Recent changes to expression_cnv

expression_cnv modified by Keith Ching

Keith Ching — Mon, 14 Mar 2016 19:54:10 -0000

--- v2
+++ v3
@@ -14,3 +14,5 @@
 Plot heatmap : render a heat map if checked (default unchecked)
 METADATA : choose metadata source and datatype to plot color bars across the heatmap. (optional)
 Colors for heatmap metadata : if you want to change the order of the colors. (default red blue green violet orange yellow black)
+
+[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=NONE&combination_id=ALL&expcore_scale=none&expcnv_numresults=50&expmirna_low=1&activehtab=1&cnvminbp=10000&compound_source=NONE&source=GSE37385&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&metadata_names=2419+subgroup+&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_cnv&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=-0.5&dataset_name=NONE&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=6&venncnvgene1=%3e1&cnvamp=2&tissues=ALL&affy_source=GSE37385&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=GSE37385&vennexpgene2=%3e10&expcore_direction=both&expcnv_heatmap=on&ic50high=500&expcnv_minsize=10&genes=ptch1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)  genes differentially expressed in PTCH1 deleted pediatric Medulloblastomas are characteristic of the SHH driven subgroup.

expression_cnv modified by Keith Ching

Keith Ching — Thu, 22 Jan 2015 01:41:07 -0000

--- v1
+++ v2
@@ -6,10 +6,11 @@
 EXPRESSION : source for expression data (required)
 CNV SOURCE : source for CNV data (required)

-Minimum size (KB) : (default 10KB)
-Max size (MB) : (default 10MB)
-group1 < : (default 1)
-group2 >= : (default 1)
-num results : (default 25) 
-Plot heatmap : (default unchecked)
-Colors for heatmap metadata : (default red blue green violet orange yellow black)
+Minimum size (KB) : the smallest fragment to use (default 10KB)
+Max size (MB) : the largest fragment size to use (default 10MB)
+group1 < : define first group as less than this mean segment value (default 1)
+group2 >= : define second group as greater than or equal to this mean segment value (default 1)
+num results : number of genes to return (default 25) 
+Plot heatmap : render a heat map if checked (default unchecked)
+METADATA : choose metadata source and datatype to plot color bars across the heatmap. (optional)
+Colors for heatmap metadata : if you want to change the order of the colors. (default red blue green violet orange yellow black)

expression_cnv modified by Keith Ching

Keith Ching — Thu, 22 Jan 2015 01:26:47 -0000

[Instructions]

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

HUGO :Enter gene in HUGO box (required)
EXPRESSION : source for expression data (required)
CNV SOURCE : source for CNV data (required)

Minimum size (KB) : (default 10KB)
Max size (MB) : (default 10MB)
group1 < : (default 1)
group2 >= : (default 1)
num results : (default 25)
Plot heatmap : (default unchecked)
Colors for heatmap metadata : (default red blue green violet orange yellow black)