Correlation between copy number variation genes (focal events) and molecular subtypes

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QC01XW

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 12 molecular subtypes across 504 patients, 187 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 40 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 187 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	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	Chi-square 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
9q	159 (32%)	345	0.00628 (1.00)	0.000826 (0.244)	1.48e-42 (7.09e-40)	5.8e-18 (2.71e-15)	5.31e-07 (0.00021)	0.000429 (0.133)	6.51e-22 (3.09e-19)	7.16e-23 (3.42e-20)	1.15e-15 (5.31e-13)	3.6e-05 (0.0127)	1.47e-08 (5.97e-06)	3.44e-06 (0.00131)
14q	227 (45%)	277	4.78e-05 (0.0166)	4.72e-05 (0.0165)	1.14e-19 (5.37e-17)	7.43e-09 (3.03e-06)	3.64e-13 (1.62e-10)	1.79e-07 (7.15e-05)	5.27e-18 (2.48e-15)	1.69e-15 (7.81e-13)	1.24e-14 (5.67e-12)	0.0676 (1.00)	0.0003 (0.0955)	0.000568 (0.174)
9p	158 (31%)	346	0.00378 (0.923)	0.00044 (0.136)	6.08e-41 (2.91e-38)	3.82e-17 (1.78e-14)	2.54e-05 (0.00908)	0.0017 (0.453)	6.25e-20 (2.95e-17)	5.43e-21 (2.57e-18)	8.53e-13 (3.76e-10)	0.00011 (0.0363)	3.3e-08 (1.33e-05)	0.000175 (0.0566)
8q	124 (25%)	380	0.172 (1.00)	0.218 (1.00)	4.83e-15 (2.23e-12)	9.92e-05 (0.0329)	1.19e-05 (0.00441)	0.0244 (1.00)	1.03e-05 (0.00386)	8.99e-05 (0.0299)	5.15e-06 (0.00195)	0.0259 (1.00)	1.58e-05 (0.00575)	6.96e-05 (0.0236)
12q	123 (24%)	381	0.0129 (1.00)	0.0142 (1.00)	6.11e-14 (2.78e-11)	6.02e-05 (0.0206)	1.87e-13 (8.38e-11)	0.00162 (0.435)	3.61e-11 (1.55e-08)	3.61e-11 (1.55e-08)	1.21e-09 (5e-07)	0.05 (1.00)	2.52e-07 (1e-04)	0.000654 (0.198)
17p	70 (14%)	434	8.7e-06 (0.00327)	3.14e-05 (0.0111)	5.44e-15 (2.5e-12)	0.145 (1.00)	0.0018 (0.476)	0.00033 (0.104)	1.02e-06 (0.000396)	1.58e-08 (6.39e-06)	3.71e-08 (1.5e-05)	6.44e-11 (2.74e-08)	0.0127 (1.00)	0.0428 (1.00)
18p	116 (23%)	388	0.0129 (1.00)	0.0376 (1.00)	1.32e-13 (5.92e-11)	0.000198 (0.0636)	1.12e-05 (0.00417)	0.0471 (1.00)	1.82e-14 (8.32e-12)	4.32e-12 (1.88e-09)	1.84e-09 (7.6e-07)	9.79e-07 (0.000383)	3.35e-05 (0.0118)	0.0173 (1.00)
18q	118 (23%)	386	0.0136 (1.00)	0.033 (1.00)	1.19e-13 (5.36e-11)	0.000451 (0.139)	9.47e-06 (0.00354)	0.061 (1.00)	8.15e-14 (3.68e-11)	6.66e-12 (2.88e-09)	2.43e-09 (1e-06)	4.95e-07 (0.000196)	1.59e-05 (0.00578)	0.00538 (1.00)
20p	118 (23%)	386	0.0457 (1.00)	0.0675 (1.00)	6.46e-22 (3.07e-19)	6.56e-05 (0.0224)	6.31e-09 (2.58e-06)	0.002 (0.517)	9.78e-15 (4.49e-12)	8.68e-13 (3.82e-10)	1.7e-12 (7.48e-10)	3.4e-05 (0.012)	1.29e-07 (5.16e-05)	0.00112 (0.314)
20q	116 (23%)	388	0.024 (1.00)	0.033 (1.00)	5.26e-24 (2.51e-21)	5.62e-05 (0.0194)	1.75e-09 (7.23e-07)	0.00134 (0.367)	5.17e-16 (2.4e-13)	2.04e-13 (9.1e-11)	1.77e-12 (7.73e-10)	3.04e-05 (0.0108)	1.29e-07 (5.16e-05)	0.00112 (0.314)
6p	110 (22%)	394	0.00526 (1.00)	0.00159 (0.427)	5.28e-18 (2.48e-15)	0.00157 (0.423)	1.07e-06 (0.000417)	0.000946 (0.273)	1.78e-06 (0.000688)	3.47e-06 (0.00132)	9.15e-10 (3.81e-07)	2.38e-05 (0.00853)	7.8e-07 (0.000306)	0.00329 (0.809)
12p	121 (24%)	383	0.0129 (1.00)	0.0142 (1.00)	1.66e-13 (7.44e-11)	0.000101 (0.0336)	3.83e-12 (1.67e-09)	0.0031 (0.766)	5.61e-11 (2.4e-08)	1.54e-10 (6.52e-08)	5.93e-09 (2.43e-06)	0.0455 (1.00)	6.65e-07 (0.000262)	0.00128 (0.352)
13q	91 (18%)	413	0.0129 (1.00)	0.0213 (1.00)	4.88e-10 (2.04e-07)	0.000741 (0.221)	5.85e-05 (0.0201)	0.047 (1.00)	2.41e-05 (0.00863)	3.13e-06 (0.0012)	1.1e-05 (0.00408)	0.000303 (0.096)	0.0409 (1.00)	0.0431 (1.00)
17q	58 (12%)	446	8.36e-05 (0.028)	0.000175 (0.0566)	1.32e-10 (5.6e-08)	0.241 (1.00)	0.13 (1.00)	0.00614 (1.00)	8.28e-05 (0.0278)	9.69e-07 (0.00038)	1.28e-05 (0.00471)	1.9e-10 (8.04e-08)	0.018 (1.00)	0.0304 (1.00)
21q	105 (21%)	399	0.116 (1.00)	0.163 (1.00)	2.08e-11 (8.93e-09)	8.91e-05 (0.0298)	0.000125 (0.041)	0.00632 (1.00)	0.000154 (0.0501)	2.21e-05 (0.00798)	0.000114 (0.0374)	0.00108 (0.306)	0.0213 (1.00)	0.0596 (1.00)
22q	79 (16%)	425	0.00432 (1.00)	0.000485 (0.149)	5.67e-14 (2.58e-11)	0.0176 (1.00)	0.0306 (1.00)	0.158 (1.00)	9.26e-06 (0.00347)	1.52e-05 (0.00555)	2.35e-06 (0.000906)	0.0125 (1.00)	0.000659 (0.198)	0.141 (1.00)
3q	158 (31%)	346	0.236 (1.00)	0.251 (1.00)	5.98e-10 (2.49e-07)	0.0104 (1.00)	0.0348 (1.00)	0.0967 (1.00)	1.22e-05 (0.0045)	8.44e-06 (0.00318)	1.59e-05 (0.00578)	0.0294 (1.00)	0.000598 (0.182)	0.0965 (1.00)
