Recent changes to mutation_table

mutation_table modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:18:31 -0000

--- v5
+++ v6
@@ -14,4 +14,4 @@
 Notation:

 \* = STOP mutation
-\- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes.  Note that the order of genes does not necessarily match the true order of the actual fusion product.  Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies.  Also fusion information is incomplete and often entered from literature or specific studies on only a few genes or suspected samples.
+\- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes.  Note that the order of genes does not necessarily match the true order of the actual fusion product.  Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies if you just count number of mutations instead of summarizing by sample.  Also fusion information is incomplete and often entered from literature or specific studies on only a few genes or suspected samples.

mutation_table modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:16:48 -0000

--- v4
+++ v5
@@ -14,4 +14,4 @@
 Notation:

 \* = STOP mutation
-\- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes.  Note that the order of genes does not necessarily match the true order of the actual fusion product.  Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies.  Also fusion information is incomplete and often entered from literature or specific studies on only a few genes.
+\- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes.  Note that the order of genes does not necessarily match the true order of the actual fusion product.  Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies.  Also fusion information is incomplete and often entered from literature or specific studies on only a few genes or suspected samples.

mutation_table modified by Keith Ching

Keith Ching — Tue, 20 Jan 2015 18:16:27 -0000

--- v3
+++ v4
@@ -10,3 +10,8 @@
 *Cell Lines* : restrict results to the given samples. eg. KASUMI2

 *Cell Type* : add columns for tumor type and tissue type. (optional) (default unchecked)
+
+Notation:
+
+\* = STOP mutation
+\- = fusion product, ie. BCR-ABL = fusion of BCR and ABL genes.  Note that the order of genes does not necessarily match the true order of the actual fusion product.  Also, often times the fusion will appear twice (eg BCR-ABL and ABL-BCR) which may distort mutation frequencies.  Also fusion information is incomplete and often entered from literature or specific studies on only a few genes.

mutation_table modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 22:26:46 -0000

--- v2
+++ v3
@@ -1,5 +1,12 @@
 [[img src=mutation_table.png alt=mutation_table]]
 [Instructions]

-mutation_table
-For cell lines, list mutations from CCLE, SANGER, and COSMIC
+mutation_table : create table of mutations.  Given a list of gene symbols, query the selected datasets for all samples containing a mutation in the given genes.  Concatenates mutations in the same gene.
+
+
+*HUGO* : list gene symbols separated by spaces. (required) eg. KRAS TP53 CDKN2A
+*MUTATION* : source of mutations to query. (required) (default ALL)
+For cell lines, use ALL to list mutations from CCLE, SANGER, and COSMIC.
+*Cell Lines* : restrict results to the given samples. eg. KASUMI2
+
+*Cell Type* : add columns for tumor type and tissue type. (optional) (default unchecked)

mutation_table modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 22:19:11 -0000

--- v1
+++ v2
@@ -1,5 +1,5 @@
-
-
+[[img src=mutation_table.png alt=mutation_table]]
 [Instructions]

 mutation_table
+For cell lines, list mutations from CCLE, SANGER, and COSMIC

mutation_table modified by Keith Ching

Keith Ching — Mon, 29 Dec 2014 22:18:00 -0000

[Instructions]

mutation_table