Correlation between copy number variations of arm-level result and molecular subtypes

Liver Hepatocellular Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Q23ZNH

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 8 molecular subtypes across 370 patients, 264 significant findings detected with P value < 0.05 and Q value < 0.25.

1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
2q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
3q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
4p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
5p gain cnv correlated to 'CN_CNMF'.
5q gain cnv correlated to 'CN_CNMF'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
7q gain cnv correlated to 'METHLYATION_CNMF'.
8p gain cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
11p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
12p gain cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q gain cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
13q gain cnv correlated to 'CN_CNMF'.
16p gain cnv correlated to 'MRNASEQ_CNMF'.
16q gain cnv correlated to 'MRNASEQ_CNMF'.
17p gain cnv correlated to 'CN_CNMF'.
17q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
18q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
19p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
19q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
22q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
xp gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
2q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q loss cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
4p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q loss cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
12q loss cnv correlated to 'CN_CNMF'.
13q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF'.
20q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
22q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
xp loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
xq loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 264 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
xq gain	60 (16%)	310	0.0117 (0.0435)	0.00978 (0.0386)	0.00106 (0.00717)	0.00451 (0.0216)	0.00085 (0.00606)	9e-05 (0.00107)	0.00599 (0.0262)	7e-05 (0.00085)
1p loss	78 (21%)	292	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	0.00014 (0.00148)	0.0199 (0.0622)	0.00087 (0.00614)	0.0161 (0.0543)
4q loss	146 (39%)	224	1e-05 (0.00016)	0.00613 (0.0265)	1e-05 (0.00016)	0.00082 (0.00591)	0.00239 (0.0134)	0.00459 (0.0218)	3e-05 (0.00041)	0.00267 (0.0145)
13q loss	122 (33%)	248	1e-05 (0.00016)	0.0383 (0.103)	0.00233 (0.0133)	0.00033 (0.00305)	0.00337 (0.017)	0.00468 (0.0219)	0.00054 (0.00412)	0.00064 (0.00472)
16p loss	108 (29%)	262	1e-05 (0.00016)	0.0001 (0.00113)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)
16q loss	145 (39%)	225	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)	1e-05 (0.00016)
19q gain	71 (19%)	299	0.154 (0.284)	0.00213 (0.0124)	0.00054 (0.00412)	3e-05 (0.00041)	0.0217 (0.0655)	0.00151 (0.00987)	4e-05 (0.000536)	0.00043 (0.00357)
9p loss	119 (32%)	251	1e-05 (0.00016)	0.0402 (0.105)	0.00014 (0.00148)	0.00604 (0.0262)	0.0101 (0.0391)	0.00845 (0.0349)	0.0992 (0.206)	0.00889 (0.0362)
9q loss	110 (30%)	260	1e-05 (0.00016)	0.00991 (0.0387)	0.00227 (0.0131)	0.00162 (0.0102)	0.0277 (0.0787)	0.00854 (0.035)	0.261 (0.398)	0.00041 (0.00354)
10q loss	78 (21%)	292	1e-05 (0.00016)	0.0448 (0.113)	1e-05 (0.00016)	3e-05 (0.00041)	0.00322 (0.0165)	0.0001 (0.00113)	0.081 (0.179)	1e-05 (0.00016)
6p gain	116 (31%)	254	1e-05 (0.00016)	0.00518 (0.0236)	0.00099 (0.00676)	0.0231 (0.0685)	0.00964 (0.0386)	0.00401 (0.0198)	0.613 (0.71)	0.226 (0.366)
19p gain	56 (15%)	314	0.245 (0.388)	0.00974 (0.0386)	0.00334 (0.017)	0.0101 (0.0391)	0.0388 (0.103)	0.00669 (0.0283)	0.00247 (0.0137)	0.0593 (0.138)
4p loss	105 (28%)	265	1e-05 (0.00016)	0.0709 (0.16)	0.00066 (0.00481)	0.0187 (0.0596)	0.133 (0.255)	0.0159 (0.0543)	0.017 (0.0558)	0.00039 (0.00341)
5q loss	37 (10%)	333	0.0122 (0.0442)	0.0153 (0.053)	0.0532 (0.129)	0.00035 (0.0031)	0.00511 (0.0236)	0.0594 (0.138)	0.00011 (0.00122)	0.00061 (0.00455)
10p loss	47 (13%)	323	0.00015 (0.00154)	0.417 (0.542)	0.00307 (0.0162)	0.00438 (0.0213)	0.0104 (0.0398)	0.0138 (0.049)	0.124 (0.24)	0.0151 (0.0524)
15q loss	67 (18%)	303	0.00042 (0.00357)	0.156 (0.286)	0.00016 (0.00161)	7e-05 (0.00085)	0.031 (0.0865)	0.249 (0.389)	0.00152 (0.00987)	0.0204 (0.063)
17p loss	185 (50%)	185	1e-05 (0.00016)	0.0837 (0.183)	0.00187 (0.0113)	0.0219 (0.0658)	0.00199 (0.0118)	0.00034 (0.00306)	0.281 (0.421)	0.00022 (0.00215)
1q gain	226 (61%)	144	1e-05 (0.00016)	0.0001 (0.00113)	3e-05 (0.00041)	0.00158 (0.0101)	0.554 (0.668)	0.0209 (0.0642)	0.714 (0.789)	0.108 (0.221)
8q gain	184 (50%)	186	3e-05 (0.00041)	0.274 (0.412)	1e-05 (0.00016)	1e-05 (0.00016)	0.446 (0.569)	0.00644 (0.0276)	0.46 (0.582)	0.00193 (0.0115)
18p gain	36 (10%)	334	0.00159 (0.0101)	0.546 (0.661)	0.0216 (0.0655)	0.0188 (0.0596)	0.0339 (0.0938)	0.192 (0.327)	0.0129 (0.0462)	0.474 (0.594)
20p gain	107 (29%)	263	1e-05 (0.00016)	0.289 (0.425)	0.015 (0.0524)	0.00177 (0.011)	0.164 (0.294)	0.0445 (0.113)	0.00043 (0.00357)	0.0512 (0.127)
3p loss	52 (14%)	318	0.1 (0.207)	0.0695 (0.158)	0.00409 (0.02)	0.00919 (0.037)	0.00371 (0.0184)	0.318 (0.445)	0.00505 (0.0235)	0.0417 (0.107)
5p loss	29 (8%)	341	0.0168 (0.0554)	0.145 (0.27)	0.14 (0.265)	0.0242 (0.071)	0.0127 (0.0459)	0.112 (0.228)	0.00987 (0.0387)	0.0161 (0.0543)
14q loss	109 (29%)	261	1e-05 (0.00016)	0.165 (0.295)	6e-05 (0.000772)	2e-05 (0.000305)	0.0554 (0.132)	0.158 (0.287)	0.00019 (0.00189)	0.00463 (0.0219)
3p gain	35 (9%)	335	0.0174 (0.0565)	0.0248 (0.0716)	0.00203 (0.0119)	0.0877 (0.189)	0.0364 (0.0987)	0.516 (0.631)	0.0681 (0.157)	0.304 (0.434)
10p gain	58 (16%)	312	0.00315 (0.0165)	0.606 (0.707)	0.00818 (0.034)	0.0201 (0.0626)	0.142 (0.266)	0.476 (0.594)	0.0533 (0.129)	0.0111 (0.0419)
12p gain	40 (11%)	330	0.611 (0.71)	0.282 (0.421)	0.00518 (0.0236)	0.0005 (0.00405)	0.0575 (0.136)	0.342 (0.471)	0.00012 (0.00131)	0.0266 (0.0761)
18q gain	28 (8%)	342	0.0466 (0.117)	0.849 (0.892)	0.0518 (0.127)	0.00318 (0.0165)	0.0171 (0.0559)	0.0544 (0.13)	0.00358 (0.0179)	0.302 (0.434)
20q gain	112 (30%)	258	1e-05 (0.00016)	0.277 (0.416)	0.118 (0.235)	0.0104 (0.0398)	0.297 (0.431)	0.039 (0.103)	0.00056 (0.00422)	0.14 (0.265)
22q gain	48 (13%)	322	0.00028 (0.00262)	0.142 (0.266)	0.0389 (0.103)	0.00187 (0.0113)	0.123 (0.24)	0.737 (0.806)	0.0119 (0.0438)	0.0688 (0.157)
7q loss	21 (6%)	349	0.158 (0.287)	0.285 (0.423)	0.0185 (0.0595)	0.0842 (0.183)	0.674 (0.759)	0.035 (0.0956)	7e-05 (0.00085)	0.00733 (0.0308)
11p loss	63 (17%)	307	0.0115 (0.0427)	0.862 (0.9)	0.0549 (0.131)	0.011 (0.0417)	0.0957 (0.201)	0.158 (0.287)	0.0146 (0.0512)	0.0161 (0.0543)