6q	135 (27%)	369	0.0194 (1.00)	0.0107 (1.00)	1.01e-17 (4.69e-15)	0.0476 (1.00)	2.1e-05 (0.00762)	0.00917 (1.00)	0.00101 (0.288)	0.00306 (0.76)	4.41e-07 (0.000175)	0.000418 (0.131)	5.88e-05 (0.0202)	0.0294 (1.00)
7q	172 (34%)	332	0.416 (1.00)	0.577 (1.00)	2.11e-13 (9.4e-11)	0.00729 (1.00)	4.52e-06 (0.00172)	0.000615 (0.186)	0.000108 (0.0357)	0.000597 (0.182)	0.00209 (0.537)	0.0463 (1.00)	0.0358 (1.00)	0.163 (1.00)
8p	165 (33%)	339	0.144 (1.00)	0.224 (1.00)	8.91e-12 (3.84e-09)	0.00124 (0.344)	0.00183 (0.482)	0.0763 (1.00)	0.000424 (0.132)	0.000826 (0.244)	1.36e-05 (0.00498)	0.0406 (1.00)	0.00185 (0.484)	0.0078 (1.00)
19p	61 (12%)	443	0.433 (1.00)	0.486 (1.00)	3.73e-13 (1.65e-10)	0.000771 (0.229)	0.00594 (1.00)	0.00168 (0.449)	0.000682 (0.204)	0.00135 (0.37)	4.75e-05 (0.0165)	0.00305 (0.76)	0.00151 (0.41)	0.353 (1.00)
1p	80 (16%)	424	0.0145 (1.00)	0.00641 (1.00)	3.89e-14 (1.78e-11)	0.125 (1.00)	0.00878 (1.00)	0.00814 (1.00)	0.0515 (1.00)	0.00142 (0.385)	0.000929 (0.269)	1.08e-09 (4.48e-07)	0.00931 (1.00)	6.92e-05 (0.0235)
1q	87 (17%)	417	0.0837 (1.00)	0.126 (1.00)	9.8e-16 (4.55e-13)	0.0846 (1.00)	0.0349 (1.00)	0.00939 (1.00)	0.0194 (1.00)	0.00937 (1.00)	4.08e-05 (0.0143)	1.32e-06 (0.000513)	0.0184 (1.00)	0.0166 (1.00)
2p	89 (18%)	415	0.0326 (1.00)	0.0513 (1.00)	4.65e-10 (1.95e-07)	0.369 (1.00)	0.000178 (0.0573)	0.0549 (1.00)	0.473 (1.00)	0.378 (1.00)	0.06 (1.00)	0.000369 (0.116)	0.00531 (1.00)	0.231 (1.00)
3p	382 (76%)	122	0.00933 (1.00)	0.00108 (0.306)	8.43e-22 (3.99e-19)	0.0382 (1.00)	0.116 (1.00)	0.0593 (1.00)	5.96e-06 (0.00225)	1.16e-08 (4.73e-06)	0.302 (1.00)	0.0372 (1.00)	0.028 (1.00)	0.00434 (1.00)
7p	170 (34%)	334	0.416 (1.00)	0.577 (1.00)	7.13e-14 (3.23e-11)	0.00453 (1.00)	3.22e-06 (0.00124)	0.00189 (0.491)	0.000147 (0.0479)	0.000893 (0.262)	0.00249 (0.629)	0.0902 (1.00)	0.00914 (1.00)	0.244 (1.00)
2q	90 (18%)	414	0.106 (1.00)	0.167 (1.00)	4.86e-08 (1.95e-05)	0.413 (1.00)	0.000326 (0.103)	0.0792 (1.00)	0.65 (1.00)	0.604 (1.00)	0.0939 (1.00)	0.00133 (0.367)	0.0169 (1.00)	0.161 (1.00)
4p	84 (17%)	420	0.82 (1.00)	0.819 (1.00)	2.41e-10 (1.01e-07)	0.000658 (0.198)	0.0251 (1.00)	0.0773 (1.00)	0.0149 (1.00)	0.0908 (1.00)	0.0957 (1.00)	0.0493 (1.00)	0.0447 (1.00)	0.453 (1.00)
10p	82 (16%)	422	0.0649 (1.00)	0.1 (1.00)	2.02e-12 (8.82e-10)	0.0389 (1.00)	0.583 (1.00)	0.161 (1.00)	0.00208 (0.537)	0.0169 (1.00)	0.00288 (0.722)	0.000829 (0.244)	0.021 (1.00)	0.173 (1.00)
15q	61 (12%)	443	0.133 (1.00)	0.143 (1.00)	5.02e-12 (2.17e-09)	0.0386 (1.00)	0.0153 (1.00)	0.0855 (1.00)	0.00111 (0.312)	0.000472 (0.145)	0.00712 (1.00)	0.0122 (1.00)	0.053 (1.00)	0.37 (1.00)
16p	115 (23%)	389	0.149 (1.00)	0.216 (1.00)	7.59e-05 (0.0257)	0.299 (1.00)	0.00785 (1.00)	0.0377 (1.00)	0.00601 (1.00)	0.000225 (0.0719)	0.0129 (1.00)	0.193 (1.00)	0.113 (1.00)	0.253 (1.00)
16q	112 (22%)	392	0.282 (1.00)	0.12 (1.00)	2.99e-06 (0.00115)	0.0884 (1.00)	0.0471 (1.00)	0.0907 (1.00)	0.00371 (0.908)	0.000244 (0.0779)	0.00105 (0.299)	0.134 (1.00)	0.0341 (1.00)	0.0975 (1.00)
19q	60 (12%)	444	0.18 (1.00)	0.302 (1.00)	2.75e-13 (1.22e-10)	0.000916 (0.267)	0.00228 (0.579)	0.00254 (0.64)	0.00105 (0.299)	0.00301 (0.752)	4.89e-05 (0.0169)	0.000965 (0.277)	0.00177 (0.468)	0.471 (1.00)
xq	75 (15%)	429	0.0775 (1.00)	0.0868 (1.00)	7.68e-05 (0.0259)	0.0197 (1.00)	0.00121 (0.337)	2.25e-05 (0.00808)	0.015 (1.00)	0.00713 (1.00)	0.0178 (1.00)	0.00093 (0.269)	0.0155 (1.00)	0.0021 (0.537)
4q	78 (15%)	426	0.544 (1.00)	0.554 (1.00)	8.35e-13 (3.69e-10)	0.000915 (0.267)	0.00924 (1.00)	0.0439 (1.00)	0.00218 (0.555)	0.0106 (1.00)	0.0167 (1.00)	0.0515 (1.00)	0.0163 (1.00)	0.235 (1.00)
5p	192 (38%)	312	0.924 (1.00)	0.878 (1.00)	3.75e-05 (0.0132)	0.0957 (1.00)	0.0677 (1.00)	0.0967 (1.00)	0.036 (1.00)	0.00186 (0.486)	0.0765 (1.00)	0.921 (1.00)	0.172 (1.00)	0.94 (1.00)
10q	98 (19%)	406	0.141 (1.00)	0.201 (1.00)	4.45e-12 (1.93e-09)	0.0102 (1.00)	0.969 (1.00)	0.0801 (1.00)	0.00631 (1.00)	0.032 (1.00)	0.0082 (1.00)	0.007 (1.00)	0.021 (1.00)	0.0732 (1.00)
11p	48 (10%)	456	0.086 (1.00)	0.126 (1.00)	9.37e-11 (3.98e-08)	0.0848 (1.00)	0.0387 (1.00)	0.15 (1.00)	0.0464 (1.00)	0.0507 (1.00)	0.0785 (1.00)	0.00713 (1.00)	0.0419 (1.00)	0.0379 (1.00)
11q	51 (10%)	453	0.173 (1.00)	0.239 (1.00)	2.9e-10 (1.22e-07)	0.103 (1.00)	0.0532 (1.00)	0.305 (1.00)	0.0433 (1.00)	0.045 (1.00)	0.0699 (1.00)	0.0141 (1.00)	0.0419 (1.00)	0.074 (1.00)
5q	205 (41%)	299	0.395 (1.00)	0.291 (1.00)	0.00421 (1.00)	0.241 (1.00)	0.271 (1.00)	0.0864 (1.00)	0.264 (1.00)	0.0157 (1.00)	0.638 (1.00)	0.918 (1.00)	0.587 (1.00)	0.868 (1.00)

