Correlation between mRNAseq expression and clinical features

Cervical Squamous Cell Carcinoma and Endocervical 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/C14B309X

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 18187 genes and 45 clinical features across 301 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 28 clinical features related to at least one genes.

30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

C1ORF59|113802 , TM2D1|83941 , RIBC2|26150 , GATS|352954 , RAD9B|144715 , ...

30 genes correlated to 'YEARS_TO_BIRTH'.

NXNL2|158046 , RHOF|54509 , LANCL1|10314 , CORO6|84940 , PGR|5241 , ...

30 genes correlated to 'PATHOLOGY_T_STAGE'.

FBXL18|80028 , CYB561D1|284613 , TRIM25|7706 , ZC3HAV1|56829 , PPFIA4|8497 , ...

1 gene correlated to 'PATHOLOGY_M_STAGE'.

ZFAND6|54469

30 genes correlated to 'HISTOLOGICAL_TYPE'.

EPCAM|4072 , TP63|8626 , DDAH1|23576 , C3ORF54|389119 , BICD2|23299 , ...

14 genes correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

?|390284 , LOC644936|644936 , TSC2|7249 , HEATR7A|727957 , GBA2|57704 , ...

30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

A2ML1|144568 , KLRG2|346689 , CD99L2|83692 , TMPRSS3|64699 , SERPINB12|89777 , ...

6 genes correlated to 'RACE'.

XKR9|389668 , LOC90784|90784 , RNF112|7732 , POM121L10P|646074 , DLX3|1747 , ...

30 genes correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.

BLOC1S1|2647 , NUBP1|4682 , IL17RA|23765 , TTPAL|79183 , SERINC3|10955 , ...

6 genes correlated to 'TUMOR_STATUS'.

MPND|84954 , SEMA5B|54437 , PCDHB17|54661 , SOCS5|9655 , FPGS|2356 , ...

30 genes correlated to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

TRIM25|7706 , ?|390284 , ZBTB3|79842 , RGS1|5996 , HNRNPA3P1|10151 , ...

30 genes correlated to 'NEOPLASM_HISTOLOGIC_GRADE'.

ABLIM1|3983 , FUT2|2524 , FUT6|2528 , WDR70|55100 , CDS1|1040 , ...

2 genes correlated to 'TOBACCO_SMOKING_YEAR_STOPPED'.

LAPTM4B|55353 , PRB3|5544

12 genes correlated to 'TOBACCO_SMOKING_HISTORY'.

GPR15|2838 , LRRC8A|56262 , METTL7B|196410 , AHRR|57491 , KIAA1045|23349 , ...

1 gene correlated to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

GAD1|2571

30 genes correlated to 'RADIATION_THERAPY_TYPE'.

?|390284 , JRK|8629 , RPL23P8|222901 , PIPSL|266971 , LOC644936|644936 , ...

1 gene correlated to 'RADIATION_THERAPY_SITE'.

CYB561D1|284613

30 genes correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

ENPP3|5169 , POU2F1|5451 , RPL19P12|100129424 , FLJ44635|392490 , SDCBP|6386 , ...

30 genes correlated to 'MENOPAUSE_STATUS'.

RIMBP3|85376 , RIMBP3C|150221 , RARB|5915 , PHGDH|26227 , C1ORF52|148423 , ...

9 genes correlated to 'LYMPHOVASCULAR_INVOLVEMENT'.

TBCE|6905 , EXOG|9941 , LOC255167|255167 , LIMD1|8994 , SUSD4|55061 , ...

30 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

A2ML1|144568 , KLRG2|346689 , CD99L2|83692 , TMPRSS3|64699 , SERPINB12|89777 , ...

30 genes correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

QKI|9444 , SYT17|51760 , MAP7D3|79649 , SPG7|6687 , FRAT2|23401 , ...

30 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

?|390284 , RPPH1|85495 , SNAPC5|10302 , C19ORF33|64073 , C9ORF171|389799 , ...

30 genes correlated to 'HEIGHT_CM_AT_DIAGNOSIS'.

RRAD|6236 , FOSB|2354 , C19ORF33|64073 , ZNF107|51427 , ?|390284 , ...

