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

Brain Lower Grade Glioma (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/C1V40SQ4

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 365 patients, 96 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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, 96 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	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test
1p	142 (39%)	223	0.00608 (1.00)	0.00067 (0.25)	2.66e-47 (1.24e-44)	1.49e-64 (6.98e-62)	0.00257 (0.886)	0.189 (1.00)	2.91e-33 (1.35e-30)	2.57e-37 (1.19e-34)	7.46e-08 (3.26e-05)	9.26e-05 (0.0373)	8.35e-09 (3.7e-06)	3.42e-07 (0.000147)
10p	93 (25%)	272	0.446 (1.00)	0.042 (1.00)	2.33e-18 (1.06e-15)	2.69e-26 (1.23e-23)	2.03e-05 (0.00837)	0.00248 (0.858)	2.51e-16 (1.13e-13)	8.14e-11 (3.65e-08)	0.000657 (0.246)	0.0102 (1.00)	1.31e-07 (5.66e-05)	2.56e-07 (0.000111)
10q	74 (20%)	291	0.0838 (1.00)	0.164 (1.00)	6.69e-24 (3.05e-21)	3.17e-30 (1.46e-27)	2e-06 (0.000849)	0.000399 (0.153)	4.77e-23 (2.17e-20)	1.13e-07 (4.9e-05)	0.0222 (1.00)	0.1 (1.00)	2.36e-11 (1.06e-08)	1.67e-05 (0.00691)
19q	166 (45%)	199	0.132 (1.00)	0.159 (1.00)	6.79e-42 (3.16e-39)	1.16e-50 (5.4e-48)	0.0714 (1.00)	0.415 (1.00)	1.42e-25 (6.48e-23)	3.25e-29 (1.5e-26)	0.000207 (0.0822)	0.000572 (0.215)	2.58e-07 (0.000111)	4.22e-05 (0.0173)
7p	91 (25%)	274	0.745 (1.00)	0.648 (1.00)	4.4e-28 (2.02e-25)	2.31e-15 (1.04e-12)	0.00039 (0.15)	0.0101 (1.00)	2.8e-12 (1.26e-09)	7.45e-06 (0.00311)	0.00136 (0.49)	0.0157 (1.00)	1.29e-05 (0.00535)	6.9e-07 (0.000296)
7q	116 (32%)	249	0.764 (1.00)	0.495 (1.00)	2.04e-28 (9.41e-26)	5.95e-14 (2.69e-11)	0.00512 (1.00)	0.0288 (1.00)	2.31e-08 (1.02e-05)	4.08e-06 (0.00171)	0.00595 (1.00)	0.0508 (1.00)	0.000523 (0.197)	4.27e-05 (0.0175)
20q	35 (10%)	330			7.58e-08 (3.3e-05)	1.03e-10 (4.61e-08)	0.000898 (0.33)	0.11 (1.00)	7.85e-09 (3.48e-06)	5.17e-05 (0.021)	0.0117 (1.00)	0.0302 (1.00)	4.62e-05 (0.0189)	0.000242 (0.0953)
4q	73 (20%)	292	1 (1.00)	0.196 (1.00)	0.00399 (1.00)	3.84e-06 (0.00162)	0.196 (1.00)	0.0934 (1.00)	2.56e-06 (0.00108)	4.08e-06 (0.00171)	0.00865 (1.00)	0.000777 (0.287)	0.000436 (0.166)	0.0695 (1.00)
5q	31 (8%)	334	0.446 (1.00)	0.0182 (1.00)	0.000123 (0.0493)	0.000257 (0.1)	0.0109 (1.00)	0.38 (1.00)	2.7e-10 (1.2e-07)	0.000326 (0.126)	0.00878 (1.00)	0.00238 (0.828)	0.00289 (0.993)	0.0418 (1.00)
4p	62 (17%)	303	0.864 (1.00)	0.648 (1.00)	0.00198 (0.7)	9.89e-07 (0.000422)	0.502 (1.00)	0.0742 (1.00)	7.15e-07 (0.000306)	1.32e-05 (0.00548)	0.0658 (1.00)	0.00412 (1.00)	0.00102 (0.371)	0.333 (1.00)