'1p' versus 'CN_CNMF'

P value = 3.89e-14 (Fisher's exact test), Q value = 1.8e-11

Table S1. Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
1P MUTATED	48	5	27
1P WILD-TYPE	123	207	94

Figure S1. Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.08e-09 (Fisher's exact test), Q value = 4.5e-07

Table S2. Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
1P MUTATED	30	23	27
1P WILD-TYPE	234	17	155

Figure S2. Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.92e-05 (Fisher's exact test), Q value = 0.024

Table S3. Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
1P MUTATED	3	18	15
1P WILD-TYPE	83	51	56

Figure S3. Get High-res Image Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 9.8e-16 (Fisher's exact test), Q value = 4.5e-13

Table S4. Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
1Q MUTATED	56	6	25
1Q WILD-TYPE	115	206	96

Figure S4. Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

'1q' versus 'MIRSEQ_CNMF'

P value = 4.08e-05 (Fisher's exact test), Q value = 0.014

Table S5. Gene #2: '1q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
1Q MUTATED	12	26	47
1Q WILD-TYPE	106	177	118

Figure S5. Get High-res Image Gene #2: '1q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00051

Table S6. Gene #2: '1q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
1Q MUTATED	34	20	31
1Q WILD-TYPE	230	20	151

Figure S6. Get High-res Image Gene #2: '1q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p' versus 'CN_CNMF'

P value = 4.65e-10 (Fisher's exact test), Q value = 1.9e-07

Table S7. Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
2P MUTATED	51	12	26
2P WILD-TYPE	120	200	95

Figure S7. Get High-res Image Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

'2p' versus 'RPPA_CNMF'

P value = 0.000178 (Chi-square test), Q value = 0.057

Table S8. Gene #3: '2p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
2P MUTATED	8	7	18	24	9	10
2P WILD-TYPE	92	81	66	51	34	47

Figure S8. Get High-res Image Gene #3: '2p' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000369 (Fisher's exact test), Q value = 0.12

Table S9. Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
2P MUTATED	47	17	25
2P WILD-TYPE	217	23	157

Figure S9. Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 4.86e-08 (Fisher's exact test), Q value = 2e-05

Table S10. Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
2Q MUTATED	49	15	26
2Q WILD-TYPE	122	197	95

Figure S10. Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'RPPA_CNMF'

P value = 0.000326 (Chi-square test), Q value = 0.1

Table S11. Gene #4: '2q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
2Q MUTATED	9	7	17	24	10	11
2Q WILD-TYPE	91	81	67	51	33	46

Figure S11. Get High-res Image Gene #4: '2q' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p' versus 'CN_CNMF'

P value = 8.43e-22 (Fisher's exact test), Q value = 4e-19

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
3P MUTATED	159	171	52
3P WILD-TYPE	12	41	69

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

'3p' versus 'MRNASEQ_CNMF'

P value = 5.96e-06 (Fisher's exact test), Q value = 0.0023

Table S13. Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
3P MUTATED	168	150	59
3P WILD-TYPE	37	39	45

Figure S13. Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-08 (Fisher's exact test), Q value = 4.7e-06

Table S14. Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
3P MUTATED	175	166	36
3P WILD-TYPE	40	40	41

Figure S14. Get High-res Image Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'CN_CNMF'

P value = 5.98e-10 (Fisher's exact test), Q value = 2.5e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
3Q MUTATED	86	43	29
3Q WILD-TYPE	85	169	92

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

'3q' versus 'MRNASEQ_CNMF'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0045

Table S16. Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
3Q MUTATED	42	80	36
3Q WILD-TYPE	163	109	68

Figure S16. Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0032

Table S17. Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
3Q MUTATED	46	89	23
3Q WILD-TYPE	169	117	54

Figure S17. Get High-res Image Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0058