1 gene correlated to 'CERVIX_SUV_RESULTS'.

HDHD1A|8226

30 genes correlated to 'AJCC_TUMOR_PATHOLOGIC_PT'.

FBXL18|80028 , TRIM25|7706 , ZC3HAV1|56829 , CYB561D1|284613 , TNFRSF10D|8793 , ...

30 genes correlated to 'AGE_AT_DIAGNOSIS'.

NXNL2|158046 , PGR|5241 , RHOF|54509 , CORO6|84940 , GPR97|222487 , ...

30 genes correlated to 'STAGE_EVENT.CLINICAL_STAGE'.

TRIM25|7706 , FBXL18|80028 , RGS1|5996 , ZC3HAV1|56829 , PPFIA4|8497 , ...

No genes correlated to 'PATHOLOGY_N_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'ETHNICITY', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'RADIATION_TOTAL_DOSE', 'RADIATION_THERAPY_STATUS', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'CORPUS_INVOLVEMENT', and 'CHEMO_CONCURRENT_TYPE'.

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=30	shorter survival	N=12	longer survival	N=18
YEARS_TO_BIRTH	Spearman correlation test	N=30	older	N=12	younger	N=18
PATHOLOGY_T_STAGE	Spearman correlation test	N=30	higher stage	N=17	lower stage	N=13
PATHOLOGY_N_STAGE	Wilcoxon test	N=0
PATHOLOGY_M_STAGE	Wilcoxon test	N=1	class1	N=1	class0	N=0
HISTOLOGICAL_TYPE	Kruskal-Wallis test	N=30
RADIATIONS_RADIATION_REGIMENINDICATION	Wilcoxon test	N=14	yes	N=14	no	N=0
NUMBER_PACK_YEARS_SMOKED	Spearman correlation test	N=0
NUMBER_OF_LYMPH_NODES	Spearman correlation test	N=30	higher number_of_lymph_nodes	N=20	lower number_of_lymph_nodes	N=10
RACE	Kruskal-Wallis test	N=6
ETHNICITY	Wilcoxon test	N=0
WEIGHT_KG_AT_DIAGNOSIS	Spearman correlation test	N=30	higher weight_kg_at_diagnosis	N=23	lower weight_kg_at_diagnosis	N=7
TUMOR_STATUS	Wilcoxon test	N=6	with tumor	N=6	tumor free	N=0
TUMOR_SAMPLE_PROCUREMENT_COUNTRY	Kruskal-Wallis test	N=30
NEOPLASM_HISTOLOGIC_GRADE	Kruskal-Wallis test	N=30
TOBACCO_SMOKING_YEAR_STOPPED	Spearman correlation test	N=2	higher tobacco_smoking_year_stopped	N=1	lower tobacco_smoking_year_stopped	N=1
TOBACCO_SMOKING_PACK_YEARS_SMOKED	Spearman correlation test	N=0
TOBACCO_SMOKING_HISTORY	Kruskal-Wallis test	N=12
PATIENT AGEBEGANSMOKINGINYEARS	Spearman correlation test	N=1	higher patient.agebegansmokinginyears	N=1	lower patient.agebegansmokinginyears	N=0
RADIATION_TOTAL_DOSE	Spearman correlation test	N=0
RADIATION_THERAPY_TYPE	Kruskal-Wallis test	N=30
RADIATION_THERAPY_STATUS	Wilcoxon test	N=0
RADIATION_THERAPY_SITE	Kruskal-Wallis test	N=1
RADIATION_ADJUVANT_UNITS	Wilcoxon test	N=0
PREGNANCIES_COUNT_TOTAL	Spearman correlation test	N=0
PREGNANCIES_COUNT_STILLBIRTH	Spearman correlation test	N=0
PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT	Spearman correlation test	N=0
PREGNANCIES_COUNT_LIVE_BIRTH	Spearman correlation test	N=30	higher pregnancies_count_live_birth	N=5	lower pregnancies_count_live_birth	N=25
PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT	Spearman correlation test	N=0
PREGNANCIES_COUNT_ECTOPIC	Spearman correlation test	N=0
POS_LYMPH_NODE_LOCATION	Kruskal-Wallis test	N=0
MENOPAUSE_STATUS	Kruskal-Wallis test	N=30
LYMPHOVASCULAR_INVOLVEMENT	Wilcoxon test	N=9	present	N=9	absent	N=0
LYMPH_NODES_EXAMINED_HE_COUNT	Spearman correlation test	N=30	higher lymph_nodes_examined_he_count	N=20	lower lymph_nodes_examined_he_count	N=10
LYMPH_NODES_EXAMINED	Spearman correlation test	N=0
KERATINIZATION_SQUAMOUS_CELL	Wilcoxon test	N=30	non-keratinizing squamous cell carcinoma	N=30	keratinizing squamous cell carcinoma	N=0
INITIAL_PATHOLOGIC_DX_YEAR	Spearman correlation test	N=30	higher initial_pathologic_dx_year	N=9	lower initial_pathologic_dx_year	N=21
HISTORY_HORMONAL_CONTRACEPTIVES_USE	Kruskal-Wallis test	N=0
HEIGHT_CM_AT_DIAGNOSIS	Spearman correlation test	N=30	higher height_cm_at_diagnosis	N=20	lower height_cm_at_diagnosis	N=10
CORPUS_INVOLVEMENT	Wilcoxon test	N=0
CHEMO_CONCURRENT_TYPE	Kruskal-Wallis test	N=0
CERVIX_SUV_RESULTS	Spearman correlation test	N=1	higher cervix_suv_results	N=1	lower cervix_suv_results	N=0
AJCC_TUMOR_PATHOLOGIC_PT	Kruskal-Wallis test	N=30
AGE_AT_DIAGNOSIS	Spearman correlation test	N=30	higher age_at_diagnosis	N=13	lower age_at_diagnosis	N=17
STAGE_EVENT CLINICAL_STAGE	Kruskal-Wallis test	N=30

Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 genes 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)	0-210.7 (median=20.2)
	censored	N = 231
	death	N = 69

	Significant markers	N = 30
	associated with shorter survival	12
	associated with longer survival	18

List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2. Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test

	HazardRatio	Wald_P	Q	C_index
C1ORF59\|113802	0.54	6.073e-09	0.00011	0.328
TM2D1\|83941	2	5.23e-08	0.00034	0.607
RIBC2\|26150	0.72	5.547e-08	0.00034	0.306
GATS\|352954	0.56	9.188e-08	0.00042	0.311
RAD9B\|144715	0.44	3.754e-07	0.0014	0.308
EGLN1\|54583	2.4	1.842e-06	0.0046	0.673
ZER1\|10444	0.22	2.067e-06	0.0046	0.34
EAF2\|55840	0.58	2.941e-06	0.0046	0.323
SPRY4\|81848	1.55	3.16e-06	0.0046	0.66
TREX1\|11277	0.51	3.32e-06	0.0046	0.309

Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

Table S3. Basic characteristics of clinical feature: 'YEARS_TO_BIRTH'


YEARS_TO_BIRTH	Mean (SD)	48.07 (14)
	Significant markers	N = 30
	pos. correlated	12
	neg. correlated	18

List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S4. Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

	SpearmanCorr	corrP	Q
NXNL2\|158046	-0.3802	6.882e-11	1.25e-06
RHOF\|54509	-0.3182	2.057e-08	0.000108
LANCL1\|10314	0.3177	2.178e-08	0.000108
CORO6\|84940	-0.3169	2.378e-08	0.000108
PGR\|5241	-0.3099	5.23e-08	0.00019
GALNT11\|63917	0.305	8.173e-08	0.00022
RARB\|5915	0.3047	8.485e-08	0.00022
CSF3\|1440	-0.3071	1.046e-07	0.000224
IL24\|11009	-0.3055	1.108e-07	0.000224
GPR97\|222487	-0.2999	1.378e-07	0.000251

Clinical variable #3: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S5. Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'