2q gain	40 (11%)	330	0.0485 (0.121)	0.481 (0.598)	0.0144 (0.0509)	0.00052 (0.00411)	0.0676 (0.156)	0.9 (0.926)	0.0816 (0.179)	0.344 (0.472)
3q gain	38 (10%)	332	0.0131 (0.0468)	0.258 (0.397)	0.00298 (0.0159)	0.0921 (0.196)	0.0306 (0.0859)	0.511 (0.627)	0.0586 (0.137)	0.718 (0.789)
4p gain	27 (7%)	343	0.43 (0.556)	0.00667 (0.0283)	0.0122 (0.0442)	0.00188 (0.0113)	0.256 (0.395)	0.443 (0.567)	0.0867 (0.187)	0.162 (0.292)
7p gain	109 (29%)	261	0.00128 (0.00857)	0.0247 (0.0716)	0.791 (0.845)	0.89 (0.922)	0.0362 (0.0985)	0.104 (0.214)	0.641 (0.734)	0.455 (0.578)
8p gain	73 (20%)	297	0.4 (0.527)	0.407 (0.531)	0.00253 (0.0139)	0.0167 (0.0553)	0.273 (0.412)	0.37 (0.499)	0.885 (0.919)	0.0279 (0.0789)
10q gain	36 (10%)	334	0.00045 (0.00369)	0.0302 (0.085)	6e-05 (0.000772)	0.12 (0.237)	0.19 (0.325)	0.0789 (0.176)	0.214 (0.352)	0.0831 (0.182)
12q gain	47 (13%)	323	0.199 (0.334)	0.716 (0.789)	0.00907 (0.0367)	0.0027 (0.0145)	0.1 (0.207)	0.624 (0.719)	0.00028 (0.00262)	0.0579 (0.136)
17q gain	93 (25%)	277	0.00587 (0.026)	0.341 (0.471)	0.306 (0.435)	0.095 (0.2)	0.0774 (0.173)	0.00093 (0.00649)	0.809 (0.861)	0.0155 (0.0533)
xp gain	41 (11%)	329	0.0244 (0.0713)	0.122 (0.24)	0.0235 (0.0694)	0.376 (0.506)	0.151 (0.279)	0.0519 (0.127)	0.847 (0.892)	0.0394 (0.103)
2p loss	33 (9%)	337	0.00545 (0.0245)	0.394 (0.523)	0.00539 (0.0244)	0.0386 (0.103)	0.254 (0.393)	0.708 (0.787)	0.392 (0.522)	0.265 (0.403)
2q loss	38 (10%)	332	0.00132 (0.00875)	0.386 (0.517)	0.00097 (0.0067)	0.0216 (0.0655)	0.58 (0.689)	0.593 (0.699)	0.901 (0.926)	0.403 (0.529)
3q loss	41 (11%)	329	0.0902 (0.193)	0.342 (0.471)	0.00566 (0.0253)	0.0539 (0.129)	0.0413 (0.107)	0.466 (0.587)	0.00811 (0.0339)	0.236 (0.379)
11q loss	72 (19%)	298	0.0391 (0.103)	0.801 (0.855)	0.195 (0.331)	0.177 (0.311)	0.438 (0.562)	0.21 (0.346)	0.012 (0.0441)	0.0493 (0.122)
18p loss	74 (20%)	296	0.0266 (0.0761)	0.00236 (0.0133)	0.567 (0.678)	0.00322 (0.0165)	0.9 (0.926)	0.712 (0.789)	0.217 (0.355)	0.291 (0.426)
18q loss	79 (21%)	291	0.0163 (0.0543)	0.00164 (0.0102)	0.519 (0.633)	0.00054 (0.00412)	0.759 (0.819)	0.404 (0.529)	0.286 (0.423)	0.282 (0.421)
21q loss	110 (30%)	260	0.0162 (0.0543)	0.592 (0.699)	0.00034 (0.00306)	0.124 (0.24)	0.455 (0.578)	0.931 (0.942)	0.0115 (0.0427)	0.113 (0.228)
xp loss	95 (26%)	275	0.286 (0.423)	0.0198 (0.0622)	0.124 (0.24)	0.0242 (0.071)	0.0717 (0.161)	0.315 (0.442)	0.0227 (0.0677)	0.203 (0.338)
6q gain	67 (18%)	303	0.00015 (0.00154)	0.156 (0.286)	0.0349 (0.0956)	0.29 (0.426)	0.238 (0.381)	0.24 (0.382)	0.649 (0.742)	0.575 (0.685)
1q loss	20 (5%)	350	0.0323 (0.0898)	0.67 (0.758)	0.29 (0.426)	0.485 (0.6)	0.25 (0.39)	0.113 (0.228)	0.516 (0.631)	0.0189 (0.0596)
7p loss	16 (4%)	354	0.397 (0.525)	0.31 (0.44)	0.12 (0.238)	0.353 (0.479)	0.863 (0.9)	0.227 (0.367)	0.0204 (0.063)	0.0404 (0.105)
8p loss	196 (53%)	174	1e-05 (0.00016)	0.182 (0.316)	0.0345 (0.0952)	0.777 (0.834)	0.771 (0.831)	0.26 (0.397)	0.302 (0.434)	0.738 (0.806)
12p loss	66 (18%)	304	2e-05 (0.000305)	0.359 (0.486)	0.0181 (0.0584)	0.302 (0.434)	0.353 (0.479)	0.124 (0.24)	0.18 (0.315)	0.21 (0.346)
19p loss	52 (14%)	318	1e-05 (0.00016)	0.859 (0.899)	0.0685 (0.157)	0.247 (0.388)	0.0765 (0.171)	0.148 (0.274)	0.316 (0.442)	0.0188 (0.0596)
22q loss	70 (19%)	300	0.00452 (0.0216)	0.177 (0.311)	0.00265 (0.0145)	0.16 (0.289)	0.831 (0.882)	0.464 (0.585)	0.566 (0.678)	0.989 (0.993)
xq loss	74 (20%)	296	0.0489 (0.122)	0.0419 (0.107)	0.202 (0.338)	0.186 (0.32)	0.357 (0.484)	0.568 (0.678)	0.619 (0.715)	0.531 (0.646)
2p gain	43 (12%)	327	0.137 (0.26)	0.249 (0.389)	0.146 (0.271)	0.00024 (0.00232)	0.0946 (0.2)	0.968 (0.974)	0.117 (0.234)	0.299 (0.433)
5p gain	134 (36%)	236	1e-05 (0.00016)	0.252 (0.39)	0.909 (0.928)	0.749 (0.812)	0.632 (0.726)	0.145 (0.27)	0.0985 (0.206)	0.554 (0.668)
5q gain	110 (30%)	260	1e-05 (0.00016)	0.0816 (0.179)	0.742 (0.807)	0.906 (0.926)	0.559 (0.671)	0.904 (0.926)	0.786 (0.841)	0.891 (0.922)
7q gain	110 (30%)	260	0.205 (0.339)	0.00051 (0.00408)	0.537 (0.652)	0.841 (0.889)	0.246 (0.388)	0.238 (0.38)	0.679 (0.761)	0.44 (0.564)
11p gain	18 (5%)	352	0.435 (0.561)	0.306 (0.435)	0.199 (0.334)	0.0227 (0.0677)	0.615 (0.712)	0.483 (0.599)	0.0579 (0.136)	0.229 (0.369)
13q gain	23 (6%)	347	0.0366 (0.0987)	0.474 (0.594)	0.169 (0.3)	0.409 (0.532)	0.0525 (0.128)	0.292 (0.426)	0.168 (0.298)	0.242 (0.384)
16p gain	32 (9%)	338	0.175 (0.309)	0.919 (0.933)	0.0451 (0.114)	0.995 (0.997)	0.208 (0.344)	0.183 (0.317)	0.117 (0.233)	0.217 (0.355)
16q gain	17 (5%)	353	0.123 (0.24)	0.07 (0.159)	0.00604 (0.0262)	0.313 (0.44)	0.936 (0.945)	0.912 (0.929)	0.19 (0.325)	0.717 (0.789)
17p gain	30 (8%)	340	0.0367 (0.0988)	0.384 (0.515)	0.457 (0.579)	0.0988 (0.206)	0.274 (0.412)	0.755 (0.816)	0.178 (0.312)	0.325 (0.451)
12q loss	36 (10%)	334	0.0267 (0.0761)	0.902 (0.926)	0.3 (0.433)	0.66 (0.751)	0.6 (0.703)	0.917 (0.932)	0.804 (0.856)	0.882 (0.917)
19q loss	39 (11%)	331	1e-05 (0.00016)	0.323 (0.45)	0.156 (0.286)	0.905 (0.926)	0.113 (0.228)	0.0949 (0.2)	0.24 (0.382)	0.135 (0.257)
20q loss	13 (4%)	357	1 (1.00)	0.259 (0.397)	0.202 (0.338)	0.113 (0.228)	0.557 (0.671)	0.638 (0.732)	0.0416 (0.107)	0.3 (0.433)
1p gain	62 (17%)	308	0.0584 (0.137)	0.238 (0.38)	0.167 (0.298)	0.659 (0.751)	0.35 (0.477)	0.105 (0.215)	0.196 (0.331)	0.0801 (0.178)
4q gain	7 (2%)	363	0.304 (0.434)	0.707 (0.787)	0.728 (0.798)	0.406 (0.531)	0.194 (0.331)	0.85 (0.892)	0.293 (0.426)	0.594 (0.699)
9p gain	19 (5%)	351	0.313 (0.44)	0.687 (0.767)	0.751 (0.813)	0.668 (0.757)	0.599 (0.703)	0.401 (0.527)	0.125 (0.241)	0.323 (0.45)
9q gain	19 (5%)	351	0.602 (0.704)	0.687 (0.767)	0.597 (0.702)	0.658 (0.751)	0.741 (0.807)	0.397 (0.525)	0.593 (0.699)	0.437 (0.562)
11q gain	20 (5%)	350	0.346 (0.473)	0.671 (0.758)	0.475 (0.594)	0.0929 (0.197)	0.782 (0.838)	0.611 (0.71)	0.0519 (0.127)	0.251 (0.39)
14q gain	22 (6%)	348	0.185 (0.319)	0.5 (0.615)	0.362 (0.488)	0.133 (0.255)	0.562 (0.674)	0.174 (0.308)	0.142 (0.266)	0.734 (0.804)
15q gain	33 (9%)	337	0.182 (0.317)	0.584 (0.693)	0.899 (0.926)	0.715 (0.789)	0.952 (0.959)	0.284 (0.423)	0.544 (0.66)	0.843 (0.891)
21q gain	26 (7%)	344	0.184 (0.318)	0.934 (0.944)	0.09 (0.193)	0.388 (0.518)	0.925 (0.938)	0.225 (0.365)	0.303 (0.434)	0.492 (0.607)
6p loss	31 (8%)	339	0.746 (0.81)	0.486 (0.6)	0.395 (0.524)	0.483 (0.599)	0.0713 (0.161)	0.85 (0.892)	0.343 (0.471)	0.394 (0.523)
6q loss	94 (25%)	276	0.203 (0.338)	0.164 (0.294)	0.427 (0.553)	0.836 (0.886)	0.126 (0.242)	0.26 (0.397)	0.664 (0.754)	0.996 (0.997)
8q loss	45 (12%)	325	0.199 (0.334)	0.224 (0.364)	0.0863 (0.187)	0.632 (0.726)	0.709 (0.787)	0.882 (0.917)	0.776 (0.834)	0.673 (0.758)
17q loss	40 (11%)	330	0.0536 (0.129)	0.457 (0.579)	0.517 (0.631)	0.249 (0.389)	0.68 (0.761)	0.612 (0.71)	0.473 (0.594)	0.339 (0.469)
20p loss	26 (7%)	344	0.42 (0.545)	0.338 (0.469)	0.271 (0.411)	0.104 (0.214)	0.263 (0.4)	0.853 (0.894)	0.675 (0.759)	0.312 (0.44)