Table S18. Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
3Q MUTATED	34	46	75
3Q WILD-TYPE	84	157	90

Figure S18. Get High-res Image Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000598 (Fisher's exact test), Q value = 0.18

Table S19. Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
3Q MUTATED	16	18	36
3Q WILD-TYPE	37	77	42

Figure S19. Get High-res Image Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p' versus 'CN_CNMF'

P value = 2.41e-10 (Fisher's exact test), Q value = 1e-07

Table S20. Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
4P MUTATED	51	11	22
4P WILD-TYPE	120	201	99

Figure S20. Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 0.000658 (Fisher's exact test), Q value = 0.2

Table S21. Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
4P MUTATED	31	13	10
4P WILD-TYPE	69	101	66

Figure S21. Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'CN_CNMF'

P value = 8.35e-13 (Fisher's exact test), Q value = 3.7e-10

Table S22. Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
4Q MUTATED	51	7	20
4Q WILD-TYPE	120	205	101

Figure S22. Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'CN_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.013

Table S23. Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
5P MUTATED	86	59	47
5P WILD-TYPE	85	153	74

Figure S23. Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 5.28e-18 (Fisher's exact test), Q value = 2.5e-15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
6P MUTATED	69	10	31
6P WILD-TYPE	102	202	90

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

'6p' versus 'RPPA_CNMF'

P value = 1.07e-06 (Chi-square test), Q value = 0.00042

Table S25. Gene #11: '6p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
6P MUTATED	18	8	17	23	6	27
6P WILD-TYPE	82	80	67	52	37	30

Figure S25. Get High-res Image Gene #11: '6p' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00069

Table S26. Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
6P MUTATED	25	63	19
6P WILD-TYPE	180	126	85

Figure S26. Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-06 (Fisher's exact test), Q value = 0.0013

Table S27. Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
6P MUTATED	26	66	15
6P WILD-TYPE	189	140	62

Figure S27. Get High-res Image Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_CNMF'

P value = 9.15e-10 (Fisher's exact test), Q value = 3.8e-07

Table S28. Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
6P MUTATED	19	23	64
6P WILD-TYPE	99	180	101

Figure S28. Get High-res Image Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.38e-05 (Fisher's exact test), Q value = 0.0085

Table S29. Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
6P MUTATED	41	19	46
6P WILD-TYPE	223	21	136

Figure S29. Get High-res Image Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.8e-07 (Fisher's exact test), Q value = 0.00031

Table S30. Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
6P MUTATED	10	6	30
6P WILD-TYPE	43	89	48

Figure S30. Get High-res Image Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'CN_CNMF'

P value = 1.01e-17 (Fisher's exact test), Q value = 4.7e-15

Table S31. Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
6Q MUTATED	84	20	31
6Q WILD-TYPE	87	192	90

Figure S31. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'6q' versus 'RPPA_CNMF'

P value = 2.1e-05 (Chi-square test), Q value = 0.0076

Table S32. Gene #12: '6q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
6Q MUTATED	29	8	24	24	8	27
6Q WILD-TYPE	71	80	60	51	35	30

Figure S32. Get High-res Image Gene #12: '6q' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q' versus 'MIRSEQ_CNMF'

P value = 4.41e-07 (Fisher's exact test), Q value = 0.00018

Table S33. Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
6Q MUTATED	23	38	70
6Q WILD-TYPE	95	165	95

Figure S33. Get High-res Image Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.13

Table S34. Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
6Q MUTATED	58	21	52
6Q WILD-TYPE	206	19	130

Figure S34. Get High-res Image Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.02

Table S35. Gene #12: '6q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
6Q MUTATED	13	14	35
6Q WILD-TYPE	40	81	43

Figure S35. Get High-res Image Gene #12: '6q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'CN_CNMF'

P value = 7.13e-14 (Fisher's exact test), Q value = 3.2e-11

Table S36. Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
7P MUTATED	88	33	49
7P WILD-TYPE	83	179	72

Figure S36. Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'RPPA_CNMF'

P value = 3.22e-06 (Chi-square test), Q value = 0.0012

Table S37. Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
7P MUTATED	21	19	34	34	11	32
7P WILD-TYPE	79	69	50	41	32	25

Figure S37. Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.048

Table S38. Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
7P MUTATED	52	85	31
7P WILD-TYPE	153	104	73

Figure S38. Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'CN_CNMF'

P value = 2.11e-13 (Fisher's exact test), Q value = 9.4e-11

Table S39. Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
7Q MUTATED	87	34	51
7Q WILD-TYPE	84	178	70

Figure S39. Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'RPPA_CNMF'

P value = 4.52e-06 (Chi-square test), Q value = 0.0017

Table S40. Gene #14: '7q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
7Q MUTATED	21	21	35	34	10	32
7Q WILD-TYPE	79	67	49	41	33	25

Figure S40. Get High-res Image Gene #14: '7q' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000615 (Fisher's exact test), Q value = 0.19

Table S41. Gene #14: '7q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
7Q MUTATED	45	61	47
7Q WILD-TYPE	141	91	62

Figure S41. Get High-res Image Gene #14: '7q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.036

Table S42. Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
7Q MUTATED	52	86	32
7Q WILD-TYPE	153	103	72

Figure S42. Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000597 (Fisher's exact test), Q value = 0.18

Table S43. Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
7Q MUTATED	56	90	24
7Q WILD-TYPE	159	116	53

Figure S43. Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 8.91e-12 (Fisher's exact test), Q value = 3.8e-09

Table S44. Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
8P MUTATED	90	39	36
8P WILD-TYPE	81	173	85

Figure S44. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.13

Table S45. Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
8P MUTATED	55	82	26
8P WILD-TYPE	150	107	78

Figure S45. Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000826 (Fisher's exact test), Q value = 0.24

Table S46. Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
8P MUTATED	56	87	20
8P WILD-TYPE	159	119	57

Figure S46. Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.005

Table S47. Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
8P MUTATED	35	49	78
8P WILD-TYPE	83	154	87

Figure S47. Get High-res Image Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q' versus 'CN_CNMF'

P value = 4.83e-15 (Fisher's exact test), Q value = 2.2e-12

Table S48. Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
8Q MUTATED	76	19	29
8Q WILD-TYPE	95	193	92

Figure S48. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 9.92e-05 (Fisher's exact test), Q value = 0.033

Table S49. Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
8Q MUTATED	41	19	14
8Q WILD-TYPE	59	95	62

Figure S49. Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q' versus 'RPPA_CNMF'

P value = 1.19e-05 (Chi-square test), Q value = 0.0044

Table S50. Gene #16: '8q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
8Q MUTATED	11	22	30	19	5	25
8Q WILD-TYPE	89	66	54	56	38	32

