Recent changes to expression_mut

expression_mut modified by Keith Ching

Keith Ching — Mon, 14 Mar 2016 19:42:09 -0000

--- v7
+++ v8
@@ -18,6 +18,6 @@
 EXPRESSION : expression source (required)
 MUTATION : mutation source (required)

-[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=TCGA-LUAD&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=expression_mut&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=5&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=TCGA-LUAD-RSEM&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=egfr&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10): MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD, HUGO = EGFR
+[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=TCGA-LUAD&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=expression_mut&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=5&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=TCGA-LUAD-RSEM&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=egfr&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10): MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD-RSEM, HUGO = EGFR

 [[img src=egfr_TCGA-LUAD.png alt=egfr]]

expression_mut modified by Keith Ching

Keith Ching — Mon, 14 Mar 2016 19:41:51 -0000

--- v6
+++ v7
@@ -18,6 +18,6 @@
 EXPRESSION : expression source (required)
 MUTATION : mutation source (required)

-example: MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD, HUGO = EGFR
+[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=TCGA-LUAD&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=expression_mut&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=5&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=TCGA-LUAD-RSEM&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=egfr&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10): MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD, HUGO = EGFR

 [[img src=egfr_TCGA-LUAD.png alt=egfr]]

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:05:40 -0000

--- v5
+++ v6
@@ -1,6 +1,6 @@
 [Instructions]

-Find which genes are statistically different between groups defined by mutation status.
+Find which genes with expression levels statistically different between groups defined by mutation status.

 If you divide samples into two groups by mutation status of a gene, find the genes that are most different by t-test.

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:05:02 -0000

--- v4
+++ v5
@@ -8,16 +8,13 @@
 Return the ranked list of genes sorted by abs(t-statistic).
 A heatmap of expression clustered by mutation status is automatically generated. Yellow bar = mutated sample. Green bar = non-mutated sample.

-HUGO : enter gene symbol here. (required) 
+
 Include mutations : if checked, only use mutations to determine groups. (ie. exclude fusions)
 Include fusions : if checked, use only fusions to determine groups. (ie. exclude mutations)
 (if both are checked, or none are checked then mutations and fusions will be used)
-
-Search for mutations associated with a gene's expression
 num results : the number of results to return (default 25)

-
-Plot heatmap : if checked, plot a heatmap of the returned genes.
+HUGO : enter gene symbol here. (required) 
 EXPRESSION : expression source (required)
 MUTATION : mutation source (required)

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:03:53 -0000

--- v3
+++ v4
@@ -9,8 +9,10 @@
 A heatmap of expression clustered by mutation status is automatically generated. Yellow bar = mutated sample. Green bar = non-mutated sample.

 HUGO : enter gene symbol here. (required) 
-Include mutations
-Include fusions
+Include mutations : if checked, only use mutations to determine groups. (ie. exclude fusions)
+Include fusions : if checked, use only fusions to determine groups. (ie. exclude mutations)
+(if both are checked, or none are checked then mutations and fusions will be used)
+
 Search for mutations associated with a gene's expression
 num results : the number of results to return (default 25)

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 17:58:00 -0000

--- v2
+++ v3
@@ -20,3 +20,5 @@
 MUTATION : mutation source (required)

 example: MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD, HUGO = EGFR
+
+[[img src=egfr_TCGA-LUAD.png alt=egfr]]

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 17:55:38 -0000

--- v1
+++ v2
@@ -1,3 +1,22 @@
 [Instructions]

 Find which genes are statistically different between groups defined by mutation status.
+
+If you divide samples into two groups by mutation status of a gene, find the genes that are most different by t-test.
+
+For each gene with expression data, do a t-test and record the t-statistic. 
+Return the ranked list of genes sorted by abs(t-statistic).
+A heatmap of expression clustered by mutation status is automatically generated. Yellow bar = mutated sample. Green bar = non-mutated sample.
+
+HUGO : enter gene symbol here. (required) 
+Include mutations
+Include fusions
+Search for mutations associated with a gene's expression
+num results : the number of results to return (default 25)
+
+
+Plot heatmap : if checked, plot a heatmap of the returned genes.
+EXPRESSION : expression source (required)
+MUTATION : mutation source (required)
+
+example: MUTATION = TCGA-LUAD, EXPRESSION = TCGA-LUAD, HUGO = EGFR

expression_mut modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 06:19:54 -0000

[Instructions]

Find which genes are statistically different between groups defined by mutation status.