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
1Q GAIN MUTATED	37	87	102
1Q GAIN WILD-TYPE	56	64	24

Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S2. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
1Q GAIN MUTATED	41	99	86
1Q GAIN WILD-TYPE	52	62	30

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00041

Table S3. Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
1Q GAIN MUTATED	39	37	58	41	46
1Q GAIN WILD-TYPE	28	49	13	30	23

Figure S3. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.01

Table S4. Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
1Q GAIN MUTATED	28	35	56	63	39
1Q GAIN WILD-TYPE	26	21	58	21	17

Figure S4. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.064

Table S5. Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
1Q GAIN MUTATED	27	46	40	74	35
1Q GAIN WILD-TYPE	17	49	16	48	13

Figure S5. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0023

Table S6. Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
2P GAIN MUTATED	13	2	6	16	4
2P GAIN WILD-TYPE	41	54	108	68	52

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.12

Table S7. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
2Q GAIN MUTATED	5	15	20
2Q GAIN WILD-TYPE	88	136	106

Figure S7. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.051

Table S8. Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
2Q GAIN MUTATED	7	2	13	8	8
2Q GAIN WILD-TYPE	60	84	58	63	61

Figure S8. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0041

Table S9. Gene #4: '2q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
2Q GAIN MUTATED	10	2	4	16	6
2Q GAIN WILD-TYPE	44	54	110	68	50

Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.057

Table S10. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
3P GAIN MUTATED	4	22	9
3P GAIN WILD-TYPE	89	129	117

Figure S10. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.072

Table S11. Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
3P GAIN MUTATED	5	23	7
3P GAIN WILD-TYPE	88	138	109

Figure S11. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.012

Table S12. Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
3P GAIN MUTATED	11	7	7	0	10
3P GAIN WILD-TYPE	56	79	64	71	59

Figure S12. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.099

Table S13. Gene #5: '3p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
3P GAIN MUTATED	5	5	2	13	5	4
3P GAIN WILD-TYPE	35	58	90	71	41	36

Figure S13. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.047

Table S14. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
3Q GAIN MUTATED	5	24	9
3Q GAIN WILD-TYPE	88	127	117

Figure S14. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.016

Table S15. Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
3Q GAIN MUTATED	14	8	6	1	9
3Q GAIN WILD-TYPE	53	78	65	70	60

Figure S15. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.086

Table S16. Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
3Q GAIN MUTATED	7	5	3	11	8	3
3Q GAIN WILD-TYPE	33	58	89	73	38	37

Figure S16. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.028

Table S17. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
4P GAIN MUTATED	5	6	16
4P GAIN WILD-TYPE	88	155	100

Figure S17. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.044

Table S18. Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
4P GAIN MUTATED	4	5	12	4	1
4P GAIN WILD-TYPE	63	81	59	67	68