Figure S50. Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0039

Table S51. Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
8Q MUTATED	35	69	18
8Q WILD-TYPE	170	120	86

Figure S51. Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.99e-05 (Fisher's exact test), Q value = 0.03

Table S52. Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
8Q MUTATED	39	71	12
8Q WILD-TYPE	176	135	65

Figure S52. Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_CNMF'

P value = 5.15e-06 (Fisher's exact test), Q value = 0.002

Table S53. Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
8Q MUTATED	27	32	63
8Q WILD-TYPE	91	171	102

Figure S53. Get High-res Image Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0058

Table S54. Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
8Q MUTATED	13	10	32
8Q WILD-TYPE	40	85	46

Figure S54. Get High-res Image Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.96e-05 (Fisher's exact test), Q value = 0.024

Table S55. Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
8Q MUTATED	8	25	22
8Q WILD-TYPE	78	44	49

Figure S55. Get High-res Image Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'MRNA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.14

Table S56. Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
9P MUTATED	2	4	14
9P WILD-TYPE	12	28	10

Figure S56. Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 6.08e-41 (Fisher's exact test), Q value = 2.9e-38

Table S57. Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
9P MUTATED	113	9	36
9P WILD-TYPE	58	203	85

Figure S57. Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 3.82e-17 (Fisher's exact test), Q value = 1.8e-14

Table S58. Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
9P MUTATED	62	9	26
9P WILD-TYPE	38	105	50

Figure S58. Get High-res Image Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p' versus 'RPPA_CNMF'

P value = 2.54e-05 (Chi-square test), Q value = 0.0091

Table S59. Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
9P MUTATED	21	25	32	21	11	34
9P WILD-TYPE	79	63	52	54	32	23

Figure S59. Get High-res Image Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 6.25e-20 (Fisher's exact test), Q value = 3e-17

Table S60. Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
9P MUTATED	30	106	19
9P WILD-TYPE	175	83	85

Figure S60. Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-21 (Fisher's exact test), Q value = 2.6e-18

Table S61. Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
9P MUTATED	30	113	12
9P WILD-TYPE	185	93	65

Figure S61. Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_CNMF'

P value = 8.53e-13 (Fisher's exact test), Q value = 3.8e-10

Table S62. Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
9P MUTATED	32	34	87
9P WILD-TYPE	86	169	78

Figure S62. Get High-res Image Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.036

Table S63. Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
9P MUTATED	62	19	72
9P WILD-TYPE	202	21	110

Figure S63. Get High-res Image Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.3e-08 (Fisher's exact test), Q value = 1.3e-05

Table S64. Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
9P MUTATED	21	12	41
9P WILD-TYPE	32	83	37

Figure S64. Get High-res Image Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.057

Table S65. Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
9P MUTATED	15	33	26
9P WILD-TYPE	71	36	45

Figure S65. Get High-res Image Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000826 (Fisher's exact test), Q value = 0.24

Table S66. Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
9Q MUTATED	3	4	14
9Q WILD-TYPE	11	28	10

Figure S66. Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 1.48e-42 (Fisher's exact test), Q value = 7.1e-40

Table S67. Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
9Q MUTATED	114	8	37
9Q WILD-TYPE	57	204	84

Figure S67. Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 5.8e-18 (Fisher's exact test), Q value = 2.7e-15

Table S68. Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
9Q MUTATED	62	8	27
9Q WILD-TYPE	38	106	49

Figure S68. Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q' versus 'RPPA_CNMF'

P value = 5.31e-07 (Chi-square test), Q value = 0.00021

Table S69. Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
9Q MUTATED	18	26	35	21	10	35
9Q WILD-TYPE	82	62	49	54	33	22

Figure S69. Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.13

Table S70. Gene #18: '9q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
9Q MUTATED	42	56	47
9Q WILD-TYPE	144	96	62

Figure S70. Get High-res Image Gene #18: '9q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q' versus 'MRNASEQ_CNMF'

P value = 6.51e-22 (Fisher's exact test), Q value = 3.1e-19

Table S71. Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
9Q MUTATED	28	109	20
9Q WILD-TYPE	177	80	84

Figure S71. Get High-res Image Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-23 (Fisher's exact test), Q value = 3.4e-20

Table S72. Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
9Q MUTATED	28	116	13
9Q WILD-TYPE	187	90	64

Figure S72. Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CNMF'

P value = 1.15e-15 (Fisher's exact test), Q value = 5.3e-13

Table S73. Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
9Q MUTATED	31	31	91
9Q WILD-TYPE	87	172	74

Figure S73. Get High-res Image Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.013

Table S74. Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
9Q MUTATED	61	20	72
9Q WILD-TYPE	203	20	110

Figure S74. Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.47e-08 (Fisher's exact test), Q value = 6e-06

Table S75. Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
9Q MUTATED	21	12	42
9Q WILD-TYPE	32	83	36

Figure S75. Get High-res Image Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.44e-06 (Fisher's exact test), Q value = 0.0013

Table S76. Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
9Q MUTATED	13	36	26
9Q WILD-TYPE	73	33	45

Figure S76. Get High-res Image Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 8.8e-10

Table S77. Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
10P MUTATED	47	7	28
10P WILD-TYPE	124	205	93

Figure S77. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000829 (Fisher's exact test), Q value = 0.24

Table S78. Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
10P MUTATED	33	15	32
10P WILD-TYPE	231	25	150

Figure S78. Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 4.45e-12 (Fisher's exact test), Q value = 1.9e-09

Table S79. Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
10Q MUTATED	56	12	30
10Q WILD-TYPE	115	200	91

Figure S79. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'CN_CNMF'

P value = 9.37e-11 (Fisher's exact test), Q value = 4e-08

Table S80. Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
11P MUTATED	30	1	17
11P WILD-TYPE	141	211	104

Figure S80. Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'CN_CNMF'

P value = 2.9e-10 (Fisher's exact test), Q value = 1.2e-07

Table S81. Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
11Q MUTATED	32	2	17
11Q WILD-TYPE	139	210	104

Figure S81. Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 1.66e-13 (Fisher's exact test), Q value = 7.4e-11

Table S82. Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
12P MUTATED	70	18	33
12P WILD-TYPE	101	194	88

Figure S82. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.034

Table S83. Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
12P MUTATED	38	15	22
12P WILD-TYPE	62	99	54

Figure S83. Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'RPPA_CNMF'

P value = 3.83e-12 (Chi-square test), Q value = 1.7e-09

Table S84. Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
12P MUTATED	4	17	31	15	7	31
12P WILD-TYPE	96	71	53	60	36	26

