matrix

[Instructions]
matrix : Output expression, CNV, and mutations in table format.

Matrix will output a html ( or TSV ) table of CNV, expression, and mutation for each gene in the HUGO box.

HUGO : list of HUGO gene symbols to query. (space separated) ( required )
CNV SOURCE : CNV dataset to use. (optional)
EXPRESSION : expression dataset to use. (optional)
MUTATION : mutation dataset to use. (optional)

At least CNV or EXPRESSION must be selected.

Cell Lines : restrict results to named samples. (space separated) (optional)
Cell Type : add columns for tissue type.
no color : if checked, output an unmarked up table instead of the html colored table. (default unchecked)
Compound / Compound Source : if selected, both values are required. Restricts output to samples for which there is an IC50 value for the compound selected. Adds IC50 value column and ascending sorts the samples by IC50. (optional)
CNV/EXP plot : if IC50 values and nocolor is checked, render a waterfall plot of the IC50 values. The same plot can also be generated from [expression_IC50]. (optional)
IC50 : instead of choosing the Compound / Compound Source from the database, paste in your own IC50 values.

example required format:

CELL,COMPOUND_IC50
ZR7530,100
HCC202,500
HT29,1000

Note:
(gene_e) Expression values are median centered. If there are few samples, there will appear to be extremes in expression which may be misleading.

(gene_c) CNV values are the mean log2R of the highest absolute value segment which overlaps the gene's coding region. The 'F' indicates a focal segment of <= 10MB in size.

(gene_m) MUT indicates any mutation of any type annotated for the gene in question.

For specific expression values and mutations, it is recommended to use [expression_plot] which provides the underlying data for the plot as a tsv file. Alternatively, [mutation_table] can be used to list specific mutations.

Example query

Codes for summary Table:
F = focal cnv size <= 10 MB
A = amplified cnv >= 1
D = deleted cnv <= -1
O = overexpressed median exp >= 1
U = underexpressed median exp <= -1
M = mutation
S = STOP mutation
P = splice site mutation