Figure S18. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.011

Table S19. Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
4P GAIN MUTATED	5	3	3	14	1
4P GAIN WILD-TYPE	49	53	111	70	55

Figure S19. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S20. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
5P GAIN MUTATED	13	63	58
5P GAIN WILD-TYPE	80	88	68

Figure S20. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S21. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
5Q GAIN MUTATED	10	46	54
5Q GAIN WILD-TYPE	83	105	72

Figure S21. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S22. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
6P GAIN MUTATED	10	57	49
6P GAIN WILD-TYPE	83	94	77

Figure S22. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.024

Table S23. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
6P GAIN MUTATED	17	57	42
6P GAIN WILD-TYPE	76	104	74

Figure S23. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0068

Table S24. Gene #11: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
6P GAIN MUTATED	25	18	28	14	31
6P GAIN WILD-TYPE	42	68	43	57	38

Figure S24. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0231 (Fisher's exact test), Q value = 0.069

Table S25. Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
6P GAIN MUTATED	16	11	31	33	25
6P GAIN WILD-TYPE	38	45	83	51	31

Figure S25. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.00964 (Fisher's exact test), Q value = 0.039

Table S26. Gene #11: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
6P GAIN MUTATED	18	15	19	35	17	11
6P GAIN WILD-TYPE	22	48	73	49	29	29

Figure S26. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00401 (Fisher's exact test), Q value = 0.02

Table S27. Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
6P GAIN MUTATED	18	18	19	37	23
6P GAIN WILD-TYPE	26	77	37	85	25

Figure S27. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S28. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
6Q GAIN MUTATED	5	36	26
6Q GAIN WILD-TYPE	88	115	100

Figure S28. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.096

Table S29. Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
6Q GAIN MUTATED	19	10	15	8	15
6Q GAIN WILD-TYPE	48	76	56	63	54

Figure S29. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0086

Table S30. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
7P GAIN MUTATED	14	51	44
7P GAIN WILD-TYPE	79	100	82

Figure S30. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.072

Table S31. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
7P GAIN MUTATED	20	59	30
7P GAIN WILD-TYPE	73	102	86

Figure S31. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.099

Table S32. Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
7P GAIN MUTATED	8	18	22	31	9	18
7P GAIN WILD-TYPE	32	45	70	53	37	22

Figure S32. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0041

Table S33. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
7Q GAIN MUTATED	21	65	24
7Q GAIN WILD-TYPE	72	96	92

Figure S33. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.014

Table S34. Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
8P GAIN MUTATED	15	6	12	18	20
8P GAIN WILD-TYPE	52	80	59	53	49

Figure S34. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.055

Table S35. Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
8P GAIN MUTATED	12	12	11	22	14
8P GAIN WILD-TYPE	42	44	103	62	42

Figure S35. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.079

Table S36. Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
8P GAIN MUTATED	19	8	22	5	15
8P GAIN WILD-TYPE	51	74	78	29	39

Figure S36. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00041

Table S37. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
8Q GAIN MUTATED	38	61	85
8Q GAIN WILD-TYPE	55	90	41

Figure S37. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S38. Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
8Q GAIN MUTATED	39	21	38	37	44
8Q GAIN WILD-TYPE	28	65	33	34	25

Figure S38. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S39. Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
8Q GAIN MUTATED	31	31	30	51	36
8Q GAIN WILD-TYPE	23	25	84	33	20

Figure S39. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00644 (Fisher's exact test), Q value = 0.028

Table S40. Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
8Q GAIN MUTATED	19	34	28	70	30
8Q GAIN WILD-TYPE	25	61	28	52	18

Figure S40. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.012

Table S41. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
8Q GAIN MUTATED	42	29	54	13	35
8Q GAIN WILD-TYPE	28	53	46	21	19

Figure S41. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.017

Table S42. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
10P GAIN MUTATED	5	29	24
10P GAIN WILD-TYPE	88	122	102

Figure S42. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.034

Table S43. Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
10P GAIN MUTATED	10	8	20	6	13
10P GAIN WILD-TYPE	57	78	51	65	56

Figure S43. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.063

Table S44. Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
10P GAIN MUTATED	11	6	10	21	9
10P GAIN WILD-TYPE	43	50	104	63	47

Figure S44. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.042

Table S45. Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
10P GAIN MUTATED	17	5	17	8	6
10P GAIN WILD-TYPE	53	77	83	26	48

Figure S45. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0037

Table S46. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
10Q GAIN MUTATED	2	12	22
10Q GAIN WILD-TYPE	91	139	104

Figure S46. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.085

Table S47. Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
10Q GAIN MUTATED	3	18	15
10Q GAIN WILD-TYPE	90	143	101

Figure S47. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00077

Table S48. Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
10Q GAIN MUTATED	2	4	17	3	10
10Q GAIN WILD-TYPE	65	82	54	68	59

Figure S48. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.068

Table S49. Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
11P GAIN MUTATED	6	2	3	7	0
11P GAIN WILD-TYPE	48	54	111	77	56

Figure S49. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.024

Table S50. Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
12P GAIN MUTATED	12	3	13	8	4
12P GAIN WILD-TYPE	55	83	58	63	65

Figure S50. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.004

Table S51. Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
12P GAIN MUTATED	14	2	9	13	2
12P GAIN WILD-TYPE	40	54	105	71	54

Figure S51. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S52. Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
12P GAIN MUTATED	19	9	1	7
12P GAIN WILD-TYPE	88	72	101	43

Figure S52. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.076

Table S53. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
12P GAIN MUTATED	13	6	12	4	1
12P GAIN WILD-TYPE	57	76	88	30	53

Figure S53. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.037

Table S54. Gene #24: '12q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
12Q GAIN MUTATED	13	5	14	11	4
12Q GAIN WILD-TYPE	54	81	57	60	65

Figure S54. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.015

Table S55. Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
12Q GAIN MUTATED	14	4	12	15	2
12Q GAIN WILD-TYPE	40	52	102	69	54

Figure S55. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0026

Table S56. Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
12Q GAIN MUTATED	23	9	3	8
12Q GAIN WILD-TYPE	84	72	99	42

Figure S56. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.099

Table S57. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
13Q GAIN MUTATED	1	12	10
13Q GAIN WILD-TYPE	92	139	116

Figure S57. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.11

Table S58. Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
16P GAIN MUTATED	7	7	2	12	4
16P GAIN WILD-TYPE	60	79	69	59	65

Figure S58. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.026

Table S59. Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
16Q GAIN MUTATED	3	2	0	9	3
16Q GAIN WILD-TYPE	64	84	71	62	66

Figure S59. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.099

Table S60. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
17P GAIN MUTATED	5	8	17
17P GAIN WILD-TYPE	88	143	109

Figure S60. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.026

Table S61. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
17Q GAIN MUTATED	13	48	32
17Q GAIN WILD-TYPE	80	103	94

Figure S61. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0065

Table S62. Gene #31: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
17Q GAIN MUTATED	21	20	17	20	15
17Q GAIN WILD-TYPE	23	75	39	102	33

Figure S62. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.053

Table S63. Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
17Q GAIN MUTATED	24	18	16	13	17
17Q GAIN WILD-TYPE	46	64	84	21	37

Figure S63. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.01

Table S64. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
18P GAIN MUTATED	2	14	20
18P GAIN WILD-TYPE	91	137	106

Figure S64. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.066

Table S65. Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
18P GAIN MUTATED	9	4	13	7	3
18P GAIN WILD-TYPE	58	82	58	64	66

Figure S65. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.06

Table S66. Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
18P GAIN MUTATED	10	4	7	13	2
18P GAIN WILD-TYPE	44	52	107	71	54

Figure S66. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.094

Table S67. Gene #32: '18p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
18P GAIN MUTATED	7	3	6	7	4	9
18P GAIN WILD-TYPE	33	60	86	77	42	31