5p	34 (9%)	331	0.873 (1.00)	0.00344 (1.00)	2.02e-06 (0.000858)	5.21e-05 (0.0211)	0.424 (1.00)	1 (1.00)	4.64e-05 (0.0189)	0.00224 (0.788)	0.0505 (1.00)	0.0125 (1.00)	0.016 (1.00)	0.448 (1.00)
8q	45 (12%)	320	0.446 (1.00)	0.0182 (1.00)	1.51e-05 (0.00627)	0.00181 (0.641)	0.0111 (1.00)	0.59 (1.00)	0.00757 (1.00)	0.000286 (0.111)	0.0545 (1.00)	0.0288 (1.00)	0.0277 (1.00)	0.00039 (0.15)
14q	59 (16%)	306	0.467 (1.00)	0.473 (1.00)	0.000232 (0.0915)	0.00228 (0.796)	0.061 (1.00)	0.163 (1.00)	0.000195 (0.0778)	0.0744 (1.00)	0.00102 (0.371)	0.00451 (1.00)	0.000426 (0.162)	0.0753 (1.00)
19p	82 (22%)	283	0.113 (1.00)	0.135 (1.00)	2.72e-05 (0.0112)	3.12e-08 (1.37e-05)	0.181 (1.00)	0.265 (1.00)	0.00051 (0.193)	0.0114 (1.00)	0.269 (1.00)	1 (1.00)	0.177 (1.00)	0.79 (1.00)
20p	37 (10%)	328	0.271 (1.00)	0.0879 (1.00)	1.5e-08 (6.63e-06)	6.54e-09 (2.91e-06)	0.000988 (0.361)	0.126 (1.00)	2.13e-06 (0.000901)	0.000815 (0.301)	0.187 (1.00)	0.133 (1.00)	0.00215 (0.755)	0.00173 (0.616)
16p	22 (6%)	343	0.271 (1.00)	0.0325 (1.00)	0.0947 (1.00)	0.248 (1.00)	0.494 (1.00)	0.853 (1.00)	1.61e-06 (0.000687)	0.626 (1.00)	0.0996 (1.00)	0.000297 (0.115)	0.387 (1.00)	0.00439 (1.00)
17p	24 (7%)	341			0.0321 (1.00)	0.231 (1.00)	0.565 (1.00)	0.853 (1.00)	7.48e-08 (3.26e-05)	0.0276 (1.00)	0.00524 (1.00)	0.000222 (0.0875)	0.00111 (0.402)	0.00535 (1.00)
22q	51 (14%)	314	0.815 (1.00)	0.106 (1.00)	0.00336 (1.00)	0.0164 (1.00)	0.000195 (0.0778)	0.0166 (1.00)	0.000215 (0.085)	0.0693 (1.00)	0.225 (1.00)	0.365 (1.00)	0.00856 (1.00)	0.163 (1.00)
2p	22 (6%)	343	0.754 (1.00)	0.749 (1.00)	0.0947 (1.00)	0.191 (1.00)	0.134 (1.00)	0.696 (1.00)	0.000762 (0.283)	0.0415 (1.00)	0.0998 (1.00)	0.000154 (0.0618)	0.119 (1.00)	0.03 (1.00)
2q	20 (5%)	345	1 (1.00)	0.212 (1.00)	0.16 (1.00)	0.0987 (1.00)	0.0203 (1.00)	1 (1.00)	0.000267 (0.104)	0.0488 (1.00)	0.0678 (1.00)	0.02 (1.00)	0.0544 (1.00)	0.0137 (1.00)
3p	27 (7%)	338			0.343 (1.00)	0.645 (1.00)	0.00793 (1.00)	0.225 (1.00)	8.38e-09 (3.71e-06)	0.0565 (1.00)	0.0514 (1.00)	0.0257 (1.00)	0.0922 (1.00)	0.0235 (1.00)
3q	29 (8%)	336	0.651 (1.00)	0.164 (1.00)	0.238 (1.00)	0.593 (1.00)	0.044 (1.00)	0.11 (1.00)	6.32e-08 (2.77e-05)	0.0624 (1.00)	0.088 (1.00)	0.0654 (1.00)	0.158 (1.00)	0.0383 (1.00)
6q	51 (14%)	314			0.000247 (0.097)	0.00158 (0.566)	0.159 (1.00)	0.431 (1.00)	0.109 (1.00)	0.0313 (1.00)	0.00177 (0.63)	0.266 (1.00)	0.175 (1.00)	0.00745 (1.00)
8p	42 (12%)	323	0.839 (1.00)	0.022 (1.00)	5.53e-05 (0.0223)	0.00225 (0.788)	0.0483 (1.00)	0.604 (1.00)	0.0128 (1.00)	0.0012 (0.435)	0.0981 (1.00)	0.0416 (1.00)	0.0118 (1.00)	0.00143 (0.514)
9p	95 (26%)	270	0.745 (1.00)	0.648 (1.00)	0.00165 (0.587)	0.000977 (0.357)	0.00591 (1.00)	0.0449 (1.00)	0.000494 (0.187)	0.187 (1.00)	0.813 (1.00)	0.126 (1.00)	0.162 (1.00)	0.0558 (1.00)
