Correlation between mRNAseq expression and clinical features

Thyroid Adenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18051RQ

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 499 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 14 clinical features related to at least one genes.

30 genes correlated to 'YEARS_TO_BIRTH'.

ZNF518B|85460 , RANBP17|64901 , MSL3L2|151507 , HCG11|493812 , ASB13|79754 , ...

30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

SLC10A4|201780 , WISP2|8839 , CYP26A1|1592 , EXOC3L2|90332 , LRRC15|131578 , ...

30 genes correlated to 'PATHOLOGY_T_STAGE'.

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

30 genes correlated to 'PATHOLOGY_N_STAGE'.

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

5 genes correlated to 'GENDER'.

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

30 genes correlated to 'HISTOLOGICAL_TYPE'.

ITGA3|3675 , SFTPB|6439 , FN1|2335 , ANXA2P2|304 , UNC5CL|222643 , ...

30 genes correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

BAT2|7916 , C6ORF162|57150 , HCFC1|3054 , IPO4|79711 , AP2A1|160 , ...

30 genes correlated to 'EXTRATHYROIDAL_EXTENSION'.

SLC10A4|201780 , SLC25A42|284439 , SRPX2|27286 , FLRT1|23769 , FOXJ1|2302 , ...

30 genes correlated to 'COMPLETENESS_OF_RESECTION'.

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

30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

CBFB|865 , PELI1|57162 , FAM60A|58516 , CREB5|9586 , CLCNKA|1187 , ...

30 genes correlated to 'MULTIFOCALITY'.

AVPI1|60370 , SCD5|79966 , AMDHD2|51005 , A2BP1|54715 , CXCL3|2921 , ...

30 genes correlated to 'TUMOR_SIZE'.

C3ORF32|51066 , ISLR2|57611 , ZC3H10|84872 , CXCL12|6387 , FOXI2|399823 , ...

30 genes correlated to 'RACE'.

XKR9|389668 , LRRC37A2|474170 , SEC1|653677 , RPS26|6231 , UTS2|10911 , ...

30 genes correlated to 'ETHNICITY'.

SNAPC3|6619 , ZFP36L1|677 , ATG12|9140 , TEC|7006 , MCF2L2|23101 , ...

No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_M_STAGE', and 'RADIATION_EXPOSURE'.

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
DAYS_TO_DEATH_OR_LAST_FUP	Cox regression test	N=0
YEARS_TO_BIRTH	Spearman correlation test	N=30	older	N=11	younger	N=19
NEOPLASM_DISEASESTAGE	Kruskal-Wallis test	N=30
PATHOLOGY_T_STAGE	Spearman correlation test	N=30	higher stage	N=1	lower stage	N=29
PATHOLOGY_N_STAGE	Wilcoxon test	N=30	n1	N=30	n0	N=0
PATHOLOGY_M_STAGE	Wilcoxon test	N=0
GENDER	Wilcoxon test	N=5	male	N=5	female	N=0
HISTOLOGICAL_TYPE	Kruskal-Wallis test	N=30
RADIATIONS_RADIATION_REGIMENINDICATION	Wilcoxon test	N=30	yes	N=30	no	N=0
RADIATION_EXPOSURE	Wilcoxon test	N=0
EXTRATHYROIDAL_EXTENSION	Kruskal-Wallis test	N=30
COMPLETENESS_OF_RESECTION	Kruskal-Wallis test	N=30
NUMBER_OF_LYMPH_NODES	Spearman correlation test	N=30	higher number_of_lymph_nodes	N=18	lower number_of_lymph_nodes	N=12
MULTIFOCALITY	Wilcoxon test	N=30	unifocal	N=30	multifocal	N=0
TUMOR_SIZE	Spearman correlation test	N=30	higher tumor_size	N=3	lower tumor_size	N=27
RACE	Kruskal-Wallis test	N=30
ETHNICITY	Wilcoxon test	N=30	not hispanic or latino	N=30	hispanic or latino	N=0

Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No gene related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

Table S1. Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'