Figure S67. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.046

Table S68. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
18P GAIN MUTATED	16	9	3	7
18P GAIN WILD-TYPE	91	72	99	43

Figure S68. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.12

Table S69. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
18Q GAIN MUTATED	2	13	13
18Q GAIN WILD-TYPE	91	138	113

Figure S69. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.017

Table S70. Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
18Q GAIN MUTATED	9	4	5	10	0
18Q GAIN WILD-TYPE	45	52	109	74	56

Figure S70. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.056

Table S71. Gene #33: '18q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
18Q GAIN MUTATED	6	4	5	3	2	8
18Q GAIN WILD-TYPE	34	59	87	81	44	32

Figure S71. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.018

Table S72. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
18Q GAIN MUTATED	14	8	1	4
18Q GAIN WILD-TYPE	93	73	101	46

Figure S72. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.039

Table S73. Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
19P GAIN MUTATED	15	15	26
19P GAIN WILD-TYPE	78	146	90

Figure S73. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.017

Table S74. Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
19P GAIN MUTATED	9	10	18	15	3
19P GAIN WILD-TYPE	58	76	53	56	66

Figure S74. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.039

Table S75. Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
19P GAIN MUTATED	11	11	11	19	3
19P GAIN WILD-TYPE	43	45	103	65	53

Figure S75. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.1

Table S76. Gene #34: '19p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
19P GAIN MUTATED	4	8	18	6	8	11
19P GAIN WILD-TYPE	36	55	74	78	38	29

Figure S76. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00669 (Fisher's exact test), Q value = 0.028

Table S77. Gene #34: '19p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
19P GAIN MUTATED	4	13	10	27	1
19P GAIN WILD-TYPE	40	82	46	95	47

Figure S77. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.014

Table S78. Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
19P GAIN MUTATED	19	16	5	11
19P GAIN WILD-TYPE	88	65	97	39

Figure S78. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.012

Table S79. Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
19Q GAIN MUTATED	19	19	33
19Q GAIN WILD-TYPE	74	142	83

Figure S79. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S80. Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
19Q GAIN MUTATED	12	11	23	19	5
19Q GAIN WILD-TYPE	55	75	48	52	64

Figure S80. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00041

Table S81. Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
19Q GAIN MUTATED	12	15	11	28	4
19Q GAIN WILD-TYPE	42	41	103	56	52

Figure S81. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.066

Table S82. Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
19Q GAIN MUTATED	6	7	23	10	11	13
19Q GAIN WILD-TYPE	34	56	69	74	35	27

Figure S82. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0099

Table S83. Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
19Q GAIN MUTATED	6	14	17	31	2
19Q GAIN WILD-TYPE	38	81	39	91	46

Figure S83. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054

Table S84. Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
19Q GAIN MUTATED	25	21	5	14
19Q GAIN WILD-TYPE	82	60	97	36

Figure S84. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0036

Table S85. Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
19Q GAIN MUTATED	20	11	27	5	2
19Q GAIN WILD-TYPE	50	71	73	29	52

Figure S85. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S86. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
20P GAIN MUTATED	8	60	39
20P GAIN WILD-TYPE	85	91	87

Figure S86. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.052

Table S87. Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
20P GAIN MUTATED	24	19	31	17	16
20P GAIN WILD-TYPE	43	67	40	54	53

Figure S87. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.011

Table S88. Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
20P GAIN MUTATED	19	15	25	38	10
20P GAIN WILD-TYPE	35	41	89	46	46

Figure S88. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.11

Table S89. Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
20P GAIN MUTATED	18	21	21	37	9
20P GAIN WILD-TYPE	26	74	35	85	39

Figure S89. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0036

Table S90. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
20P GAIN MUTATED	36	22	16	24
20P GAIN WILD-TYPE	71	59	86	26

Figure S90. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S91. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
20Q GAIN MUTATED	8	63	41
20Q GAIN WILD-TYPE	85	88	85

Figure S91. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.04

Table S92. Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
20Q GAIN MUTATED	17	15	32	38	10
20Q GAIN WILD-TYPE	37	41	82	46	46

Figure S92. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.1

Table S93. Gene #37: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
20Q GAIN MUTATED	19	23	23	36	10
20Q GAIN WILD-TYPE	25	72	33	86	38

Figure S93. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0042

Table S94. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
20Q GAIN MUTATED	39	21	18	24
20Q GAIN WILD-TYPE	68	60	84	26

Figure S94. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0026

Table S95. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
22Q GAIN MUTATED	2	27	19
22Q GAIN WILD-TYPE	91	124	107

Figure S95. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.1

Table S96. Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
22Q GAIN MUTATED	8	8	18	7	7
22Q GAIN WILD-TYPE	59	78	53	64	62

Figure S96. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S97. Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
22Q GAIN MUTATED	14	5	8	17	4
22Q GAIN WILD-TYPE	40	51	106	67	52

Figure S97. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.044

Table S98. Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
22Q GAIN MUTATED	16	11	5	11
22Q GAIN WILD-TYPE	91	70	97	39

Figure S98. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.071

Table S99. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
XP GAIN MUTATED	7	12	22
XP GAIN WILD-TYPE	86	139	104

Figure S99. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.069

Table S100. Gene #40: 'xp gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
XP GAIN MUTATED	5	6	6	8	16
XP GAIN WILD-TYPE	62	80	65	63	53

Figure S100. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.1

Table S101. Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
XP GAIN MUTATED	9	4	10	3	12
XP GAIN WILD-TYPE	61	78	90	31	42

Figure S101. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.043

Table S102. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
XQ GAIN MUTATED	14	16	30
XQ GAIN WILD-TYPE	79	135	96

Figure S102. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.039

Table S103. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
XQ GAIN MUTATED	7	35	18
XQ GAIN WILD-TYPE	86	126	98

Figure S103. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0072

Table S104. Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
XQ GAIN MUTATED	7	13	8	8	24
XQ GAIN WILD-TYPE	60	73	63	63	45

Figure S104. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00451 (Fisher's exact test), Q value = 0.022

Table S105. Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
XQ GAIN MUTATED	5	6	20	10	19
XQ GAIN WILD-TYPE	49	50	94	74	37

Figure S105. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0061

Table S106. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
XQ GAIN MUTATED	3	11	10	27	5	3
XQ GAIN WILD-TYPE	37	52	82	57	41	37

Figure S106. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S107. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
XQ GAIN MUTATED	5	13	9	12	20
XQ GAIN WILD-TYPE	39	82	47	110	28

Figure S107. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.026

Table S108. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
XQ GAIN MUTATED	15	7	27	5
XQ GAIN WILD-TYPE	92	74	75	45

Figure S108. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00085

Table S109. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
XQ GAIN MUTATED	12	9	9	3	21
XQ GAIN WILD-TYPE	58	73	91	31	33

Figure S109. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S110. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
1P LOSS MUTATED	4	32	42
1P LOSS WILD-TYPE	89	119	84

Figure S110. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S111. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
1P LOSS MUTATED	8	26	44
1P LOSS WILD-TYPE	85	135	72

Figure S111. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S112. Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
1P LOSS MUTATED	8	11	37	14	7
1P LOSS WILD-TYPE	59	75	34	57	62

Figure S112. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S113. Gene #42: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
1P LOSS MUTATED	11	8	15	37	6
1P LOSS WILD-TYPE	43	48	99	47	50

Figure S113. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S114. Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
1P LOSS MUTATED	5	8	15	14	17	18
1P LOSS WILD-TYPE	35	55	77	70	29	22

Figure S114. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.062

Table S115. Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
1P LOSS MUTATED	5	17	15	35	5
1P LOSS WILD-TYPE	39	78	41	87	43

Figure S115. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0061

Table S116. Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
1P LOSS MUTATED	27	18	10	18
1P LOSS WILD-TYPE	80	63	92	32

Figure S116. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.054

Table S117. Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
1P LOSS MUTATED	16	15	32	4	6
1P LOSS WILD-TYPE	54	67	68	30	48