Figure S84. Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 5.61e-11 (Fisher's exact test), Q value = 2.4e-08

Table S85. Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
12P MUTATED	24	77	19
12P WILD-TYPE	181	112	85

Figure S85. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-10 (Fisher's exact test), Q value = 6.5e-08

Table S86. Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
12P MUTATED	26	81	13
12P WILD-TYPE	189	125	64

Figure S86. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 5.93e-09 (Fisher's exact test), Q value = 2.4e-06

Table S87. Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
12P MUTATED	23	28	68
12P WILD-TYPE	95	175	97

Figure S87. Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.65e-07 (Fisher's exact test), Q value = 0.00026

Table S88. Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
12P MUTATED	10	8	33
12P WILD-TYPE	43	87	45

Figure S88. Get High-res Image Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'CN_CNMF'

P value = 6.11e-14 (Fisher's exact test), Q value = 2.8e-11

Table S89. Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
12Q MUTATED	71	18	34
12Q WILD-TYPE	100	194	87

Figure S89. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 6.02e-05 (Fisher's exact test), Q value = 0.021

Table S90. Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
12Q MUTATED	39	15	22
12Q WILD-TYPE	61	99	54

Figure S90. Get High-res Image Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q' versus 'RPPA_CNMF'

P value = 1.87e-13 (Chi-square test), Q value = 8.4e-11

Table S91. Gene #24: '12q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
12Q MUTATED	4	17	31	15	7	33
12Q WILD-TYPE	96	71	53	60	36	24

Figure S91. Get High-res Image Gene #24: '12q' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 3.61e-11 (Fisher's exact test), Q value = 1.5e-08

Table S92. Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
12Q MUTATED	24	78	20
12Q WILD-TYPE	181	111	84

Figure S92. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-11 (Fisher's exact test), Q value = 1.5e-08

Table S93. Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
12Q MUTATED	26	83	13
12Q WILD-TYPE	189	123	64

Figure S93. Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_CNMF'

P value = 1.21e-09 (Fisher's exact test), Q value = 5e-07

Table S94. Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
12Q MUTATED	23	28	70
12Q WILD-TYPE	95	175	95

Figure S94. Get High-res Image Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.52e-07 (Fisher's exact test), Q value = 1e-04

Table S95. Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
12Q MUTATED	10	8	34
12Q WILD-TYPE	43	87	44

Figure S95. Get High-res Image Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000654 (Fisher's exact test), Q value = 0.2

Table S96. Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
12Q MUTATED	10	26	16
12Q WILD-TYPE	76	43	55

Figure S96. Get High-res Image Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 4.88e-10 (Fisher's exact test), Q value = 2e-07

Table S97. Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
13Q MUTATED	48	12	31
13Q WILD-TYPE	123	200	90

Figure S97. Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000741 (Fisher's exact test), Q value = 0.22

Table S98. Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
13Q MUTATED	30	12	20
13Q WILD-TYPE	70	102	56

Figure S98. Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'RPPA_CNMF'

P value = 5.85e-05 (Chi-square test), Q value = 0.02

Table S99. Gene #25: '13q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
13Q MUTATED	6	16	19	15	4	21
13Q WILD-TYPE	94	72	65	60	39	36

Figure S99. Get High-res Image Gene #25: '13q' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.0086

Table S100. Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
13Q MUTATED	19	50	22
13Q WILD-TYPE	186	139	82

Figure S100. Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.0012

Table S101. Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
13Q MUTATED	19	56	16
13Q WILD-TYPE	196	150	61

Figure S101. Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0041

Table S102. Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
13Q MUTATED	22	19	47
13Q WILD-TYPE	96	184	118

Figure S102. Get High-res Image Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.096

Table S103. Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
13Q MUTATED	35	16	37
13Q WILD-TYPE	229	24	145

Figure S103. Get High-res Image Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MRNA_CNMF'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.017

Table S104. Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
14Q MUTATED	10	20	3
14Q WILD-TYPE	23	4	10

Figure S104. Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q' versus 'MRNA_CHIERARCHICAL'

P value = 4.72e-05 (Fisher's exact test), Q value = 0.016

Table S105. Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
14Q MUTATED	4	9	20
14Q WILD-TYPE	10	23	4

Figure S105. Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 1.14e-19 (Fisher's exact test), Q value = 5.4e-17

Table S106. Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
14Q MUTATED	123	53	51
14Q WILD-TYPE	48	159	70

Figure S106. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 7.43e-09 (Fisher's exact test), Q value = 3e-06

Table S107. Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
14Q MUTATED	62	26	40
14Q WILD-TYPE	38	88	36

Figure S107. Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'RPPA_CNMF'

P value = 3.64e-13 (Chi-square test), Q value = 1.6e-10

Table S108. Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
14Q MUTATED	28	30	63	30	13	41
14Q WILD-TYPE	72	58	21	45	30	16

Figure S108. Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q' versus 'RPPA_CHIERARCHICAL'

P value = 1.79e-07 (Fisher's exact test), Q value = 7.1e-05

Table S109. Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
14Q MUTATED	57	90	58
14Q WILD-TYPE	129	62	51

Figure S109. Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q' versus 'MRNASEQ_CNMF'

P value = 5.27e-18 (Fisher's exact test), Q value = 2.5e-15

Table S110. Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
14Q MUTATED	67	131	24
14Q WILD-TYPE	138	58	80

Figure S110. Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.69e-15 (Fisher's exact test), Q value = 7.8e-13

Table S111. Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
14Q MUTATED	68	136	18
14Q WILD-TYPE	147	70	59

Figure S111. Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 1.24e-14 (Fisher's exact test), Q value = 5.7e-12

Table S112. Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
14Q MUTATED	39	65	116
14Q WILD-TYPE	79	138	49

Figure S112. Get High-res Image Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.096

Table S113. Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
14Q MUTATED	23	32	50
14Q WILD-TYPE	30	63	28

Figure S113. Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000568 (Fisher's exact test), Q value = 0.17

Table S114. Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	86	69	71
14Q MUTATED	30	45	30
14Q WILD-TYPE	56	24	41

Figure S114. Get High-res Image Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 5.02e-12 (Fisher's exact test), Q value = 2.2e-09

Table S115. Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
15Q MUTATED	40	3	18
15Q WILD-TYPE	131	209	103

Figure S115. Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000472 (Fisher's exact test), Q value = 0.15

Table S116. Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
15Q MUTATED	15	39	6
15Q WILD-TYPE	200	167	71

Figure S116. Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.026

Table S117. Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
16P MUTATED	54	29	32
16P WILD-TYPE	117	183	89