DAYS_TO_DEATH_OR_LAST_FUP	Duration (Months)	0.1-169.3 (median=20.3)
	censored	N = 484
	death	N = 14

	Significant markers	N = 0

Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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


YEARS_TO_BIRTH	Mean (SD)	47.22 (16)
	Significant markers	N = 30
	pos. correlated	11
	neg. correlated	19

List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

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

	SpearmanCorr	corrP	Q
ZNF518B\|85460	-0.3446	2.322e-15	4.18e-11
RANBP17\|64901	-0.3315	3.485e-14	3.13e-10
MSL3L2\|151507	-0.3279	5.703e-14	3.42e-10
HCG11\|493812	-0.2954	1.65e-11	7.42e-08
ASB13\|79754	0.2842	9.964e-11	3.59e-07
C12ORF52\|84934	0.2811	1.622e-10	4.86e-07
ST3GAL1\|6482	-0.2794	2.121e-10	5.45e-07
LHFPL4\|375323	0.2903	2.638e-10	5.93e-07
C1ORF59\|113802	-0.2745	4.498e-10	8.99e-07
DDIT4L\|115265	0.2642	2.134e-09	3.84e-06

Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

Table S4. Basic characteristics of clinical feature: 'NEOPLASM_DISEASESTAGE'


NEOPLASM_DISEASESTAGE	Labels	N
	STAGE I	282
	STAGE II	53
	STAGE III	108
	STAGE IV	2
	STAGE IVA	46
	STAGE IVC	6

	Significant markers	N = 30

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'

	kruskal_wallis_P	Q
SLC10A4\|201780	4.051e-11	7.29e-07
WISP2\|8839	4.445e-10	3.16e-06
CYP26A1\|1592	5.706e-10	3.16e-06
EXOC3L2\|90332	7.036e-10	3.16e-06
LRRC15\|131578	1.134e-09	3.5e-06
KDR\|3791	1.662e-09	3.5e-06
TM4SF18\|116441	1.784e-09	3.5e-06
IQCE\|23288	2.302e-09	3.5e-06
COL10A1\|1300	2.312e-09	3.5e-06
UNC5CL\|222643	2.55e-09	3.5e-06

Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S6. Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'


PATHOLOGY_T_STAGE	Mean (SD)	2.14 (0.89)
		N
	T1	141
	T2	166
	T3	167
	T4	23

	Significant markers	N = 30
	pos. correlated	1
	neg. correlated	29

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	-0.2987	1.055e-11	1.15e-07
LTF\|4057	-0.2975	1.301e-11	1.15e-07
VIPR1\|7433	-0.2951	1.91e-11	1.15e-07
SPCS3\|60559	-0.2907	3.93e-11	1.77e-07
SLCO2A1\|6578	-0.2786	2.609e-10	8.06e-07
LRRC4\|64101	-0.278	2.969e-10	8.06e-07
SYT15\|83849	-0.2774	3.137e-10	8.06e-07
GNG7\|2788	-0.2757	4.041e-10	8.83e-07
LOC653566\|653566	-0.2751	4.415e-10	8.83e-07
KDR\|3791	-0.2741	5.161e-10	9.28e-07

Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S8. Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'


PATHOLOGY_N_STAGE	Labels	N
	N0	225
	N1	224

	Significant markers	N = 30
	Higher in N1	30
	Higher in N0	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 'N1')	wilcoxontestP	Q	AUC
CBFB\|865	37535	2.911e-19	5.24e-15	0.7447
CREB5\|9586	36759	4.186e-17	3.64e-13	0.7293
CLCNKA\|1187	13627	6.068e-17	3.64e-13	0.7284
PELI1\|57162	36504	2e-16	9e-13	0.7243
ZNF346\|23567	13974	3.205e-16	1.15e-12	0.7227
MLEC\|9761	14103	6.943e-16	2.08e-12	0.7202
TFAP2C\|7022	36251	9.127e-16	2.09e-12	0.7193
TMEM117\|84216	36248	9.291e-16	2.09e-12	0.7192
FN1\|2335	36101	2.21e-15	4.06e-12	0.7163
GPER\|2852	14303	2.262e-15	4.06e-12	0.7162

Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

Table S10. Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'


PATHOLOGY_M_STAGE	Labels	N
	class0	277
	class1	9

	Significant markers	N = 0

Clinical variable #7: 'GENDER'

5 genes related to 'GENDER'.