Figure S117. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.09

Table S118. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
1Q LOSS MUTATED	1	13	6
1Q LOSS WILD-TYPE	92	138	120

Figure S118. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.06

Table S119. Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
1Q LOSS MUTATED	1	7	10	1	0
1Q LOSS WILD-TYPE	69	75	90	33	54

Figure S119. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 0.024

Table S120. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
2P LOSS MUTATED	3	22	8
2P LOSS WILD-TYPE	90	129	118

Figure S120. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00539 (Fisher's exact test), Q value = 0.024

Table S121. Gene #44: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
2P LOSS MUTATED	11	9	7	6	0
2P LOSS WILD-TYPE	56	77	64	65	69

Figure S121. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.1

Table S122. Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
2P LOSS MUTATED	6	7	10	10	0
2P LOSS WILD-TYPE	48	49	104	74	56

Figure S122. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0087

Table S123. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
2Q LOSS MUTATED	4	26	8
2Q LOSS WILD-TYPE	89	125	118

Figure S123. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0067

Table S124. Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
2Q LOSS MUTATED	10	14	9	5	0
2Q LOSS WILD-TYPE	57	72	62	66	69

Figure S124. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.066

Table S125. Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
2Q LOSS MUTATED	5	7	16	10	0
2Q LOSS WILD-TYPE	49	49	98	74	56

Figure S125. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.02

Table S126. Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
3P LOSS MUTATED	8	6	18	14	5
3P LOSS WILD-TYPE	59	80	53	57	64

Figure S126. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.037

Table S127. Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
3P LOSS MUTATED	14	5	10	17	5
3P LOSS WILD-TYPE	40	51	104	67	51

Figure S127. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.018

Table S128. Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
3P LOSS MUTATED	4	4	15	8	6	14
3P LOSS WILD-TYPE	36	59	77	76	40	26

Figure S128. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.023

Table S129. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
3P LOSS MUTATED	20	17	6	4
3P LOSS WILD-TYPE	87	64	96	46

Figure S129. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.11

Table S130. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
3P LOSS MUTATED	13	9	20	2	3
3P LOSS WILD-TYPE	57	73	80	32	51

Figure S130. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00566 (Fisher's exact test), Q value = 0.025

Table S131. Gene #47: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
3Q LOSS MUTATED	7	5	17	7	4
3Q LOSS WILD-TYPE	60	81	54	64	65

Figure S131. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.11

Table S132. Gene #47: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
3Q LOSS MUTATED	3	4	11	7	4	11
3Q LOSS WILD-TYPE	37	59	81	77	42	29

Figure S132. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00811 (Fisher's exact test), Q value = 0.034

Table S133. Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
3Q LOSS MUTATED	19	10	5	2
3Q LOSS WILD-TYPE	88	71	97	48

Figure S133. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S134. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
4P LOSS MUTATED	3	65	37
4P LOSS WILD-TYPE	90	86	89

Figure S134. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0048

Table S135. Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
4P LOSS MUTATED	26	26	29	12	11
4P LOSS WILD-TYPE	41	60	42	59	58

Figure S135. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.06

Table S136. Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
4P LOSS MUTATED	15	11	36	33	9
4P LOSS WILD-TYPE	39	45	78	51	47

Figure S136. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.054

Table S137. Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
4P LOSS MUTATED	14	25	25	33	7
4P LOSS WILD-TYPE	30	70	31	89	41

Figure S137. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.056

Table S138. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
4P LOSS MUTATED	40	18	21	18
4P LOSS WILD-TYPE	67	63	81	32

Figure S138. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0034

Table S139. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
4P LOSS MUTATED	33	25	22	10	7
4P LOSS WILD-TYPE	37	57	78	24	47

Figure S139. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S140. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
4Q LOSS MUTATED	4	91	51
4Q LOSS WILD-TYPE	89	60	75

Figure S140. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.026

Table S141. Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
4Q LOSS MUTATED	28	59	59
4Q LOSS WILD-TYPE	65	102	57

Figure S141. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S142. Gene #49: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
4Q LOSS MUTATED	33	33	46	17	15
4Q LOSS WILD-TYPE	34	53	25	54	54

Figure S142. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0059

Table S143. Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
4Q LOSS MUTATED	24	19	42	47	12
4Q LOSS WILD-TYPE	30	37	72	37	44

Figure S143. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.013

Table S144. Gene #49: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
4Q LOSS MUTATED	18	22	30	25	26	24
4Q LOSS WILD-TYPE	22	41	62	59	20	16

Figure S144. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00459 (Fisher's exact test), Q value = 0.022

Table S145. Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
4Q LOSS MUTATED	18	35	30	53	9
4Q LOSS WILD-TYPE	26	60	26	69	39

Figure S145. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00041

Table S146. Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
4Q LOSS MUTATED	53	28	26	31
4Q LOSS WILD-TYPE	54	53	76	19

Figure S146. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.014

Table S147. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
4Q LOSS MUTATED	39	33	42	13	11
4Q LOSS WILD-TYPE	31	49	58	21	43

Figure S147. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.055

Table S148. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
5P LOSS MUTATED	2	18	9
5P LOSS WILD-TYPE	91	133	117

Figure S148. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.071

Table S149. Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
5P LOSS MUTATED	7	1	7	12	2
5P LOSS WILD-TYPE	47	55	107	72	54

Figure S149. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.046

Table S150. Gene #50: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
5P LOSS MUTATED	5	3	3	4	7	7
5P LOSS WILD-TYPE	35	60	89	80	39	33

Figure S150. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00987 (Fisher's exact test), Q value = 0.039

Table S151. Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
5P LOSS MUTATED	14	2	4	6
5P LOSS WILD-TYPE	93	79	98	44

Figure S151. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.054

Table S152. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
5P LOSS MUTATED	11	5	7	3	0
5P LOSS WILD-TYPE	59	77	93	31	54

Figure S152. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.044

Table S153. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
5Q LOSS MUTATED	3	22	12
5Q LOSS WILD-TYPE	90	129	114

Figure S153. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.053

Table S154. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
5Q LOSS MUTATED	9	9	19
5Q LOSS WILD-TYPE	84	152	97

Figure S154. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0031

Table S155. Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
5Q LOSS MUTATED	12	1	8	14	2
5Q LOSS WILD-TYPE	42	55	106	70	54

Figure S155. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.024

Table S156. Gene #51: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
5Q LOSS MUTATED	5	4	4	6	8	10
5Q LOSS WILD-TYPE	35	59	88	78	38	30

Figure S156. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0012

Table S157. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
5Q LOSS MUTATED	21	3	3	7
5Q LOSS WILD-TYPE	86	78	99	43

Figure S157. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0045

Table S158. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
5Q LOSS MUTATED	16	7	9	2	0
5Q LOSS WILD-TYPE	54	75	91	32	54

Figure S158. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.063

Table S159. Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
7P LOSS MUTATED	10	2	1	3
7P LOSS WILD-TYPE	97	79	101	47

Figure S159. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.1

Table S160. Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
7P LOSS MUTATED	7	5	2	2	0
7P LOSS WILD-TYPE	63	77	98	32	54

Figure S160. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.06

Table S161. Gene #55: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
7Q LOSS MUTATED	8	1	7	3	2
7Q LOSS WILD-TYPE	59	85	64	68	67

Figure S161. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.096

Table S162. Gene #55: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
7Q LOSS MUTATED	5	6	6	4	0
7Q LOSS WILD-TYPE	39	89	50	118	48

Figure S162. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00085

Table S163. Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
7Q LOSS MUTATED	15	3	0	3
7Q LOSS WILD-TYPE	92	78	102	47

Figure S163. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.031

Table S164. Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
7Q LOSS MUTATED	8	5	3	5	0
7Q LOSS WILD-TYPE	62	77	97	29	54

Figure S164. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S165. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
8P LOSS MUTATED	30	82	84
8P LOSS WILD-TYPE	63	69	42