PATHOLOGY_T_STAGE	Mean (SD)	1.58 (0.82)
		N
	T1	139
	T2	69
	T3	20
	T4	10

	Significant markers	N = 30
	pos. correlated	17
	neg. correlated	13

List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S6. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
FBXL18\|80028	0.377	1.88e-09	3.42e-05
CYB561D1\|284613	0.3631	7.932e-09	7.21e-05
TRIM25\|7706	0.3538	1.997e-08	0.000121
ZC3HAV1\|56829	0.3466	4.01e-08	0.000182
PPFIA4\|8497	0.342	6.218e-08	0.000226
TMEM220\|388335	-0.3393	8.015e-08	0.000243
CCNF\|899	0.3155	6.722e-07	0.00175
ZNF487\|642819	-0.3137	8.725e-07	0.00198
PPIG\|9360	-0.3076	1.308e-06	0.00232
TBC1D15\|64786	-0.307	1.378e-06	0.00232

Clinical variable #4: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

Table S7. Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'


PATHOLOGY_N_STAGE	Labels	N
	N0	131
	N1	59

	Significant markers	N = 0

Clinical variable #5: 'PATHOLOGY_M_STAGE'

One gene related to 'PATHOLOGY_M_STAGE'.

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


PATHOLOGY_M_STAGE	Labels	N
	class0	115
	class1	10

	Significant markers	N = 1
	Higher in class1	1
	Higher in class0	0

List of one gene differentially expressed by 'PATHOLOGY_M_STAGE'

Table S9. Get Full Table List of one gene differentially expressed by 'PATHOLOGY_M_STAGE'

	W(pos if higher in 'class1')	wilcoxontestP	Q	AUC
ZFAND6\|54469	94	1.227e-05	0.223	0.9183

Clinical variable #6: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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


HISTOLOGICAL_TYPE	Labels	N
	ADENOSQUAMOUS	4
	CERVICAL SQUAMOUS CELL CARCINOMA	251
	ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE	6
	ENDOCERVICAL TYPE OF ADENOCARCINOMA	22
	ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX	3
	MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE	15

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S11. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

	kruskal_wallis_P	Q
EPCAM\|4072	2.833e-22	3.68e-18
TP63\|8626	4.049e-22	3.68e-18
DDAH1\|23576	7.435e-22	4.51e-18
C3ORF54\|389119	1.147e-21	5.07e-18
BICD2\|23299	1.555e-21	5.07e-18
GM2A\|2760	1.672e-21	5.07e-18
CLDN3\|1365	2.136e-21	5.55e-18
CLCA2\|9635	3.579e-21	8.14e-18
CSTA\|1475	7.929e-21	1.57e-17
KRT6A\|3853	8.656e-21	1.57e-17

Clinical variable #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

14 genes related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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


RADIATIONS_RADIATION_REGIMENINDICATION	Labels	N
	NO	35
	YES	266

	Significant markers	N = 14
	Higher in YES	14
	Higher in NO	0

List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S13. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

	W(pos if higher in 'YES')	wilcoxontestP	Q	AUC
?\|390284	2226	7.719e-07	0.014	0.7573
LOC644936\|644936	2400	3.199e-06	0.0291	0.7422
TSC2\|7249	6785	1.086e-05	0.0658	0.7288
HEATR7A\|727957	6716	2.074e-05	0.0943	0.7214
GBA2\|57704	6680	2.884e-05	0.105	0.7175
LOC341056\|341056	2652	3.519e-05	0.107	0.7151
RPL23P8\|222901	2672	4.209e-05	0.109	0.713
ZFYVE27\|118813	6582	6.892e-05	0.15	0.707
RXFP4\|339403	3444.5	7.401e-05	0.15	0.7374
ALDOB\|229	4824	9.314e-05	0.169	0.7171

Clinical variable #8: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S14. Basic characteristics of clinical feature: 'NUMBER_PACK_YEARS_SMOKED'


NUMBER_PACK_YEARS_SMOKED	Mean (SD)	17.38 (14)
	Significant markers	N = 0

Clinical variable #9: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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


NUMBER_OF_LYMPH_NODES	Mean (SD)	1.05 (2.4)
	Significant markers	N = 30
	pos. correlated	20
	neg. correlated	10

List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S16. Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