Figure S117. Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.072

Table S118. Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
16P MUTATED	31	60	24
16P WILD-TYPE	184	146	53

Figure S118. Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.0012

Table S119. Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
16Q MUTATED	55	25	32
16Q WILD-TYPE	116	187	89

Figure S119. Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000244 (Fisher's exact test), Q value = 0.078

Table S120. Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
16Q MUTATED	30	61	21
16Q WILD-TYPE	185	145	56

Figure S120. Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MRNA_CNMF'

P value = 8.7e-06 (Fisher's exact test), Q value = 0.0033

Table S121. Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
17P MUTATED	1	5	9
17P WILD-TYPE	32	19	4

Figure S121. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'MRNA_CHIERARCHICAL'

P value = 3.14e-05 (Fisher's exact test), Q value = 0.011

Table S122. Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
17P MUTATED	9	1	5
17P WILD-TYPE	5	31	19

Figure S122. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 5.44e-15 (Fisher's exact test), Q value = 2.5e-12

Table S123. Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
17P MUTATED	41	2	27
17P WILD-TYPE	130	210	94

Figure S123. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.1

Table S124. Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
17P MUTATED	15	17	27
17P WILD-TYPE	171	135	82

Figure S124. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 4e-04

Table S125. Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
17P MUTATED	10	37	23
17P WILD-TYPE	195	152	81

Figure S125. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-08 (Fisher's exact test), Q value = 6.4e-06

Table S126. Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
17P MUTATED	10	37	23
17P WILD-TYPE	205	169	54

Figure S126. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 3.71e-08 (Fisher's exact test), Q value = 1.5e-05

Table S127. Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
17P MUTATED	16	10	43
17P WILD-TYPE	102	193	122

Figure S127. Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.44e-11 (Fisher's exact test), Q value = 2.7e-08

Table S128. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
17P MUTATED	21	22	26
17P WILD-TYPE	243	18	156

Figure S128. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MRNA_CNMF'

P value = 8.36e-05 (Fisher's exact test), Q value = 0.028

Table S129. Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
17Q MUTATED	1	5	8
17Q WILD-TYPE	32	19	5

Figure S129. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.057

Table S130. Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
17Q MUTATED	8	1	5
17Q WILD-TYPE	6	31	19

Figure S130. Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 1.32e-10 (Fisher's exact test), Q value = 5.6e-08

Table S131. Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
17Q MUTATED	31	3	24
17Q WILD-TYPE	140	209	97

Figure S131. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 8.28e-05 (Fisher's exact test), Q value = 0.028

Table S132. Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
17Q MUTATED	10	27	21
17Q WILD-TYPE	195	162	83

Figure S132. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.69e-07 (Fisher's exact test), Q value = 0.00038

Table S133. Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
17Q MUTATED	10	27	21
17Q WILD-TYPE	205	179	56

Figure S133. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0047

Table S134. Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
17Q MUTATED	15	9	33
17Q WILD-TYPE	103	194	132

Figure S134. Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.9e-10 (Fisher's exact test), Q value = 8e-08

Table S135. Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
17Q MUTATED	17	20	20
17Q WILD-TYPE	247	20	162

Figure S135. Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 1.32e-13 (Fisher's exact test), Q value = 5.9e-11

Table S136. Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
18P MUTATED	67	16	33
18P WILD-TYPE	104	196	88

Figure S136. Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.064

Table S137. Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
18P MUTATED	32	13	24
18P WILD-TYPE	68	101	52

Figure S137. Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'RPPA_CNMF'

P value = 1.12e-05 (Chi-square test), Q value = 0.0042

Table S138. Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
18P MUTATED	12	17	27	18	5	26
18P WILD-TYPE	88	71	57	57	38	31

Figure S138. Get High-res Image Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p' versus 'MRNASEQ_CNMF'

P value = 1.82e-14 (Fisher's exact test), Q value = 8.3e-12

Table S139. Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
18P MUTATED	18	79	18
18P WILD-TYPE	187	110	86

Figure S139. Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.32e-12 (Fisher's exact test), Q value = 1.9e-09

Table S140. Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
18P MUTATED	21	80	14
18P WILD-TYPE	194	126	63

Figure S140. Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_CNMF'

P value = 1.84e-09 (Fisher's exact test), Q value = 7.6e-07

Table S141. Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
18P MUTATED	32	21	62
18P WILD-TYPE	86	182	103

Figure S141. Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.79e-07 (Fisher's exact test), Q value = 0.00038

Table S142. Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
18P MUTATED	41	20	54
18P WILD-TYPE	223	20	128

Figure S142. Get High-res Image Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.012

Table S143. Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
18P MUTATED	13	10	31
18P WILD-TYPE	40	85	47

Figure S143. Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'CN_CNMF'

P value = 1.19e-13 (Fisher's exact test), Q value = 5.4e-11

Table S144. Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
18Q MUTATED	69	17	32
18Q WILD-TYPE	102	195	89

Figure S144. Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 0.000451 (Fisher's exact test), Q value = 0.14

Table S145. Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
18Q MUTATED	32	14	24
18Q WILD-TYPE	68	100	52

Figure S145. Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'RPPA_CNMF'

P value = 9.47e-06 (Chi-square test), Q value = 0.0035

Table S146. Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
18Q MUTATED	12	16	27	19	7	27
18Q WILD-TYPE	88	72	57	56	36	30

Figure S146. Get High-res Image Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 8.15e-14 (Fisher's exact test), Q value = 3.7e-11

Table S147. Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
18Q MUTATED	19	79	19
18Q WILD-TYPE	186	110	85

Figure S147. Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-12 (Fisher's exact test), Q value = 2.9e-09

Table S148. Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
18Q MUTATED	21	80	16
18Q WILD-TYPE	194	126	61

Figure S148. Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_CNMF'

P value = 2.43e-09 (Fisher's exact test), Q value = 1e-06

Table S149. Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
18Q MUTATED	32	22	63
18Q WILD-TYPE	86	181	102

Figure S149. Get High-res Image Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.95e-07 (Fisher's exact test), Q value = 2e-04

Table S150. Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
18Q MUTATED	42	21	54
18Q WILD-TYPE	222	19	128

Figure S150. Get High-res Image Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0058

Table S151. Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
18Q MUTATED	12	10	32
18Q WILD-TYPE	41	85	46

Figure S151. Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'CN_CNMF'

P value = 3.73e-13 (Fisher's exact test), Q value = 1.7e-10

Table S152. Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
19P MUTATED	40	2	19
19P WILD-TYPE	131	210	102

Figure S152. Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 0.000771 (Fisher's exact test), Q value = 0.23

Table S153. Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
19P MUTATED	24	7	9
19P WILD-TYPE	76	107	67