9q	51 (14%)	314	1 (1.00)	0.212 (1.00)	0.209 (1.00)	0.622 (1.00)	0.135 (1.00)	0.59 (1.00)	0.000401 (0.153)	0.611 (1.00)	0.846 (1.00)	0.0282 (1.00)	0.137 (1.00)	0.779 (1.00)
12q	46 (13%)	319	1 (1.00)	0.00815 (1.00)	8.12e-06 (0.00339)	0.00497 (1.00)	1 (1.00)	0.912 (1.00)	0.192 (1.00)	0.000871 (0.321)	0.271 (1.00)	0.145 (1.00)	0.078 (1.00)	0.493 (1.00)
13q	89 (24%)	276	0.18 (1.00)	0.000618 (0.232)	0.0501 (1.00)	0.0119 (1.00)	0.0284 (1.00)	0.517 (1.00)	0.0485 (1.00)	0.205 (1.00)	0.214 (1.00)	0.0531 (1.00)	0.0531 (1.00)	0.174 (1.00)
15q	40 (11%)	325	0.574 (1.00)	0.404 (1.00)	0.121 (1.00)	0.00772 (1.00)	0.0471 (1.00)	0.0174 (1.00)	0.000272 (0.106)	0.0237 (1.00)	0.04 (1.00)	0.0568 (1.00)	0.49 (1.00)	0.0601 (1.00)
17q	21 (6%)	344			0.201 (1.00)	0.664 (1.00)	0.785 (1.00)	0.708 (1.00)	0.000163 (0.0652)	0.189 (1.00)	0.00595 (1.00)	0.0127 (1.00)	0.00313 (1.00)	0.00338 (1.00)
1q	33 (9%)	332	0.0942 (1.00)	0.212 (1.00)	0.0352 (1.00)	0.0758 (1.00)	0.188 (1.00)	0.652 (1.00)	0.00529 (1.00)	0.916 (1.00)	0.393 (1.00)	0.0155 (1.00)	0.385 (1.00)	0.447 (1.00)
6p	29 (8%)	336			0.118 (1.00)	0.101 (1.00)	0.0585 (1.00)	0.683 (1.00)	0.0932 (1.00)	0.173 (1.00)	0.0526 (1.00)	0.511 (1.00)	0.433 (1.00)	0.000751 (0.279)
11p	71 (19%)	294	0.552 (1.00)	0.068 (1.00)	0.0305 (1.00)	0.0119 (1.00)	0.249 (1.00)	0.25 (1.00)	0.00349 (1.00)	0.244 (1.00)	0.223 (1.00)	0.0499 (1.00)	0.194 (1.00)	0.19 (1.00)
11q	59 (16%)	306	0.0708 (1.00)	0.00315 (1.00)	0.87 (1.00)	0.588 (1.00)	0.689 (1.00)	0.139 (1.00)	0.03 (1.00)	0.72 (1.00)	0.908 (1.00)	0.0349 (1.00)	0.819 (1.00)	0.35 (1.00)
12p	42 (12%)	323	0.508 (1.00)	0.106 (1.00)	0.00242 (0.839)	0.0367 (1.00)	0.366 (1.00)	0.843 (1.00)	0.301 (1.00)	0.00735 (1.00)	0.0435 (1.00)	0.00381 (1.00)	0.0143 (1.00)	0.0818 (1.00)
16q	29 (8%)	336	0.651 (1.00)	0.164 (1.00)	0.036 (1.00)	0.0167 (1.00)	0.426 (1.00)	0.528 (1.00)	0.00824 (1.00)	0.294 (1.00)	0.902 (1.00)	0.0467 (1.00)	0.716 (1.00)	0.015 (1.00)
18p	59 (16%)	306	0.552 (1.00)	0.00351 (1.00)	1 (1.00)	0.0853 (1.00)	0.222 (1.00)	0.184 (1.00)	0.0607 (1.00)	0.72 (1.00)	0.765 (1.00)	0.0192 (1.00)	0.551 (1.00)	0.612 (1.00)
18q	51 (14%)	314	0.0942 (1.00)	0.0286 (1.00)	0.32 (1.00)	0.0474 (1.00)	0.217 (1.00)	0.299 (1.00)	0.00549 (1.00)	0.347 (1.00)	0.755 (1.00)	0.018 (1.00)	0.78 (1.00)	0.876 (1.00)
21q	46 (13%)	319	1 (1.00)	0.0138 (1.00)	0.262 (1.00)	0.0568 (1.00)	0.0912 (1.00)	0.37 (1.00)	0.0265 (1.00)	0.0252 (1.00)	0.0576 (1.00)	0.0965 (1.00)	0.142 (1.00)	0.271 (1.00)
xq	79 (22%)	286	0.745 (1.00)	0.0422 (1.00)	0.533 (1.00)	0.163 (1.00)	0.0123 (1.00)	0.0155 (1.00)	0.145 (1.00)	0.018 (1.00)	0.207 (1.00)	0.369 (1.00)	0.0312 (1.00)	0.0376 (1.00)