Table S11. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	365
	MALE	134

	Significant markers	N = 5
	Higher in MALE	5
	Higher in FEMALE	0

List of 5 genes differentially expressed by 'GENDER'

Table S12. Get Full Table List of 5 genes differentially expressed by 'GENDER'. 25 significant gene(s) located in sex chromosomes is(are) filtered out.

	W(pos if higher in 'MALE')	wilcoxontestP	Q	AUC
HDHD1A\|8226	4092	3.674e-46	1.1e-42	0.9163
NCRNA00183\|554203	5138.5	1.029e-41	2.06e-38	0.8949
CA5BP\|340591	9674	4.026e-25	3.45e-22	0.8022
CYORF15A\|246126	5719	7.298e-23	5.97e-20	1
CYORF15B\|84663	3724	1.022e-16	6.81e-14	1

Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S13. Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'


HISTOLOGICAL_TYPE	Labels	N
	OTHER SPECIFY	9
	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	355
	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	100
	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)	35

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S14. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

	kruskal_wallis_P	Q
ITGA3\|3675	6.979e-35	9.71e-31
SFTPB\|6439	1.08e-34	9.71e-31
FN1\|2335	6.725e-33	4.03e-29
ANXA2P2\|304	1.241e-32	4.44e-29
UNC5CL\|222643	1.351e-32	4.44e-29
AHNAK2\|113146	1.722e-32	4.44e-29
SERPINA1\|5265	1.726e-32	4.44e-29
ERBB3\|2065	3.503e-32	7.88e-29
CYP2S1\|29785	5.002e-32	1e-28
KCNN4\|3783	4.634e-31	8.3e-28

Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 genes related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

Table S15. Basic characteristics of clinical feature: 'RADIATIONS_RADIATION_REGIMENINDICATION'


RADIATIONS_RADIATION_REGIMENINDICATION	Labels	N
	NO	14
	YES	485

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

List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S16. 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	697	3.948e-07	0.00193	0.8973
C6ORF162\|57150	6080	4.488e-07	0.00193	0.8954
HCFC1\|3054	719	4.903e-07	0.00193	0.8941
IPO4\|79711	736	5.789e-07	0.00193	0.8916
AP2A1\|160	751	6.698e-07	0.00193	0.8894
CUL7\|9820	762	7.45e-07	0.00193	0.8878
SMARCA4\|6597	763	7.522e-07	0.00193	0.8876
BAT3\|7917	788	9.566e-07	0.00215	0.8839
ENPP3\|5169	5862	2.022e-06	0.00348	0.8723
POM121C\|100101267	871	2.092e-06	0.00348	0.8717

Clinical variable #10: 'RADIATION_EXPOSURE'

No gene related to 'RADIATION_EXPOSURE'.

Table S17. Basic characteristics of clinical feature: 'RADIATION_EXPOSURE'


RADIATION_EXPOSURE	Labels	N
	NO	420
	YES	17

	Significant markers	N = 0

Clinical variable #11: 'EXTRATHYROIDAL_EXTENSION'

30 genes related to 'EXTRATHYROIDAL_EXTENSION'.

