...
Networks
...
dissimilarity
...
measure
...
as
...
it
...
is
...
defined
...
...
.
Beta vs M value (-batch, |
...
center, |
...
plate |
...
column |
...
and |
...
row |
...
(BCRC)) |
...
0.32 |
...
Beta |
...
vs |
...
M |
...
value |
...
(-batch, |
...
plate |
...
column |
...
and |
...
row |
...
(CENTER)) |
...
0.27 |
...
M |
...
value |
...
(BCRC) |
...
vs |
...
M |
...
value |
...
(CENTER) |
...
0.12 |
...
Beta
...
(vertical)
...
vs
...
M
...
value
...
(-batch,
...
center,
...
plate
...
column
...
and
...
row
...
(BCRC))
...
(horizontal):
...
| Wiki Markup |
|---|
{csv}Modules,grey,turquoise,blue,brown,yellow,black,pink,magenta,red,purple,greenyellow,tan,green,salmon,midnightblue,cyan,lightcyan,grey60,lightgreen
grey,20981,2126,1039,60,227,108,97,92,89,89,86,85,82,46,42,4,34,33,32
turquoise,787,19,0,552,0,0,0,0,24,0,0,0,0,0,1,39,0,0,0
blue,255,0,8,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
brown,1,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0
yellow,0,0,159,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
green,0,0,0,0,0,0,0,0,0,0,0,0,39,0,0,0,0,0,0
black,32,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
pink,30,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
red,29,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0{csv} |
...
Beta
...
vs
...
M
...
value
...
(CENTER):
...
| Wiki Markup |
|---|
{csv}"Modules","grey","turquoise","blue","brown","yellow","green","red","black","pink"
"grey",22469,1726,774,166,2,96,45,41,33
"turquoise",1247,19,0,0,155,0,0,0,1
"blue",259,0,5,0,0,0,0,0,0
"brown",1,0,0,242,0,0,0,0,0
"yellow",0,0,159,0,0,0,0,0,0
"green",0,0,0,0,0,39,0,0,0
"black",32,0,0,0,0,0,0,0,0
"red",30,5,0,0,0,0,0,0,0
"pink",30,0,0,0,2,0,0,0,0
{csv} |
...
M
...
value
...
(BCRC)
...
vs
...
M
...
value
...
(Center):
...
| Wiki Markup |
|---|
{csv}"Modules","grey","turquoise","blue","brown","yellow","green","red","black","pink"
"grey",22104,2,1,0,3,3,0,2,0
"turquoise",389,1746,16,0,0,0,0,0,0
"blue",283,2,921,0,0,0,0,0,0
"brown",459,0,0,0,156,0,0,0,0
"yellow",61,0,0,408,0,0,0,0,0
"black",108,0,0,0,0,0,0,0,0
"magenta",92,0,0,0,0,0,0,0,0
"tan",85,0,0,0,0,0,0,0,0
"greenyellow",85,0,0,0,0,0,0,1,0
"green",38,0,0,0,0,83,0,0,0
"red",68,0,0,0,0,0,45,0,0
"pink",59,0,0,0,0,0,0,38,0
"purple",40,0,0,0,0,49,0,0,0
"salmon",46,0,0,0,0,0,0,0,0
"cyan",43,0,0,0,0,0,0,0,0
"midnightblue",9,0,0,0,0,0,0,0,34
"lightcyan",34,0,0,0,0,0,0,0,0
"grey60",33,0,0,0,0,0,0,0,0
"lightgreen",32,0,0,0,0,0,0,0,0
{csv} |
...
of
...
network
...
modules
...
correlations
...
with
...
clinical
...
traits:
...
traits | Beta | M value (BCRC) |
|---|
...
M |
|---|
...
value |
|---|
...
(BCR) |
|---|
...
mb | mbc | ||||
|---|---|---|---|---|---|
% variance explained | 60-73% | 45-80% | 45-80% | 15-60% | 15-66% |
number of modules | 8 | 18 | 8 | 65 | 79 |
survival (P value=0.05) |
...
0 | 0 | 0 (red=0.0509) |
...
6 | 8 | ||||
primary therapy outcome | 0 | 0 | 1 (red) |
|
|
age | 1 | 6 | 1 |
|
|
tumor grade | 1 | 1 | 0 |
|
|
tumor stage | 0 | 0 | 0 |
|
|
Tumor residual disease | 0 | 1 | 1 |
|
|
Chromosomal clustering | 2 | 4 | 1 (brown) | 27 | 52 |
Gene Ontology | keratinization | keratinization | keratinization | weak | weak |
November 16th, 2011 update: We decided to choose M value as a measure for methylation and normalization -batch, -center, -plate row, -plate column for all further analyses.