Recent changes to expression_meta

expression_meta modified by Keith Ching

Keith Ching — Mon, 20 Jun 2016 20:54:10 -0000

--- v5
+++ v6
@@ -13,3 +13,7 @@
 Generate table of meta specific gene expression : deprecated.
 Include Normal Tissue : if checked, do not remove sample data from normal tissues (default do not include normals)
 Include No Value : if checked, do not remove sample data that has no meta value recorded (default do not include data from samples with missing meta values)
+
+Development:
+
+Multiple meta data combinations:  If you already know the gene you want to plot vs. metadata, you can show all combinations of two or more meta categories by adding additional meta values. Note there is a limit because the combinations can quickly increase.

expression_meta modified by Keith Ching

Keith Ching — Mon, 14 Mar 2016 22:43:54 -0000

--- v4
+++ v5
@@ -5,7 +5,7 @@

 [For 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&metadata_names=235+gender+&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_meta&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&dataset_name=NONE&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=8&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=TCGA-LUAD&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10), it is easy to find sex specific gene expression by using the gender meta data type.

-
+[Enter a specific gene to get a plot](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&metadata_names=235+gender+&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_meta&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&dataset_name=NONE&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=8&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=TCGA-LUAD&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)

 HUGO: gene symbol to check. If no gene selected, will search all genes.
 EXPRESSION : Source of gene expression

expression_meta modified by Keith Ching

Keith Ching — Mon, 14 Mar 2016 22:42:52 -0000

--- v3
+++ v4
@@ -3,7 +3,7 @@

 Find genes correlated or enriched between groups defined by meta data.

-For example, it is easy to find sex specific gene expression by using the gender meta data type.
+[For 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&metadata_names=235+gender+&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_meta&rppa_source=NONE&METACOLORS=green+blue&venn_segment=none&sort=mean&fisher_mutation_low=4&combo_high=500&expcnv_low=1&dataset_name=NONE&expcore_top=100&expcore_datasets=10&fisher_mutation_high=10&active_Expression=8&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=TCGA-LUAD&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10), it is easy to find sex specific gene expression by using the gender meta data type.

expression_meta modified by Keith Ching

Keith Ching — Thu, 19 Feb 2015 21:44:13 -0000

--- v2
+++ v3
@@ -2,6 +2,8 @@

 Find genes correlated or enriched between groups defined by meta data.
+
+For example, it is easy to find sex specific gene expression by using the gender meta data type.

expression_meta modified by Keith Ching

Keith Ching — Fri, 13 Feb 2015 20:11:00 -0000

--- v1
+++ v2
@@ -8,6 +8,6 @@
 HUGO: gene symbol to check. If no gene selected, will search all genes.
 EXPRESSION : Source of gene expression
 META : Choose the matching metadata set. If no specific Metadata type selected, will test all metadata via F-test else pairwise t-test.
-Generate table of meta specific gene expression :
+Generate table of meta specific gene expression : deprecated.
 Include Normal Tissue : if checked, do not remove sample data from normal tissues (default do not include normals)
 Include No Value : if checked, do not remove sample data that has no meta value recorded (default do not include data from samples with missing meta values)

expression_meta modified by Keith Ching

Keith Ching — Fri, 13 Feb 2015 19:58:43 -0000

[Instructions]

Find genes correlated or enriched between groups defined by meta data.

HUGO: gene symbol to check. If no gene selected, will search all genes.
EXPRESSION : Source of gene expression
META : Choose the matching metadata set. If no specific Metadata type selected, will test all metadata via F-test else pairwise t-test.
Generate table of meta specific gene expression :
Include Normal Tissue : if checked, do not remove sample data from normal tissues (default do not include normals)
Include No Value : if checked, do not remove sample data that has no meta value recorded (default do not include data from samples with missing meta values)