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


EXTRATHYROIDAL_EXTENSION	Labels	N
	MINIMAL (T3)	132
	MODERATE/ADVANCED (T4A)	18
	NONE	330
	VERY ADVANCED (T4B)	1

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

Table S19. Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

	kruskal_wallis_P	Q
SLC10A4\|201780	6.989e-15	1.26e-10
SLC25A42\|284439	2.149e-14	1.93e-10
SRPX2\|27286	1.451e-13	8.7e-10
FLRT1\|23769	3.814e-13	1.51e-09
FOXJ1\|2302	4.202e-13	1.51e-09
BAG3\|9531	6.367e-13	1.67e-09
FN1\|2335	6.485e-13	1.67e-09
BEGAIN\|57596	7.885e-13	1.77e-09
COL1A1\|1277	9.274e-13	1.85e-09
LOX\|4015	1.14e-12	1.92e-09

Clinical variable #12: 'COMPLETENESS_OF_RESECTION'

30 genes related to 'COMPLETENESS_OF_RESECTION'.

Table S20. Basic characteristics of clinical feature: 'COMPLETENESS_OF_RESECTION'


COMPLETENESS_OF_RESECTION	Labels	N
	R0	381
	R1	52
	R2	4
	RX	30

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

Table S21. Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

	kruskal_wallis_P	Q
SHOX2\|6474	2.069e-06	0.0323
APCDD1L\|164284	6.524e-06	0.0323
SLC10A4\|201780	7.023e-06	0.0323
LGR5\|8549	7.179e-06	0.0323
WNT2\|7472	9.154e-06	0.0329
RCBTB2\|1102	2.855e-05	0.0856
COL12A1\|1303	4.681e-05	0.0931
CA4\|762	4.745e-05	0.0931
COL5A1\|1289	4.988e-05	0.0931
CYP26A1\|1592	5.175e-05	0.0931

Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

Table S22. Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'


NUMBER_OF_LYMPH_NODES	Mean (SD)	3.67 (6.2)
	Significant markers	N = 30
	pos. correlated	18
	neg. correlated	12

List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S23. Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

	SpearmanCorr	corrP	Q
CBFB\|865	0.3703	7.4e-14	1.33e-09
PELI1\|57162	0.3602	3.82e-13	3.44e-09
FAM60A\|58516	0.3574	5.911e-13	3.55e-09
CREB5\|9586	0.3548	8.938e-13	3.71e-09
CLCNKA\|1187	-0.3543	1.031e-12	3.71e-09
FECH\|2235	-0.3463	3.326e-12	8.59e-09
TAGLN2\|8407	0.3463	3.341e-12	8.59e-09
GPR153\|387509	0.3429	5.609e-12	1.11e-08
WFS1\|7466	-0.3407	7.71e-12	1.11e-08
PI15\|51050	0.349	7.803e-12	1.11e-08

Clinical variable #14: 'MULTIFOCALITY'

30 genes related to 'MULTIFOCALITY'.

Table S24. Basic characteristics of clinical feature: 'MULTIFOCALITY'


MULTIFOCALITY	Labels	N
	MULTIFOCAL	225
	UNIFOCAL	264

	Significant markers	N = 30
	Higher in UNIFOCAL	30
	Higher in MULTIFOCAL	0

List of top 10 genes differentially expressed by 'MULTIFOCALITY'

Table S25. Get Full Table List of top 10 genes differentially expressed by 'MULTIFOCALITY'

	W(pos if higher in 'UNIFOCAL')	wilcoxontestP	Q	AUC
AVPI1\|60370	37125	1.868e-06	0.0336	0.625
SCD5\|79966	22942	1.432e-05	0.0839	0.6138
AMDHD2\|51005	36390	1.745e-05	0.0839	0.6126
A2BP1\|54715	18171.5	1.865e-05	0.0839	0.6185
CXCL3\|2921	32818	2.97e-05	0.103	0.6123
SLC35F1\|222553	23154	3.433e-05	0.103	0.6087
C18ORF1\|753	23413	5.425e-05	0.124	0.6058
TMTC1\|83857	23420	5.53e-05	0.124	0.6057
LZTR1\|8216	35935	6.251e-05	0.125	0.605
FAM169A\|26049	23539	7.633e-05	0.126	0.6037

Clinical variable #15: 'TUMOR_SIZE'

30 genes related to 'TUMOR_SIZE'.