Figure S165. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.095

Table S166. Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
8P LOSS MUTATED	37	44	48	30	33
8P LOSS WILD-TYPE	30	42	23	41	36

Figure S166. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S167. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
9P LOSS MUTATED	7	67	45
9P LOSS WILD-TYPE	86	84	81

Figure S167. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.1

Table S168. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
9P LOSS MUTATED	26	45	48
9P LOSS WILD-TYPE	67	116	68

Figure S168. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S169. Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
9P LOSS MUTATED	25	24	36	22	10
9P LOSS WILD-TYPE	42	62	35	49	59

Figure S169. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00604 (Fisher's exact test), Q value = 0.026

Table S170. Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
9P LOSS MUTATED	21	17	31	38	10
9P LOSS WILD-TYPE	33	39	83	46	46

Figure S170. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.039

Table S171. Gene #58: '9p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
9P LOSS MUTATED	15	15	31	18	21	19
9P LOSS WILD-TYPE	25	48	61	66	25	21

Figure S171. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00845 (Fisher's exact test), Q value = 0.035

Table S172. Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
9P LOSS MUTATED	16	28	22	47	6
9P LOSS WILD-TYPE	28	67	34	75	42

Figure S172. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00889 (Fisher's exact test), Q value = 0.036

Table S173. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
9P LOSS MUTATED	30	25	38	13	8
9P LOSS WILD-TYPE	40	57	62	21	46

Figure S173. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S174. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
9Q LOSS MUTATED	7	61	42
9Q LOSS WILD-TYPE	86	90	84

Figure S174. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.039

Table S175. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
9Q LOSS MUTATED	22	41	47
9Q LOSS WILD-TYPE	71	120	69

Figure S175. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.013

Table S176. Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
9Q LOSS MUTATED	24	25	30	21	9
9Q LOSS WILD-TYPE	43	61	41	50	60

Figure S176. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.01

Table S177. Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
9Q LOSS MUTATED	20	15	31	36	7
9Q LOSS WILD-TYPE	34	41	83	48	49

Figure S177. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.079

Table S178. Gene #59: '9q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
9Q LOSS MUTATED	15	15	27	16	17	18
9Q LOSS WILD-TYPE	25	48	65	68	29	22

Figure S178. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.035

Table S179. Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
9Q LOSS MUTATED	15	25	21	42	5
9Q LOSS WILD-TYPE	29	70	35	80	43

Figure S179. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0035

Table S180. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
9Q LOSS MUTATED	29	21	35	13	5
9Q LOSS WILD-TYPE	41	61	65	21	49

Figure S180. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S181. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
10P LOSS MUTATED	5	33	9
10P LOSS WILD-TYPE	88	118	117

Figure S181. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.016

Table S182. Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
10P LOSS MUTATED	15	13	5	11	2
10P LOSS WILD-TYPE	52	73	66	60	67

Figure S182. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.021

Table S183. Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
10P LOSS MUTATED	12	4	21	7	2
10P LOSS WILD-TYPE	42	52	93	77	54

Figure S183. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.04

Table S184. Gene #60: '10p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
10P LOSS MUTATED	4	15	9	4	9	6
10P LOSS WILD-TYPE	36	48	83	80	37	34

Figure S184. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.049

Table S185. Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
10P LOSS MUTATED	4	20	3	18	2
10P LOSS WILD-TYPE	40	75	53	104	46

Figure S185. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.052

Table S186. Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
10P LOSS MUTATED	7	19	14	3	2
10P LOSS WILD-TYPE	63	63	86	31	52

Figure S186. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S187. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
10Q LOSS MUTATED	10	56	12
10Q LOSS WILD-TYPE	83	95	114

Figure S187. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.11

Table S188. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
10Q LOSS MUTATED	28	31	19
10Q LOSS WILD-TYPE	65	130	97

Figure S188. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S189. Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
10Q LOSS MUTATED	30	21	6	15	4
10Q LOSS WILD-TYPE	37	65	65	56	65

Figure S189. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00041

Table S190. Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
10Q LOSS MUTATED	23	8	30	10	5
10Q LOSS WILD-TYPE	31	48	84	74	51

Figure S190. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.017

Table S191. Gene #61: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
10Q LOSS MUTATED	10	23	15	9	9	12
10Q LOSS WILD-TYPE	30	40	77	75	37	28

Figure S191. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S192. Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
10Q LOSS MUTATED	10	34	8	24	2
10Q LOSS WILD-TYPE	34	61	48	98	46

Figure S192. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S193. Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
10Q LOSS MUTATED	16	31	19	9	1
10Q LOSS WILD-TYPE	54	51	81	25	53

Figure S193. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.043

Table S194. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
11P LOSS MUTATED	7	32	24
11P LOSS WILD-TYPE	86	119	102

Figure S194. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.042

Table S195. Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
11P LOSS MUTATED	14	5	15	22	6
11P LOSS WILD-TYPE	40	51	99	62	50

Figure S195. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.051

Table S196. Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
11P LOSS MUTATED	27	12	9	9
11P LOSS WILD-TYPE	80	69	93	41

Figure S196. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.054

Table S197. Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
11P LOSS MUTATED	21	13	15	4	4
11P LOSS WILD-TYPE	49	69	85	30	50

Figure S197. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.1

Table S198. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
11Q LOSS MUTATED	10	35	27
11Q LOSS WILD-TYPE	83	116	99

Figure S198. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.044

Table S199. Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
11Q LOSS MUTATED	32	12	13	9
11Q LOSS WILD-TYPE	75	69	89	41

Figure S199. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.12

Table S200. Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
11Q LOSS MUTATED	21	19	15	5	6
11Q LOSS WILD-TYPE	49	63	85	29	48

Figure S200. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S201. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
12P LOSS MUTATED	4	40	22
12P LOSS WILD-TYPE	89	111	104

Figure S201. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.058

Table S202. Gene #64: '12p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
12P LOSS MUTATED	19	21	9	10	7
12P LOSS WILD-TYPE	48	65	62	61	62

Figure S202. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.076

Table S203. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
12Q LOSS MUTATED	3	20	13
12Q LOSS WILD-TYPE	90	131	113

Figure S203. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S204. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
13Q LOSS MUTATED	13	72	37
13Q LOSS WILD-TYPE	80	79	89

Figure S204. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.1

Table S205. Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
13Q LOSS MUTATED	31	43	48
13Q LOSS WILD-TYPE	62	118	68

Figure S205. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.013

Table S206. Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
13Q LOSS MUTATED	30	24	28	26	11
13Q LOSS WILD-TYPE	37	62	43	45	58

Figure S206. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.003

Table S207. Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
13Q LOSS MUTATED	24	11	38	37	9
13Q LOSS WILD-TYPE	30	45	76	47	47

Figure S207. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.017

Table S208. Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
13Q LOSS MUTATED	18	25	34	14	13	17
13Q LOSS WILD-TYPE	22	38	58	70	33	23

Figure S208. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00468 (Fisher's exact test), Q value = 0.022

Table S209. Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
13Q LOSS MUTATED	19	35	15	46	6
13Q LOSS WILD-TYPE	25	60	41	76	42

Figure S209. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S210. Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
13Q LOSS MUTATED	40	37	19	20
13Q LOSS WILD-TYPE	67	44	83	30

Figure S210. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0047

Table S211. Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
13Q LOSS MUTATED	23	30	42	15	6
13Q LOSS WILD-TYPE	47	52	58	19	48

Figure S211. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S212. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
14Q LOSS MUTATED	5	72	32
14Q LOSS WILD-TYPE	88	79	94

Figure S212. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00077

Table S213. Gene #67: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
14Q LOSS MUTATED	32	17	27	22	10
14Q LOSS WILD-TYPE	35	69	44	49	59

Figure S213. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S214. Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
14Q LOSS MUTATED	30	11	26	33	8
14Q LOSS WILD-TYPE	24	45	88	51	48

