Correlation between mRNAseq expression and clinical features

Thyroid Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BC3XH0

Overview

Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 17991 genes and 17 clinical features across 495 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one genes.

196 genes correlated to 'AGE'.

ZNF518B|85460 , RANBP17|64901 , MSL3L2|151507 , HCG11|493812 , C12ORF52|84934 , ...

516 genes correlated to 'NEOPLASM.DISEASESTAGE'.

SLC10A4|201780 , CYP26A1|1592 , EXOC3L2|90332 , WISP2|8839 , PIK3R3|8503 , ...

774 genes correlated to 'PATHOLOGY.T.STAGE'.

FBXO9|26268 , LTF|4057 , VIPR1|7433 , SPCS3|60559 , SLCO2A1|6578 , ...

2897 genes correlated to 'PATHOLOGY.N.STAGE'.

CBFB|865 , CREB5|9586 , CLCNKA|1187 , PELI1|57162 , ZNF346|23567 , ...

24 genes correlated to 'PATHOLOGY.M.STAGE'.

ST6GALNAC1|55808 , CYP21A2|1589 , SELP|6403 , C19ORF76|199800 , RARRES1|5918 , ...

12 genes correlated to 'GENDER'.

HDHD1A|8226 , NCRNA00183|554203 , CA5BP|340591 , CYORF15A|246126 , CYORF15B|84663 , ...

6223 genes correlated to 'HISTOLOGICAL.TYPE'.

ITGA3|3675 , SFTPB|6439 , FN1|2335 , ANXA2P2|304 , ERBB3|2065 , ...

30 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

BAT2|7916 , C6ORF162|57150 , HCFC1|3054 , IPO4|79711 , SMARCA4|6597 , ...

1474 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

SLC10A4|201780 , SLC25A42|284439 , SRPX2|27286 , FLRT1|23769 , COL1A1|1277 , ...

5 genes correlated to 'COMPLETENESS.OF.RESECTION'.

SHOX2|6474 , LGR5|8549 , WNT2|7472 , APCDD1L|164284 , SLC10A4|201780

1675 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

PELI1|57162 , CBFB|865 , FAM60A|58516 , CREB5|9586 , FECH|2235 , ...

2 genes correlated to 'MULTIFOCALITY'.

AVPI1|60370 , SCD5|79966

24 genes correlated to 'TUMOR.SIZE'.

C3ORF32|51066 , ISLR2|57611 , ZC3H10|84872 , CXCL12|6387 , LRRC55|219527 , ...

44 genes correlated to 'RACE'.

XKR9|389668 , SEC1|653677 , LRRC37A2|474170 , RPS26|6231 , ATAD3C|219293 , ...

13 genes correlated to 'ETHNICITY'.

SNAPC3|6619 , ZFP36L1|677 , ATG12|9140 , TEC|7006 , CHRNA10|57053 , ...

No genes correlated to 'Time to Death', and 'RADIATIONEXPOSURE'.

Results

Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature	Statistical test	Significant genes	Associated with		Associated with
Time to Death	Cox regression test	N=0
AGE	Spearman correlation test	N=196	older	N=91	younger	N=105
NEOPLASM DISEASESTAGE	Kruskal-Wallis test	N=516
PATHOLOGY T STAGE	Spearman correlation test	N=774	higher stage	N=167	lower stage	N=607
PATHOLOGY N STAGE	Wilcoxon test	N=2897	class1	N=2897	class0	N=0
PATHOLOGY M STAGE	Kruskal-Wallis test	N=24
GENDER	Wilcoxon test	N=12	male	N=12	female	N=0
HISTOLOGICAL TYPE	Kruskal-Wallis test	N=6223
RADIATIONS RADIATION REGIMENINDICATION	Wilcoxon test	N=30	yes	N=30	no	N=0
RADIATIONEXPOSURE	Wilcoxon test	N=0
EXTRATHYROIDAL EXTENSION	Kruskal-Wallis test	N=1474
COMPLETENESS OF RESECTION	Kruskal-Wallis test	N=5
NUMBER OF LYMPH NODES	Spearman correlation test	N=1675	higher number.of.lymph.nodes	N=897	lower number.of.lymph.nodes	N=778
MULTIFOCALITY	Wilcoxon test	N=2	unifocal	N=2	multifocal	N=0
TUMOR SIZE	Spearman correlation test	N=24	higher tumor.size	N=3	lower tumor.size	N=21
RACE	Kruskal-Wallis test	N=44
ETHNICITY	Wilcoxon test	N=13	not hispanic or latino	N=13	hispanic or latino	N=0

Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1. Basic characteristics of clinical feature: 'Time to Death'


Time to Death	Duration (Months)	0-158.8 (median=16.6)
	censored	N = 477
	death	N = 14

	Significant markers	N = 0

Clinical variable #2: 'AGE'

196 genes related to 'AGE'.

Table S2. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	47.13 (16)
	Significant markers	N = 196
	pos. correlated	91
	neg. correlated	105

List of top 10 genes differentially expressed by 'AGE'

Table S3. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
ZNF518B\|85460	-0.3361	1.542e-14	2.77e-10
RANBP17\|64901	-0.3279	8.45e-14	1.52e-09
MSL3L2\|151507	-0.3221	2.071e-13	3.73e-09
HCG11\|493812	-0.2909	4.148e-11	7.46e-07
C12ORF52\|84934	0.2863	8.637e-11	1.55e-06
ASB13\|79754	0.2834	1.351e-10	2.43e-06
LHFPL4\|375323	0.2897	3.149e-10	5.66e-06
C1ORF59\|113802	-0.273	6.532e-10	1.17e-05
DDIT4L\|115265	0.2685	1.335e-09	2.4e-05
ST3GAL1\|6482	-0.2655	1.96e-09	3.52e-05

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

516 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'


NEOPLASM.DISEASESTAGE	Labels	N
	STAGE I	280
	STAGE II	52
	STAGE III	108
	STAGE IV	2
	STAGE IVA	45
	STAGE IVC	6

	Significant markers	N = 516

List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S5. Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

	ANOVA_P	Q
SLC10A4\|201780	3.86e-10	6.94e-06
CYP26A1\|1592	1.192e-09	2.14e-05
EXOC3L2\|90332	2.971e-09	5.34e-05
WISP2\|8839	3.131e-09	5.63e-05
PIK3R3\|8503	5.808e-09	0.000104
IQCE\|23288	6.619e-09	0.000119
LRRC15\|131578	6.981e-09	0.000126
KDR\|3791	7.543e-09	0.000136
TM4SF18\|116441	8.817e-09	0.000159
PLP2\|5355	1.022e-08	0.000184

Clinical variable #4: 'PATHOLOGY.T.STAGE'

774 genes related to 'PATHOLOGY.T.STAGE'.

Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'


PATHOLOGY.T.STAGE	Mean (SD)	2.14 (0.88)
		N
	1	140
	2	166
	3	165
	4	21

	Significant markers	N = 774
	pos. correlated	167
	neg. correlated	607

List of top 10 genes differentially expressed by 'PATHOLOGY.T.STAGE'

Table S7. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
FBXO9\|26268	-0.2959	2.136e-11	3.84e-07
LTF\|4057	-0.2852	1.163e-10	2.09e-06
VIPR1\|7433	-0.2839	1.421e-10	2.56e-06
SPCS3\|60559	-0.2826	1.74e-10	3.13e-06
SLCO2A1\|6578	-0.2728	7.636e-10	1.37e-05
GNG7\|2788	-0.2701	1.131e-09	2.03e-05
IPCEF1\|26034	-0.2673	1.706e-09	3.07e-05
LOC653566\|653566	-0.2669	1.802e-09	3.24e-05
SYT15\|83849	-0.2664	1.928e-09	3.47e-05
FAM65C\|140876	-0.2655	2.218e-09	3.99e-05

Clinical variable #5: 'PATHOLOGY.N.STAGE'

2897 genes related to 'PATHOLOGY.N.STAGE'.

Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'


PATHOLOGY.N.STAGE	Labels	N
	class0	224
	class1	221

	Significant markers	N = 2897
	Higher in class1	2897
	Higher in class0	0

List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S9. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

	W(pos if higher in 'class1')	wilcoxontestP	Q	AUC
CBFB\|865	36978	2.005e-19	3.61e-15	0.747
CREB5\|9586	36160	4.102e-17	7.38e-13	0.7304
CLCNKA\|1187	13326	5.812e-17	1.05e-12	0.7296
PELI1\|57162	35884	2.278e-16	4.1e-12	0.7249
ZNF346\|23567	13715	4.071e-16	7.32e-12	0.723
TMEM117\|84216	35712	6.494e-16	1.17e-11	0.7214
MLEC\|9761	13837	8.52e-16	1.53e-11	0.7205
FAM60A\|58516	35641	9.962e-16	1.79e-11	0.72
DIRAS2\|54769	13661.5	1.79e-15	3.22e-11	0.719
FN1\|2335	35518	2.077e-15	3.74e-11	0.7175

Clinical variable #6: 'PATHOLOGY.M.STAGE'

24 genes related to 'PATHOLOGY.M.STAGE'.

Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'


PATHOLOGY.M.STAGE	Labels	N
	M0	273
	M1	9
	MX	212

	Significant markers	N = 24

List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S11. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

	ANOVA_P	Q
ST6GALNAC1\|55808	3.058e-07	0.0055
CYP21A2\|1589	1.093e-06	0.0197
SELP\|6403	1.204e-06	0.0217
C19ORF76\|199800	1.602e-06	0.0288
RARRES1\|5918	1.797e-06	0.0323
C1QTNF7\|114905	1.83e-06	0.0329
MAPRE1\|22919	1.917e-06	0.0345
EIF4H\|7458	2.106e-06	0.0379
EDN1\|1906	2.803e-06	0.0504
ANKRD35\|148741	2.878e-06	0.0517

Clinical variable #7: 'GENDER'

12 genes related to 'GENDER'.

Table S12. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	363
	MALE	132

	Significant markers	N = 12
	Higher in MALE	12
	Higher in FEMALE	0

List of top 10 genes differentially expressed by 'GENDER'

Table S13. Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 43 significant gene(s) located in sex chromosomes is(are) filtered out.

	W(pos if higher in 'MALE')	wilcoxontestP	Q	AUC
HDHD1A\|8226	3772	1.173e-46	2.11e-42	0.9213
NCRNA00183\|554203	5107.5	6.527e-41	1.17e-36	0.8934
CA5BP\|340591	9506	9.734e-25	1.75e-20	0.8016
CYORF15A\|246126	5633	8.784e-23	1.58e-18	1
CYORF15B\|84663	3537	3.164e-16	5.68e-12	1
C2ORF84\|653140	31104	2.798e-07	0.00502	0.6509
TFRC\|7037	16808	3.769e-07	0.00677	0.6492
C1ORF93\|127281	31061	4.491e-07	0.00806	0.6482
C21ORF7\|56911	30884	8.607e-07	0.0154	0.6445
LOC90110\|90110	30840.5	1.007e-06	0.0181	0.6436

Clinical variable #8: 'HISTOLOGICAL.TYPE'

6223 genes related to 'HISTOLOGICAL.TYPE'.

Table S14. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	OTHER SPECIFY	9
	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	352
	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	100
	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)	34

	Significant markers	N = 6223

List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S15. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

	ANOVA_P	Q
ITGA3\|3675	9.36e-35	1.68e-30
SFTPB\|6439	2.713e-34	4.88e-30
FN1\|2335	1.417e-32	2.55e-28
ANXA2P2\|304	2.858e-32	5.14e-28
ERBB3\|2065	3.051e-32	5.49e-28
UNC5CL\|222643	3.098e-32	5.57e-28
AHNAK2\|113146	4.078e-32	7.33e-28
SERPINA1\|5265	4.756e-32	8.55e-28
CYP2S1\|29785	1.1e-31	1.98e-27
KCNN4\|3783	1.026e-30	1.85e-26