	SpearmanCorr	corrP	Q
A2ML1\|144568	0.3287	2.963e-05	0.121
KLRG2\|346689	0.3257	3.55e-05	0.121
CD99L2\|83692	-0.323	3.698e-05	0.121
TMPRSS3\|64699	-0.3205	4.281e-05	0.121
SERPINB12\|89777	0.3899	4.668e-05	0.121
APC2\|10297	0.317	5.518e-05	0.121
METTL8\|79828	0.3156	5.664e-05	0.121
NCAM2\|4685	0.3342	5.793e-05	0.121
FLJ35390\|255031	0.3126	6.74e-05	0.121
PHC2\|1912	-0.3108	7.43e-05	0.121

Clinical variable #10: 'RACE'

6 genes related to 'RACE'.

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


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	7
	ASIAN	19
	BLACK OR AFRICAN AMERICAN	30
	NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER	2
	WHITE	208

	Significant markers	N = 6

List of 6 genes differentially expressed by 'RACE'

Table S18. Get Full Table List of 6 genes differentially expressed by 'RACE'

	kruskal_wallis_P	Q
XKR9\|389668	1.517e-06	0.0254
LOC90784\|90784	2.79e-06	0.0254
RNF112\|7732	1.713e-05	0.104
POM121L10P\|646074	2.437e-05	0.111
DLX3\|1747	3.359e-05	0.122
RPS26\|6231	7.036e-05	0.213

Clinical variable #11: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S19. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	24
	NOT HISPANIC OR LATINO	167

	Significant markers	N = 0

Clinical variable #12: 'WEIGHT_KG_AT_DIAGNOSIS'

30 genes related to 'WEIGHT_KG_AT_DIAGNOSIS'.

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


WEIGHT_KG_AT_DIAGNOSIS	Mean (SD)	73.08 (21)
	Significant markers	N = 30
	pos. correlated	23
	neg. correlated	7

List of top 10 genes differentially expressed by 'WEIGHT_KG_AT_DIAGNOSIS'

Table S21. Get Full Table List of top 10 genes significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test

	SpearmanCorr	corrP	Q
BLOC1S1\|2647	0.3135	1.228e-07	0.00223
NUBP1\|4682	0.2915	9.501e-07	0.00827
IL17RA\|23765	-0.2875	1.364e-06	0.00827
TTPAL\|79183	-0.2802	2.561e-06	0.00903
SERINC3\|10955	-0.2778	3.139e-06	0.00903
ZRSR2\|8233	0.2768	3.418e-06	0.00903
GNRHR2\|114814	0.2766	3.475e-06	0.00903
IK\|3550	0.2732	4.614e-06	0.0105
NCKAP1\|10787	-0.2687	6.718e-06	0.0136
PIN4\|5303	0.2664	8.116e-06	0.0148

Clinical variable #13: 'TUMOR_STATUS'

6 genes related to 'TUMOR_STATUS'.

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


TUMOR_STATUS	Labels	N
	TUMOR FREE	137
	WITH TUMOR	44

	Significant markers	N = 6
	Higher in WITH TUMOR	6
	Higher in TUMOR FREE	0

List of 6 genes differentially expressed by 'TUMOR_STATUS'

Table S23. Get Full Table List of 6 genes differentially expressed by 'TUMOR_STATUS'

	W(pos if higher in 'WITH TUMOR')	wilcoxontestP	Q	AUC
MPND\|84954	1733	2.286e-05	0.212	0.7125
SEMA5B\|54437	4221	4.33e-05	0.212	0.7054
PCDHB17\|54661	2980	4.476e-05	0.212	0.7261
SOCS5\|9655	4243	4.845e-05	0.212	0.7039
FPGS\|2356	1803	6.243e-05	0.212	0.7009
SMEK2\|57223	4217	6.98e-05	0.212	0.6996

Clinical variable #14: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

30 genes related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.