Table S26. Basic characteristics of clinical feature: 'TUMOR_SIZE'


TUMOR_SIZE	Mean (SD)	2.99 (1.6)
	Significant markers	N = 30
	pos. correlated	3
	neg. correlated	27

List of top 10 genes differentially expressed by 'TUMOR_SIZE'

Table S27. Get Full Table List of top 10 genes significantly correlated to 'TUMOR_SIZE' by Spearman correlation test

	SpearmanCorr	corrP	Q
C3ORF32\|51066	-0.2775	2.509e-08	0.000451
ISLR2\|57611	-0.2607	1.185e-07	0.000834
ZC3H10\|84872	-0.2593	1.391e-07	0.000834
CXCL12\|6387	-0.2562	1.968e-07	0.000885
FOXI2\|399823	-0.2522	3.804e-07	0.00126
LRRC55\|219527	-0.2506	4.216e-07	0.00126
CLDN2\|9075	-0.2482	5.48e-07	0.00141
SLC14A1\|6563	-0.2429	8.525e-07	0.00173
GPR34\|2857	-0.2428	8.636e-07	0.00173
PI16\|221476	-0.2416	1.177e-06	0.00212

Clinical variable #16: 'RACE'

30 genes related to 'RACE'.

Table S28. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	1
	ASIAN	51
	BLACK OR AFRICAN AMERICAN	27
	WHITE	326

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'RACE'

Table S29. Get Full Table List of top 10 genes differentially expressed by 'RACE'

	kruskal_wallis_P	Q
XKR9\|389668	4.247e-12	7.64e-08
LRRC37A2\|474170	1.113e-10	1e-06
SEC1\|653677	4.703e-10	2.82e-06
RPS26\|6231	8.988e-10	4.04e-06
UTS2\|10911	1.167e-08	4.15e-05
ATAD3C\|219293	1.385e-08	4.15e-05
LRRC19\|64922	2.597e-08	6.67e-05
DDX11L2\|84771	3.813e-08	8.57e-05
MKX\|283078	5.425e-08	0.000108
TMX4\|56255	6.876e-08	0.000124

Clinical variable #17: 'ETHNICITY'

30 genes related to 'ETHNICITY'.

Table S30. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	38
	NOT HISPANIC OR LATINO	357

	Significant markers	N = 30
	Higher in NOT HISPANIC OR LATINO	30
	Higher in HISPANIC OR LATINO	0

List of top 10 genes differentially expressed by 'ETHNICITY'

Table S31. 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("3500", "9.298e-07")	c("3500", "9.298e-07")	0.00678	0.742
ZFP36L1\|677	c("3513", "1.026e-06")	c("3513", "1.026e-06")	0.00678	0.741
ATG12\|9140	c("3545", "1.307e-06")	c("3545", "1.307e-06")	0.00678	0.7387
TEC\|7006	c("3564", "1.507e-06")	c("3564", "1.507e-06")	0.00678	0.7373
MCF2L2\|23101	c("3650", "3.074e-06")	c("3650", "3.074e-06")	0.00858	0.7302
CHRNA10\|57053	c("9894", "3.338e-06")	c("9894", "3.338e-06")	0.00858	0.7293
RIMBP3\|85376	c("9894", "3.338e-06")	c("9894", "3.338e-06")	0.00858	0.7293
SLC19A2\|10560	c("3733", "5.172e-06")	c("3733", "5.172e-06")	0.0103	0.7248
SNW1\|22938	c("3733", "5.172e-06")	c("3733", "5.172e-06")	0.0103	0.7248
FAM45A\|404636	c("3767", "6.579e-06")	c("3767", "6.579e-06")	0.0118	0.7223

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 = 499
Number of genes = 17991
Number of clinical features = 17

Selected clinical features

For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .
Survival time data

Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.

if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

if 'vital_status'==0(alive),

if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

if 'vital_status'==NA,excludes this case in survival analysis and report the case.

cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .

This analysis excluded clinical variables that has only NA values.

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

Wilcoxon rank sum test (Mann-Whitney U test)

For two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.

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] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)

[4] 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)

Made with Nozzle