Figure S153. Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 0.000682 (Fisher's exact test), Q value = 0.2

Table S154. Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
19P MUTATED	12	33	16
19P WILD-TYPE	193	156	88

Figure S154. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MIRSEQ_CNMF'

P value = 4.75e-05 (Fisher's exact test), Q value = 0.017

Table S155. Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
19P MUTATED	15	11	34
19P WILD-TYPE	103	192	131

Figure S155. Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'CN_CNMF'

P value = 2.75e-13 (Fisher's exact test), Q value = 1.2e-10

Table S156. Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
19Q MUTATED	41	2	17
19Q WILD-TYPE	130	210	104

Figure S156. Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'MIRSEQ_CNMF'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.017

Table S157. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
19Q MUTATED	13	11	34
19Q WILD-TYPE	105	192	131

Figure S157. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'CN_CNMF'

P value = 6.46e-22 (Fisher's exact test), Q value = 3.1e-19

Table S158. Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
20P MUTATED	73	8	37
20P WILD-TYPE	98	204	84

Figure S158. Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 6.56e-05 (Fisher's exact test), Q value = 0.022

Table S159. Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
20P MUTATED	35	12	19
20P WILD-TYPE	65	102	57

Figure S159. Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'RPPA_CNMF'

P value = 6.31e-09 (Chi-square test), Q value = 2.6e-06

Table S160. Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
20P MUTATED	7	22	20	18	7	31
20P WILD-TYPE	93	66	64	57	36	26

Figure S160. Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 9.78e-15 (Fisher's exact test), Q value = 4.5e-12

Table S161. Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
20P MUTATED	19	81	18
20P WILD-TYPE	186	108	86

Figure S161. Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.68e-13 (Fisher's exact test), Q value = 3.8e-10

Table S162. Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
20P MUTATED	22	83	13
20P WILD-TYPE	193	123	64

Figure S162. Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CNMF'

P value = 1.7e-12 (Fisher's exact test), Q value = 7.5e-10

Table S163. Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
20P MUTATED	29	19	69
20P WILD-TYPE	89	184	96

Figure S163. Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.012

Table S164. Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
20P MUTATED	43	16	58
20P WILD-TYPE	221	24	124

Figure S164. Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 5.2e-05

Table S165. Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
20P MUTATED	10	6	32
20P WILD-TYPE	43	89	46

Figure S165. Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'CN_CNMF'

P value = 5.26e-24 (Fisher's exact test), Q value = 2.5e-21

Table S166. Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
20Q MUTATED	74	6	36
20Q WILD-TYPE	97	206	85

Figure S166. Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.019

Table S167. Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
20Q MUTATED	34	11	18
20Q WILD-TYPE	66	103	58

Figure S167. Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'RPPA_CNMF'

P value = 1.75e-09 (Chi-square test), Q value = 7.2e-07

Table S168. Gene #37: '20q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
20Q MUTATED	7	21	21	18	5	31
20Q WILD-TYPE	93	67	63	57	38	26

Figure S168. Get High-res Image Gene #37: '20q' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 5.17e-16 (Fisher's exact test), Q value = 2.4e-13

Table S169. Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
20Q MUTATED	18	82	16
20Q WILD-TYPE	187	107	88

Figure S169. Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.04e-13 (Fisher's exact test), Q value = 9.1e-11

Table S170. Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
20Q MUTATED	21	83	12
20Q WILD-TYPE	194	123	65

Figure S170. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 1.77e-12 (Fisher's exact test), Q value = 7.7e-10

Table S171. Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
20Q MUTATED	27	19	69
20Q WILD-TYPE	91	184	96

Figure S171. Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.011

Table S172. Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	264	40	182
20Q MUTATED	42	16	57
20Q WILD-TYPE	222	24	125

Figure S172. Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 5.2e-05

Table S173. Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
20Q MUTATED	10	6	32
20Q WILD-TYPE	43	89	46

Figure S173. Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'CN_CNMF'

P value = 2.08e-11 (Fisher's exact test), Q value = 8.9e-09

Table S174. Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
21Q MUTATED	59	15	31
21Q WILD-TYPE	112	197	90

Figure S174. Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 8.91e-05 (Fisher's exact test), Q value = 0.03

Table S175. Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	114	76
21Q MUTATED	36	13	16
21Q WILD-TYPE	64	101	60

Figure S175. Get High-res Image Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q' versus 'RPPA_CNMF'

P value = 0.000125 (Chi-square test), Q value = 0.041

Table S176. Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
21Q MUTATED	10	10	21	19	8	22
21Q WILD-TYPE	90	78	63	56	35	35

Figure S176. Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q' versus 'MRNASEQ_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.05

Table S177. Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
21Q MUTATED	24	52	26
21Q WILD-TYPE	181	137	78

Figure S177. Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.21e-05 (Fisher's exact test), Q value = 0.008

Table S178. Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
21Q MUTATED	24	58	20
21Q WILD-TYPE	191	148	57

Figure S178. Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.037

Table S179. Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
21Q MUTATED	23	28	53
21Q WILD-TYPE	95	175	112

Figure S179. Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000485 (Fisher's exact test), Q value = 0.15

Table S180. Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
22Q MUTATED	4	0	8
22Q WILD-TYPE	10	32	16

Figure S180. Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 5.67e-14 (Fisher's exact test), Q value = 2.6e-11

Table S181. Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
22Q MUTATED	48	5	26
22Q WILD-TYPE	123	207	95

Figure S181. Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 9.26e-06 (Fisher's exact test), Q value = 0.0035

Table S182. Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	205	189	104
22Q MUTATED	16	48	15
22Q WILD-TYPE	189	141	89

Figure S182. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0056

Table S183. Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	206	77
22Q MUTATED	16	48	15
22Q WILD-TYPE	199	158	62

Figure S183. Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CNMF'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.00091

Table S184. Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	203	165
22Q MUTATED	15	17	46
22Q WILD-TYPE	103	186	119

Figure S184. Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000659 (Fisher's exact test), Q value = 0.2

Table S185. Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	95	78
22Q MUTATED	9	4	18
22Q WILD-TYPE	44	91	60

Figure S185. Get High-res Image Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq' versus 'CN_CNMF'

P value = 7.68e-05 (Fisher's exact test), Q value = 0.026

Table S186. Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	212	121
XQ MUTATED	41	17	17
XQ WILD-TYPE	130	195	104

Figure S186. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'RPPA_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0081

Table S187. Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
XQ MUTATED	14	19	30
XQ WILD-TYPE	172	133	79

Figure S187. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = KIRC-TP.transferedmergedcluster.txt
Number of patients = 504
Number of significantly focal cnvs = 40
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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