Figure S214. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0019

Table S215. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
14Q LOSS MUTATED	44	28	15	17
14Q LOSS WILD-TYPE	63	53	87	33

Figure S215. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.022

Table S216. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
14Q LOSS MUTATED	29	21	35	12	7
14Q LOSS WILD-TYPE	41	61	65	22	47

Figure S216. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0036

Table S217. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
15Q LOSS MUTATED	7	40	20
15Q LOSS WILD-TYPE	86	111	106

Figure S217. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S218. Gene #68: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
15Q LOSS MUTATED	22	9	20	9	6
15Q LOSS WILD-TYPE	45	77	51	62	63

Figure S218. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00085

Table S219. Gene #68: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
15Q LOSS MUTATED	20	5	12	22	7
15Q LOSS WILD-TYPE	34	51	102	62	49

Figure S219. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.086

Table S220. Gene #68: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
15Q LOSS MUTATED	6	11	10	13	13	13
15Q LOSS WILD-TYPE	34	52	82	71	33	27

Figure S220. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0099

Table S221. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
15Q LOSS MUTATED	27	11	10	16
15Q LOSS WILD-TYPE	80	70	92	34

Figure S221. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.063

Table S222. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
15Q LOSS MUTATED	20	12	23	5	4
15Q LOSS WILD-TYPE	50	70	77	29	50

Figure S222. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S223. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
16P LOSS MUTATED	6	60	42
16P LOSS WILD-TYPE	87	91	84

Figure S223. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S224. Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
16P LOSS MUTATED	26	31	51
16P LOSS WILD-TYPE	67	130	65

Figure S224. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S225. Gene #69: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
16P LOSS MUTATED	24	16	51	11	4
16P LOSS WILD-TYPE	43	70	20	60	65

Figure S225. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S226. Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
16P LOSS MUTATED	22	13	24	44	3
16P LOSS WILD-TYPE	32	43	90	40	53

Figure S226. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S227. Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
16P LOSS MUTATED	9	12	16	17	30	23
16P LOSS WILD-TYPE	31	51	76	67	16	17

Figure S227. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S228. Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
16P LOSS MUTATED	10	20	27	48	2
16P LOSS WILD-TYPE	34	75	29	74	46

Figure S228. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S229. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
16P LOSS MUTATED	39	20	13	31
16P LOSS WILD-TYPE	68	61	89	19

Figure S229. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S230. Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
16P LOSS MUTATED	32	18	41	7	5
16P LOSS WILD-TYPE	38	64	59	27	49

Figure S230. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S231. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
16Q LOSS MUTATED	6	75	64
16Q LOSS WILD-TYPE	87	76	62

Figure S231. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S232. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
16Q LOSS MUTATED	26	48	71
16Q LOSS WILD-TYPE	67	113	45

Figure S232. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S233. Gene #70: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
16Q LOSS MUTATED	33	26	60	17	7
16Q LOSS WILD-TYPE	34	60	11	54	62

Figure S233. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S234. Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
16Q LOSS MUTATED	23	16	46	53	5
16Q LOSS WILD-TYPE	31	40	68	31	51

Figure S234. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S235. Gene #70: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
16Q LOSS MUTATED	15	25	27	20	31	26
16Q LOSS WILD-TYPE	25	38	65	64	15	14

Figure S235. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S236. Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
16Q LOSS MUTATED	15	33	33	60	3
16Q LOSS WILD-TYPE	29	62	23	62	45

Figure S236. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S237. Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
16Q LOSS MUTATED	59	28	21	31
16Q LOSS WILD-TYPE	48	53	81	19

Figure S237. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S238. Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
16Q LOSS MUTATED	41	32	48	10	8
16Q LOSS WILD-TYPE	29	50	52	24	46

Figure S238. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S239. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
17P LOSS MUTATED	32	119	34
17P LOSS WILD-TYPE	61	32	92

Figure S239. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S240. Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
17P LOSS MUTATED	45	50	31	29	27
17P LOSS WILD-TYPE	22	36	40	42	42

Figure S240. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.066

Table S241. Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
17P LOSS MUTATED	32	23	68	36	23
17P LOSS WILD-TYPE	22	33	46	48	33

Figure S241. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.012

Table S242. Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	40	63	92	84	46	40
17P LOSS MUTATED	29	40	38	34	24	19
17P LOSS WILD-TYPE	11	23	54	50	22	21

Figure S242. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0031

Table S243. Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	44	95	56	122	48
17P LOSS MUTATED	34	54	23	52	21
17P LOSS WILD-TYPE	10	41	33	70	27

Figure S243. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0022

Table S244. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
17P LOSS MUTATED	30	51	46	27	22
17P LOSS WILD-TYPE	40	31	54	7	32

Figure S244. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.076

Table S245. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
18P LOSS MUTATED	11	39	24
18P LOSS WILD-TYPE	82	112	102

Figure S245. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.013

Table S246. Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
18P LOSS MUTATED	13	25	36
18P LOSS WILD-TYPE	80	136	80

Figure S246. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.017

Table S247. Gene #73: '18p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
18P LOSS MUTATED	10	5	18	29	12
18P LOSS WILD-TYPE	44	51	96	55	44

Figure S247. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.054

Table S248. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
18Q LOSS MUTATED	11	41	27
18Q LOSS WILD-TYPE	82	110	99

Figure S248. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.01

Table S249. Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
18Q LOSS MUTATED	13	28	38
18Q LOSS WILD-TYPE	80	133	78

Figure S249. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0041

Table S250. Gene #74: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
18Q LOSS MUTATED	8	5	21	32	13
18Q LOSS WILD-TYPE	46	51	93	52	43

Figure S250. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S251. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
19P LOSS MUTATED	3	37	12
19P LOSS WILD-TYPE	90	114	114

Figure S251. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.06

Table S252. Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	70	82	100	34	54
19P LOSS MUTATED	15	12	10	9	3
19P LOSS WILD-TYPE	55	70	90	25	51

Figure S252. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S253. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
19Q LOSS MUTATED	2	30	7
19Q LOSS WILD-TYPE	91	121	119

Figure S253. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.11

Table S254. Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
20Q LOSS MUTATED	8	3	1	0
20Q LOSS WILD-TYPE	99	78	101	50

Figure S254. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.054

Table S255. Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
21Q LOSS MUTATED	17	50	43
21Q LOSS WILD-TYPE	76	101	83

Figure S255. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0031

Table S256. Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
21Q LOSS MUTATED	34	15	22	17	19
21Q LOSS WILD-TYPE	33	71	49	54	50

Figure S256. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.043

Table S257. Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
21Q LOSS MUTATED	43	23	21	19
21Q LOSS WILD-TYPE	64	58	81	31

Figure S257. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.022

Table S258. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
22Q LOSS MUTATED	16	40	14
22Q LOSS WILD-TYPE	77	111	112

Figure S258. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.014

Table S259. Gene #80: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	67	86	71	71	69
22Q LOSS MUTATED	24	17	8	13	8
22Q LOSS WILD-TYPE	43	69	63	58	61

Figure S259. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.062

Table S260. Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
XP LOSS MUTATED	14	46	35
XP LOSS WILD-TYPE	79	115	81

Figure S260. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.071

Table S261. Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	54	56	114	84	56
XP LOSS MUTATED	14	11	40	13	16
XP LOSS WILD-TYPE	40	45	74	71	40

Figure S261. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.068

Table S262. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	107	81	102	50
XP LOSS MUTATED	27	16	37	8
XP LOSS WILD-TYPE	80	65	65	42

Figure S262. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.12

Table S263. Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	151	126
XQ LOSS MUTATED	11	37	26
XQ LOSS WILD-TYPE	82	114	100

Figure S263. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.11

Table S264. Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	161	116
XQ LOSS MUTATED	12	31	31
XQ LOSS WILD-TYPE	81	130	85

Figure S264. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22531240/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/22542932/LIHC-TP.transferedmergedcluster.txt
Number of patients = 370
Number of significantly arm-level cnvs = 82
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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