'1p' versus 'MRNA_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.25

Table S1. Gene #1: '1p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
1P MUTATED	7	2	1	1
1P WILD-TYPE	0	4	9	3

Figure S1. Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p' versus 'CN_CNMF'

P value = 2.66e-47 (Fisher's exact test), Q value = 1.2e-44

Table S2. Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
1P MUTATED	8	17	117
1P WILD-TYPE	130	70	23

Figure S2. Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'CN_CNMF'

'1p' versus 'METHLYATION_CNMF'

P value = 1.49e-64 (Fisher's exact test), Q value = 7e-62

Table S3. Gene #1: '1p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
1P MUTATED	9	9	107	14
1P WILD-TYPE	152	46	1	22

Figure S3. Get High-res Image Gene #1: '1p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p' versus 'MRNASEQ_CNMF'

P value = 2.91e-33 (Chi-square test), Q value = 1.3e-30

Table S4. Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
1P MUTATED	3	13	64	50	3	9
1P WILD-TYPE	91	57	1	59	4	9

Figure S4. Get High-res Image Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-37 (Fisher's exact test), Q value = 1.2e-34

Table S5. Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
1P MUTATED	60	21	61
1P WILD-TYPE	1	153	67

Figure S5. Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_CNMF'

P value = 7.46e-08 (Chi-square test), Q value = 3.3e-05

Table S6. Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	77	61	100	16	49
1P MUTATED	21	10	50	14	18
1P WILD-TYPE	56	51	50	2	31

Figure S6. Get High-res Image Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.037

Table S7. Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	169	132
1P MUTATED	2	47	64
1P WILD-TYPE	0	122	68

Figure S7. Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.35e-09 (Chi-square test), Q value = 3.7e-06

Table S8. Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
1P MUTATED	2	13	17	39	22	11	1	8
1P WILD-TYPE	47	34	27	42	6	23	3	8

Figure S8. Get High-res Image Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.42e-07 (Fisher's exact test), Q value = 0.00015

Table S9. Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
1P MUTATED	1	44	68
1P WILD-TYPE	9	125	56

Figure S9. Get High-res Image Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.062

Table S10. Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	169	132
2P MUTATED	2	15	3
2P WILD-TYPE	0	154	129

Figure S10. Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Chi-square test), Q value = 0.1

