Recent changes to expression_IC50

expression_IC50 modified by Keith Ching

Keith Ching — Sat, 29 Oct 2016 19:05:10 -0000

--- v4
+++ v5
@@ -17,3 +17,5 @@
 IC50 : fill in box for custom IC50 values. see [matrix]
 HUGO : spike in selected gene symbols to see how they rank. (optional)
 Tissues : limit to selected tissue type.
+
+Dev:  Select samples based on a metadata value.  If a metadata dataset is chosen and a metadata field is chosen, the Filter pulldown will be populated with the available values from the field.  If you select one of the values, the samples will be filtered to those containing that specific field.

expression_IC50 modified by Keith Ching

Keith Ching — Mon, 02 Feb 2015 20:27:46 -0000

--- v3
+++ v4
@@ -3,6 +3,8 @@
 Find genes correlated or enriched between groups defined by IC50 cutoffs.
 Performs t-test on expression values between low and high groups.
 Combines mutation and CNV values into table and ranks genes using Fisher's exact test.
+
+Outputs: Summary of IC50 values, IC50 waterfall plot, expression table, expression heatmap, mutation/cnv pvalue table, and combined mutation/cnv, IC50, table.

 IC50 nM low: cutoff for samples in low group (required) (default 100nM)
 IC50 nM high: cutoff for samples in high group (required) (default 500nM)
@@ -11,7 +13,7 @@
 EXPRESSION : source for expression data (required)
 MUTATION : source for mutation data
 CNV : source for CNV data
-META : select META data to overlay colored bars on heatmap.
+META : select META data to overlay colored bars on expression heatmap.  If you choose this option, the IC50 colored bars will be replaced with the META data colors and the samples will instead be suffixed with either _LOW or _HIGH to indicate group membership.  
 IC50 : fill in box for custom IC50 values. see [matrix]
-HUGO : spike in selected gene symbols to see how they ranks (optional)
-Tissues : limit to tissue types.
+HUGO : spike in selected gene symbols to see how they rank. (optional)
+Tissues : limit to selected tissue type.

expression_IC50 modified by Keith Ching

Keith Ching — Mon, 02 Feb 2015 20:21:52 -0000

--- v2
+++ v3
@@ -14,3 +14,4 @@
 META : select META data to overlay colored bars on heatmap.
 IC50 : fill in box for custom IC50 values. see [matrix]
 HUGO : spike in selected gene symbols to see how they ranks (optional)
+Tissues : limit to tissue types.

expression_IC50 modified by Keith Ching

Keith Ching — Mon, 02 Feb 2015 20:19:58 -0000

--- v1
+++ v2
@@ -1,3 +1,16 @@
 [Instructions]

-Find genes correlated or enriched between groups defined by IC50 cutoffs
+Find genes correlated or enriched between groups defined by IC50 cutoffs.
+Performs t-test on expression values between low and high groups.
+Combines mutation and CNV values into table and ranks genes using Fisher's exact test.
+
+IC50 nM low: cutoff for samples in low group (required) (default 100nM)
+IC50 nM high: cutoff for samples in high group (required) (default 500nM)
+
+Compound : select compound to analyze (required)
+EXPRESSION : source for expression data (required)
+MUTATION : source for mutation data
+CNV : source for CNV data
+META : select META data to overlay colored bars on heatmap.
+IC50 : fill in box for custom IC50 values. see [matrix]
+HUGO : spike in selected gene symbols to see how they ranks (optional)

expression_IC50 modified by Keith Ching

Keith Ching — Mon, 02 Feb 2015 19:37:38 -0000

[Instructions]

Find genes correlated or enriched between groups defined by IC50 cutoffs