question.
+
+For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file.

matrix modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 09:40:16 -0000

--- v3
+++ v4
@@ -23,3 +23,10 @@
 ZR7530,100
 HCC202,500
 HT29,1000
+
+
+Note: Expression values are median centered.  If there are few samples, there will appear to be extremes in expression which may be misleading.
+
+CNV values are the mean log2R of the highest absolute value segment which overlaps the gene's coding region.  The 'F' indicates a focal segment of <= 10MB in size.
+
+MUT indicates any mutation of any type annotated for the gene in question.

matrix modified by Keith Ching

Keith Ching — Sun, 28 Dec 2014 20:15:41 -0000

--- v2
+++ v3
@@ -19,3 +19,7 @@

 example required format:

+CELL,COMPOUND_IC50
+ZR7530,100
+HCC202,500
+HT29,1000

matrix modified by Keith Ching

Keith Ching — Sun, 28 Dec 2014 19:40:16 -0000

--- v1
+++ v2
@@ -15,3 +15,7 @@
 *no color* : if checked, output an unmarked up table instead of the html colored table. (default unchecked)
 *Compound* / *Compound Source* : if selected, both values are required. Restricts output to samples for which there is an IC50 value for the compound selected. Adds IC50 value column and ascending sorts the samples by IC50. (optional)
 *CNV/EXP plot* : if IC50 values and nocolor is checked, render a waterfall plot of the IC50 values. The same plot can also be generated from [expression_IC50]. (optional)
+*IC50* :  instead of choosing the Compound / Compound Source from the database, paste in your own IC50 values.
+
+example required format:
+