Table S11. Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
2Q MUTATED	6	6	2	3	3	0
2Q WILD-TYPE	88	64	63	106	4	18

Figure S11. Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p' versus 'MRNASEQ_CNMF'

P value = 8.38e-09 (Chi-square test), Q value = 3.7e-06

Table S12. Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
3P MUTATED	4	8	4	5	5	1
3P WILD-TYPE	90	62	61	104	2	17

Figure S12. Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'MRNASEQ_CNMF'

P value = 6.32e-08 (Chi-square test), Q value = 2.8e-05

Table S13. Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
3Q MUTATED	6	8	3	6	5	1
3Q WILD-TYPE	88	62	62	103	2	17

Figure S13. Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 9.89e-07 (Fisher's exact test), Q value = 0.00042

Table S14. Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
4P MUTATED	22	3	36	1
4P WILD-TYPE	139	52	72	35

Figure S14. Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 7.15e-07 (Chi-square test), Q value = 0.00031

Table S15. Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
4P MUTATED	11	4	24	17	4	1
4P WILD-TYPE	83	66	41	92	3	17

Figure S15. Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0055

Table S16. Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
4P MUTATED	23	17	21
4P WILD-TYPE	38	157	107

Figure S16. Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'METHLYATION_CNMF'

P value = 3.84e-06 (Fisher's exact test), Q value = 0.0016

Table S17. Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
4Q MUTATED	28	3	39	3
4Q WILD-TYPE	133	52	69	33

Figure S17. Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 2.56e-06 (Chi-square test), Q value = 0.0011

Table S18. Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
4Q MUTATED	14	4	26	22	4	2
4Q WILD-TYPE	80	66	39	87	3	16

Figure S18. Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0017

Table S19. Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
4Q MUTATED	25	19	28
4Q WILD-TYPE	36	155	100

Figure S19. Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000436 (Chi-square test), Q value = 0.17

Table S20. Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
4Q MUTATED	2	4	15	17	11	8	1	1
4Q WILD-TYPE	47	43	29	64	17	26	3	15

Figure S20. Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'CN_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.00086

Table S21. Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
5P MUTATED	22	11	1
5P WILD-TYPE	116	76	139

Figure S21. Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.021

Table S22. Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
5P MUTATED	26	6	1	1
5P WILD-TYPE	135	49	107	35

Figure S22. Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CNMF'

P value = 4.64e-05 (Chi-square test), Q value = 0.019

Table S23. Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
5P MUTATED	9	9	1	7	4	3
5P WILD-TYPE	85	61	64	102	3	15

Figure S23. Get High-res Image Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'CN_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.049

Table S24. Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
5Q MUTATED	19	10	2
5Q WILD-TYPE	119	77	138

Figure S24. Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.1

Table S25. Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
5Q MUTATED	23	6	1	1
5Q WILD-TYPE	138	49	107	35

Figure S25. Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 2.7e-10 (Chi-square test), Q value = 1.2e-07

Table S26. Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
5Q MUTATED	8	11	1	2	5	3
5Q WILD-TYPE	86	59	64	107	2	15

Figure S26. Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000326 (Fisher's exact test), Q value = 0.13

Table S27. Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
5Q MUTATED	0	24	6
5Q WILD-TYPE	61	150	122

Figure S27. Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'CN_CNMF'

P value = 0.000247 (Fisher's exact test), Q value = 0.097

Table S28. Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
6Q MUTATED	22	21	8
6Q WILD-TYPE	116	66	132

Figure S28. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 4.4e-28 (Fisher's exact test), Q value = 2e-25

Table S29. Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
7P MUTATED	21	62	8
7P WILD-TYPE	117	25	132

Figure S29. Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 2.31e-15 (Fisher's exact test), Q value = 1e-12

Table S30. Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
7P MUTATED	30	40	13	6
7P WILD-TYPE	131	15	95	30

Figure S30. Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S31. Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
7P MUTATED	13	28	12	11
7P WILD-TYPE	39	34	56	63

Figure S31. Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 2.8e-12 (Chi-square test), Q value = 1.3e-09

Table S32. Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
7P MUTATED	17	41	7	19	4	1
7P WILD-TYPE	77	29	58	90	3	17

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

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.45e-06 (Fisher's exact test), Q value = 0.0031

