Recent changes to expression_mirna

expression_mirna modified by Keith Ching

Keith Ching — Thu, 21 Apr 2016 21:16:29 -0000

--- v2
+++ v3
@@ -17,3 +17,5 @@
 EXPRESSION : expression source (required)
 MIRNA : miRNA source (required)
 META : set meta source and value to color samples on heatmap. (optional) Note: in order for the metavalue dropdown menu to show up, you must select the metasource and submit once so the menu can be populated from the source selection.
+
+HUGO: Enter the miRNA id.  TCGA uses the format hsa-xxx-xxxx : microRNA ids start with hsa eg.( hsa-mir-1200, hsa-mir-103-1-as, hsa-let-7e, hsa-let-7a-1 ). If you don't know the exact ID, enter what you can and similar ID names will be returned. (eg. mir-10a)

expression_mirna modified by Keith Ching

Keith Ching — Thu, 19 Feb 2015 21:53:56 -0000

--- v1
+++ v2
@@ -2,3 +2,18 @@

 Find which genes are statistically different between groups defined by mirna status.
+Similar to [expression_stat] except miRNA values are used to define the groups.
+
+If you divide samples into two groups, find the genes that are most different by t-test.
+To use this method, first decide on cutoff values for samples less than a certain value for group A.
+
+Then set a cutoff for samples higher than a certain value for group B. Samples that do not meet either cutoff will be ignored. 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).
+group1 less than : lower expression cutoff (required) default 4
+group2 greater than : higher expression cutff (required) default 10
+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)
+MIRNA : miRNA source (required)
+META : set meta source and value to color samples on heatmap. (optional) Note: in order for the metavalue dropdown menu to show up, you must select the metasource and submit once so the menu can be populated from the source selection.

expression_mirna modified by Keith Ching

Keith Ching — Thu, 19 Feb 2015 21:46:30 -0000

[Instructions]

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