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

30 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	14
	YES	481

	Significant markers	N = 30
	Higher in YES	30
	Higher in NO	0

List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

	W(pos if higher in 'YES')	wilcoxontestP	Q	AUC
BAT2\|7916	694	4.071e-07	0.00731	0.8969
C6ORF162\|57150	6032	4.408e-07	0.00792	0.8958
HCFC1\|3054	714	4.964e-07	0.00891	0.894
IPO4\|79711	731	5.869e-07	0.0105	0.8914
SMARCA4\|6597	745	6.732e-07	0.0121	0.8894
AP2A1\|160	746	6.798e-07	0.0122	0.8892
CUL7\|9820	753	7.279e-07	0.0131	0.8882
BAT3\|7917	777	9.188e-07	0.0165	0.8846
POM121C\|100101267	855	1.932e-06	0.0347	0.873
ENPP3\|5169	5811	2.07e-06	0.0372	0.872

Clinical variable #10: 'RADIATIONEXPOSURE'

No gene related to 'RADIATIONEXPOSURE'.

Table S18. Basic characteristics of clinical feature: 'RADIATIONEXPOSURE'


RADIATIONEXPOSURE	Labels	N
	NO	416
	YES	17

	Significant markers	N = 0

Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

1474 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S19. Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'


EXTRATHYROIDAL.EXTENSION	Labels	N
	MINIMAL (T3)	130
	MODERATE/ADVANCED (T4A)	16
	NONE	328
	VERY ADVANCED (T4B)	1

	Significant markers	N = 1474

List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S20. Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

	ANOVA_P	Q
SLC10A4\|201780	6.055e-14	1.09e-09
SLC25A42\|284439	1.935e-13	3.48e-09
SRPX2\|27286	6.096e-13	1.1e-08
FLRT1\|23769	2.603e-12	4.68e-08
COL1A1\|1277	2.902e-12	5.22e-08
FAM69C\|125704	2.904e-12	5.22e-08
FN1\|2335	3.771e-12	6.78e-08
BEGAIN\|57596	4.268e-12	7.67e-08
KDM4B\|23030	4.275e-12	7.69e-08
LOX\|4015	5.26e-12	9.46e-08

Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

5 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S21. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'


COMPLETENESS.OF.RESECTION	Labels	N
	R0	378
	R1	51
	R2	4
	RX	30

	Significant markers	N = 5

List of 5 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S22. Get Full Table List of 5 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

	ANOVA_P	Q
SHOX2\|6474	2.776e-06	0.0499
LGR5\|8549	6.503e-06	0.117
WNT2\|7472	9.096e-06	0.164
APCDD1L\|164284	9.58e-06	0.172
SLC10A4\|201780	9.956e-06	0.179

Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

1675 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S23. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'


NUMBER.OF.LYMPH.NODES	Mean (SD)	3.56 (6.2)
	Significant markers	N = 1675
	pos. correlated	897
	neg. correlated	778

List of top 10 genes differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S24. Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

	SpearmanCorr	corrP	Q
PELI1\|57162	0.3844	3.477e-15	6.26e-11
CBFB\|865	0.3835	4.122e-15	7.42e-11
FAM60A\|58516	0.3781	1.067e-14	1.92e-10
CREB5\|9586	0.3727	2.707e-14	4.87e-10
FECH\|2235	-0.3673	6.67e-14	1.2e-09
TAGLN2\|8407	0.364	1.167e-13	2.1e-09
CLCNKA\|1187	-0.3633	1.4e-13	2.52e-09
GPR153\|387509	0.3619	1.649e-13	2.97e-09
TMEM99\|147184	-0.359	2.637e-13	4.74e-09
S100A10\|6281	0.3569	3.699e-13	6.65e-09

Clinical variable #14: 'MULTIFOCALITY'

2 genes related to 'MULTIFOCALITY'.

Table S25. Basic characteristics of clinical feature: 'MULTIFOCALITY'


MULTIFOCALITY	Labels	N
	MULTIFOCAL	224
	UNIFOCAL	261

	Significant markers	N = 2
	Higher in UNIFOCAL	2
	Higher in MULTIFOCAL	0

List of 2 genes differentially expressed by 'MULTIFOCALITY'

Table S26. Get Full Table List of 2 genes differentially expressed by 'MULTIFOCALITY'

	W(pos if higher in 'UNIFOCAL')	wilcoxontestP	Q	AUC
AVPI1\|60370	36463	2.616e-06	0.0471	0.6237
SCD5\|79966	22588	1.579e-05	0.284	0.6136

Clinical variable #15: 'TUMOR.SIZE'

24 genes related to 'TUMOR.SIZE'.