Table S33. Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
7P MUTATED	6	62	21
7P WILD-TYPE	55	112	107

Figure S33. Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0054

Table S34. Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
7P MUTATED	9	25	13	11	4	13	1	1
7P WILD-TYPE	40	22	31	70	24	21	3	15

Figure S34. Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.9e-07 (Fisher's exact test), Q value = 3e-04

Table S35. Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
7P MUTATED	8	53	16
7P WILD-TYPE	2	116	108

Figure S35. Get High-res Image Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 2.04e-28 (Fisher's exact test), Q value = 9.4e-26

Table S36. Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
7Q MUTATED	31	70	15
7Q WILD-TYPE	107	17	125

Figure S36. Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 5.95e-14 (Fisher's exact test), Q value = 2.7e-11

Table S37. Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
7Q MUTATED	45	43	19	7
7Q WILD-TYPE	116	12	89	29

Figure S37. Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 2.31e-08 (Chi-square test), Q value = 1e-05

Table S38. Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
7Q MUTATED	28	43	10	26	4	3
7Q WILD-TYPE	66	27	55	83	3	15

Figure S38. Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0017

Table S39. Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
7Q MUTATED	9	76	29
7Q WILD-TYPE	52	98	99

Figure S39. Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.2

Table S40. Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
7Q MUTATED	12	26	17	16	8	16	1	2
7Q WILD-TYPE	37	21	27	65	20	18	3	14

Figure S40. Get High-res Image Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.017

Table S41. Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
7Q MUTATED	8	64	26
7Q WILD-TYPE	2	105	98

Figure S41. Get High-res Image Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.022

Table S42. Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
8P MUTATED	23	15	4
8P WILD-TYPE	115	72	136

Figure S42. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.0063

Table S43. Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
8Q MUTATED	25	16	4
8Q WILD-TYPE	113	71	136

Figure S43. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000286 (Fisher's exact test), Q value = 0.11

Table S44. Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
8Q MUTATED	1	33	11
8Q WILD-TYPE	60	141	117

Figure S44. Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S45. Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
8Q MUTATED	2	33	6
8Q WILD-TYPE	8	136	118

Figure S45. Get High-res Image Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'MRNASEQ_CNMF'

P value = 0.000494 (Chi-square test), Q value = 0.19

Table S46. Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
9P MUTATED	24	20	12	28	7	4
9P WILD-TYPE	70	50	53	81	0	14

Figure S46. Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 0.000401 (Chi-square test), Q value = 0.15

Table S47. Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
9Q MUTATED	9	12	11	12	5	2
9Q WILD-TYPE	85	58	54	97	2	16

Figure S47. Get High-res Image Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'CN_CNMF'

P value = 2.33e-18 (Fisher's exact test), Q value = 1.1e-15

Table S48. Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
10P MUTATED	36	50	7
10P WILD-TYPE	102	37	133

Figure S48. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 2.69e-26 (Fisher's exact test), Q value = 1.2e-23

Table S49. Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
10P MUTATED	35	47	6	4
10P WILD-TYPE	126	8	102	32

Figure S49. Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p' versus 'RPPA_CNMF'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.0084

Table S50. Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
10P MUTATED	15	29	11	9
10P WILD-TYPE	37	33	57	65

Figure S50. Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.51e-16 (Chi-square test), Q value = 1.1e-13

Table S51. Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
10P MUTATED	19	45	2	19	4	3
10P WILD-TYPE	75	25	63	90	3	15

Figure S51. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.14e-11 (Fisher's exact test), Q value = 3.6e-08

Table S52. Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
10P MUTATED	2	70	20
10P WILD-TYPE	59	104	108

Figure S52. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 0.000657 (Chi-square test), Q value = 0.25

Table S53. Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	77	61	100	16	49
10P MUTATED	30	23	16	1	11
10P WILD-TYPE	47	38	84	15	38

Figure S53. Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.31e-07 (Chi-square test), Q value = 5.7e-05

Table S54. Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
10P MUTATED	12	30	8	14	2	9	2	4
10P WILD-TYPE	37	17	36	67	26	25	2	12

Figure S54. Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.56e-07 (Fisher's exact test), Q value = 0.00011

Table S55. Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
10P MUTATED	7	59	15
10P WILD-TYPE	3	110	109

Figure S55. Get High-res Image Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 6.69e-24 (Fisher's exact test), Q value = 3.1e-21

Table S56. Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
10Q MUTATED	15	53	6
10Q WILD-TYPE	123	34	134

Figure S56. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 3.17e-30 (Fisher's exact test), Q value = 1.5e-27

Table S57. Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
10Q MUTATED	17	47	6	3
10Q WILD-TYPE	144	8	102	33

Figure S57. Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'RPPA_CNMF'

P value = 2e-06 (Fisher's exact test), Q value = 0.00085

Table S58. Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
10Q MUTATED	7	28	9	7
10Q WILD-TYPE	45	34	59	67

Figure S58. Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000399 (Fisher's exact test), Q value = 0.15

Table S59. Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	129	119
10Q MUTATED	1	38	12
10Q WILD-TYPE	7	91	107

Figure S59. Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q' versus 'MRNASEQ_CNMF'

P value = 4.77e-23 (Chi-square test), Q value = 2.2e-20

Table S60. Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
10Q MUTATED	6	45	2	16	3	1
10Q WILD-TYPE	88	25	63	93	4	17

Figure S60. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-07 (Fisher's exact test), Q value = 4.9e-05

Table S61. Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
10Q MUTATED	2	55	16
10Q WILD-TYPE	59	119	112

Figure S61. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.36e-11 (Chi-square test), Q value = 1.1e-08

Table S62. Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
10Q MUTATED	3	29	4	12	2	11	1	3
10Q WILD-TYPE	46	18	40	69	26	23	3	13

Figure S62. Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.0069

Table S63. Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
10Q MUTATED	7	44	14
10Q WILD-TYPE	3	125	110

Figure S63. Get High-res Image Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 8.12e-06 (Fisher's exact test), Q value = 0.0034

Table S64. Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
12Q MUTATED	32	8	6
12Q WILD-TYPE	106	79	134

Figure S64. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000618 (Fisher's exact test), Q value = 0.23

Table S65. Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
13Q MUTATED	0	0	5	4
13Q WILD-TYPE	7	6	5	0

Figure S65. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.092

Table S66. Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
14Q MUTATED	15	27	17
14Q WILD-TYPE	123	60	123

Figure S66. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.000195 (Chi-square test), Q value = 0.078

Table S67. Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
14Q MUTATED	8	24	7	15	2	2
14Q WILD-TYPE	86	46	58	94	5	16

Figure S67. Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000426 (Chi-square test), Q value = 0.16

Table S68. Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
14Q MUTATED	5	20	6	10	3	4	1	3
14Q WILD-TYPE	44	27	38	71	25	30	3	13

Figure S68. Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 0.000272 (Chi-square test), Q value = 0.11

Table S69. Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
15Q MUTATED	7	9	15	5	3	1
15Q WILD-TYPE	87	61	50	104	4	17

Figure S69. Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 1.61e-06 (Chi-square test), Q value = 0.00069

Table S70. Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
16P MUTATED	2	5	4	6	4	1
16P WILD-TYPE	92	65	61	103	3	17

Figure S70. Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000297 (Fisher's exact test), Q value = 0.12

Table S71. Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	169	132
16P MUTATED	2	6	13
16P WILD-TYPE	0	163	119

Figure S71. Get High-res Image Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 7.48e-08 (Chi-square test), Q value = 3.3e-05

Table S72. Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
17P MUTATED	3	10	4	2	4	1
17P WILD-TYPE	91	60	61	107	3	17

Figure S72. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.088

Table S73. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	169	132
17P MUTATED	2	17	4
17P WILD-TYPE	0	152	128

Figure S73. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Chi-square test), Q value = 0.065

Table S74. Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
17Q MUTATED	3	7	5	2	3	1
17Q WILD-TYPE	91	63	60	107	4	17

Figure S74. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'CN_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.011

Table S75. Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
19P MUTATED	14	27	41
19P WILD-TYPE	124	60	99

Figure S75. Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 3.12e-08 (Fisher's exact test), Q value = 1.4e-05

Table S76. Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
19P MUTATED	16	22	38	4
19P WILD-TYPE	145	33	70	32

Figure S76. Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Chi-square test), Q value = 0.19