Table S27. Basic characteristics of clinical feature: 'TUMOR.SIZE'


TUMOR.SIZE	Mean (SD)	2.98 (1.6)
	Significant markers	N = 24
	pos. correlated	3
	neg. correlated	21

List of top 10 genes differentially expressed by 'TUMOR.SIZE'

Table S28. Get Full Table List of top 10 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

	SpearmanCorr	corrP	Q
C3ORF32\|51066	-0.2785	2.63e-08	0.000473
ISLR2\|57611	-0.2583	1.8e-07	0.00324
ZC3H10\|84872	-0.2574	1.997e-07	0.00359
CXCL12\|6387	-0.2482	5.502e-07	0.0099
LRRC55\|219527	-0.2445	9.296e-07	0.0167
SLC14A1\|6563	-0.2412	1.158e-06	0.0208
FOXI2\|399823	-0.2422	1.252e-06	0.0225
CLDN2\|9075	-0.2396	1.547e-06	0.0278
GPR34\|2857	-0.2378	1.647e-06	0.0296
KCNJ5\|3762	-0.2378	1.706e-06	0.0307

Clinical variable #16: 'RACE'

44 genes related to 'RACE'.

Table S29. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	1
	ASIAN	48
	BLACK OR AFRICAN AMERICAN	26
	WHITE	322

	Significant markers	N = 44

List of top 10 genes differentially expressed by 'RACE'

Table S30. Get Full Table List of top 10 genes differentially expressed by 'RACE'

	ANOVA_P	Q
XKR9\|389668	3.295e-12	5.93e-08
SEC1\|653677	3.273e-10	5.89e-06
LRRC37A2\|474170	3.497e-10	6.29e-06
RPS26\|6231	2.446e-09	4.4e-05
ATAD3C\|219293	4.759e-09	8.56e-05
MKX\|283078	1.556e-08	0.00028
UTS2\|10911	3.543e-08	0.000637
CORO6\|84940	1.053e-07	0.00189
LRRC19\|64922	1.189e-07	0.00214
DDX11L2\|84771	1.397e-07	0.00251

Clinical variable #17: 'ETHNICITY'

13 genes related to 'ETHNICITY'.

Table S31. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	38
	NOT HISPANIC OR LATINO	349

	Significant markers	N = 13
	Higher in NOT HISPANIC OR LATINO	13
	Higher in HISPANIC OR LATINO	0

List of top 10 genes differentially expressed by 'ETHNICITY'

Table S32. Get Full Table List of top 10 genes differentially expressed by 'ETHNICITY'

	W(pos if higher in 'NOT HISPANIC OR LATINO')	wilcoxontestP	Q	AUC
SNAPC3\|6619	c("3407", "8.539e-07")	c("3407", "8.539e-07")	0.0154	0.7431
ZFP36L1\|677	c("3450", "1.192e-06")	c("3450", "1.192e-06")	0.0214	0.7399
ATG12\|9140	c("3479", "1.489e-06")	c("3479", "1.489e-06")	0.0268	0.7377
TEC\|7006	c("3506", "1.829e-06")	c("3506", "1.829e-06")	0.0329	0.7356
CHRNA10\|57053	c("9728", "2.26e-06")	c("9728", "2.26e-06")	0.0406	0.7335
MCF2L2\|23101	c("3595", "3.854e-06")	c("3595", "3.854e-06")	0.0693	0.7281
RIMBP3\|85376	c("9636", "4.471e-06")	c("9636", "4.471e-06")	0.0804	0.7266
SLC19A2\|10560	c("3655", "5.522e-06")	c("3655", "5.522e-06")	0.0993	0.7244
SNW1\|22938	c("3656", "5.562e-06")	c("3656", "5.562e-06")	0.1	0.7243
FAM45A\|404636	c("3660", "5.726e-06")	c("3660", "5.726e-06")	0.103	0.724

Methods & Data

Input

Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Clinical data file = THCA-TP.merged_data.txt
Number of patients = 495
Number of genes = 17991
Number of clinical features = 17

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.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] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)

[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)

[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)

[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[5] 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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