Table S77. Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
19P MUTATED	8	22	24	23	2	3
19P WILD-TYPE	86	48	41	86	5	15

Figure S77. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'CN_CNMF'

P value = 6.79e-42 (Fisher's exact test), Q value = 3.2e-39

Table S78. Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
19Q MUTATED	17	26	123
19Q WILD-TYPE	121	61	17

Figure S78. Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 1.16e-50 (Fisher's exact test), Q value = 5.4e-48

Table S79. Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
19Q MUTATED	22	18	107	15
19Q WILD-TYPE	139	37	1	21

Figure S79. Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 1.42e-25 (Chi-square test), Q value = 6.5e-23

Table S80. Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
19Q MUTATED	12	20	64	56	2	11
19Q WILD-TYPE	82	50	1	53	5	7

Figure S80. Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-29 (Fisher's exact test), Q value = 1.5e-26

Table S81. Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
19Q MUTATED	60	37	68
19Q WILD-TYPE	1	137	60

Figure S81. Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 0.000207 (Chi-square test), Q value = 0.082

Table S82. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	77	61	100	16	49
19Q MUTATED	23	22	55	13	20
19Q WILD-TYPE	54	39	45	3	29

Figure S82. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000572 (Fisher's exact test), Q value = 0.22

Table S83. Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	169	132
19Q MUTATED	0	60	73
19Q WILD-TYPE	2	109	59

Figure S83. Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.58e-07 (Chi-square test), Q value = 0.00011

Table S84. Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
19Q MUTATED	4	18	22	42	22	14	2	9
19Q WILD-TYPE	45	29	22	39	6	20	2	7

Figure S84. Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.22e-05 (Fisher's exact test), Q value = 0.017

Table S85. Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
19Q MUTATED	3	57	73
19Q WILD-TYPE	7	112	51

Figure S85. Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 1.5e-08 (Fisher's exact test), Q value = 6.6e-06

Table S86. Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
20P MUTATED	10	24	3
20P WILD-TYPE	128	63	137

Figure S86. Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 6.54e-09 (Fisher's exact test), Q value = 2.9e-06

Table S87. Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
20P MUTATED	11	21	4	1
20P WILD-TYPE	150	34	104	35

Figure S87. Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 2.13e-06 (Chi-square test), Q value = 9e-04

Table S88. Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
20P MUTATED	5	18	3	8	3	0
20P WILD-TYPE	89	52	62	101	4	18

Figure S88. Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'CN_CNMF'

P value = 7.58e-08 (Fisher's exact test), Q value = 3.3e-05

Table S89. Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	87	140
20Q MUTATED	8	23	4
20Q WILD-TYPE	130	64	136

Figure S89. Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.03e-10 (Fisher's exact test), Q value = 4.6e-08

Table S90. Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	161	55	108	36
20Q MUTATED	9	22	4	0
20Q WILD-TYPE	152	33	104	36

Figure S90. Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 7.85e-09 (Chi-square test), Q value = 3.5e-06

Table S91. Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
20Q MUTATED	4	21	3	5	2	0
20Q WILD-TYPE	90	49	62	104	5	18

Figure S91. Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.17e-05 (Fisher's exact test), Q value = 0.021

Table S92. Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	174	128
20Q MUTATED	1	29	5
20Q WILD-TYPE	60	145	123

Figure S92. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.62e-05 (Chi-square test), Q value = 0.019

Table S93. Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	49	47	44	81	28	34	4	16
20Q MUTATED	1	12	4	1	2	8	1	1
20Q WILD-TYPE	48	35	40	80	26	26	3	15

Figure S93. Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S94. Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	10	169	124
20Q MUTATED	4	22	4
20Q WILD-TYPE	6	147	120

Figure S94. Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'RPPA_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.078

Table S95. Gene #39: '22q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
22Q MUTATED	3	20	7	6
22Q WILD-TYPE	49	42	61	68

Figure S95. Get High-res Image Gene #39: '22q' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 0.000215 (Chi-square test), Q value = 0.085

Table S96. Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	94	70	65	109	7	18
22Q MUTATED	7	20	9	10	3	1
22Q WILD-TYPE	87	50	56	99	4	17

Figure S96. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LGG-TP.transferedmergedcluster.txt
Number of patients = 365
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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