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


TUMOR_SAMPLE_PROCUREMENT_COUNTRY	Labels	N
	BRAZIL	53
	CANADA	5
	NIGERIA	1
	RUSSIA	12
	UKRAINE	7
	UNITED STATES	209
	VIETNAM	14

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'

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

	kruskal_wallis_P	Q
TRIM25\|7706	2.757e-11	5.01e-07
?\|390284	1.367e-10	1.24e-06
ZBTB3\|79842	5.585e-10	2.82e-06
RGS1\|5996	7.043e-10	2.82e-06
HNRNPA3P1\|10151	7.744e-10	2.82e-06
CYB561D1\|284613	1.405e-09	4.26e-06
FLJ44635\|392490	3.314e-09	8.61e-06
ANXA2P3\|305	4.371e-09	9.94e-06
RAB6C\|84084	5.612e-09	1.13e-05
RPL19P12\|100129424	7.67e-09	1.31e-05

Clinical variable #15: 'NEOPLASM_HISTOLOGIC_GRADE'

30 genes related to 'NEOPLASM_HISTOLOGIC_GRADE'.

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


NEOPLASM_HISTOLOGIC_GRADE	Labels	N
	G1	18
	G2	135
	G3	116
	G4	1
	GX	24

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

Table S27. Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'

	kruskal_wallis_P	Q
ABLIM1\|3983	3.895e-07	0.00708
FUT2\|2524	1.038e-06	0.00734
FUT6\|2528	1.211e-06	0.00734
WDR70\|55100	4.222e-06	0.0192
CDS1\|1040	6.407e-06	0.0198
ARHGEF37\|389337	6.943e-06	0.0198
CLINT1\|9685	7.637e-06	0.0198
FAHD2B\|151313	1.732e-05	0.0353
SOHLH2\|54937	1.749e-05	0.0353
SCARNA2\|677766	2.263e-05	0.0412

Clinical variable #16: 'TOBACCO_SMOKING_YEAR_STOPPED'

2 genes related to 'TOBACCO_SMOKING_YEAR_STOPPED'.

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


TOBACCO_SMOKING_YEAR_STOPPED	Mean (SD)	1999.69 (14)
	Significant markers	N = 2
	pos. correlated	1
	neg. correlated	1

List of 2 genes differentially expressed by 'TOBACCO_SMOKING_YEAR_STOPPED'

Table S29. Get Full Table List of 2 genes significantly correlated to 'TOBACCO_SMOKING_YEAR_STOPPED' by Spearman correlation test

	SpearmanCorr	corrP	Q
LAPTM4B\|55353	0.6149	1.475e-05	0.139
PRB3\|5544	-0.773	1.529e-05	0.139

Clinical variable #17: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'

No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.

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


TOBACCO_SMOKING_PACK_YEARS_SMOKED	Mean (SD)	17.38 (14)
	Significant markers	N = 0

Clinical variable #18: 'TOBACCO_SMOKING_HISTORY'

12 genes related to 'TOBACCO_SMOKING_HISTORY'.

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


TOBACCO_SMOKING_HISTORY	Labels	N
	CURRENT REFORMED SMOKER FOR < OR = 15 YEARS	39
	CURRENT REFORMED SMOKER FOR > 15 YEARS	9
	CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED	4
	CURRENT SMOKER	64
	LIFELONG NON-SMOKER	143

	Significant markers	N = 12

List of top 10 genes differentially expressed by 'TOBACCO_SMOKING_HISTORY'

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

	kruskal_wallis_P	Q
GPR15\|2838	3.061e-10	5.57e-06
LRRC8A\|56262	5.453e-06	0.0496
METTL7B\|196410	5.591e-05	0.271
AHRR\|57491	5.957e-05	0.271
KIAA1045\|23349	7.813e-05	0.271
IL1RL1\|9173	9.418e-05	0.271
FRMD6\|122786	0.0001207	0.271
SLC6A12\|6539	0.0001274	0.271
SH3PXD2A\|9644	0.0001376	0.271
HSD3B7\|80270	0.0001488	0.271

Clinical variable #19: 'PATIENT.AGEBEGANSMOKINGINYEARS'

One gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.

Table S33. Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'


PATIENT.AGEBEGANSMOKINGINYEARS	Mean (SD)	21.14 (7.7)
	Significant markers	N = 1
	pos. correlated	1
	neg. correlated	0

List of one gene differentially expressed by 'PATIENT.AGEBEGANSMOKINGINYEARS'

Table S34. Get Full Table List of one gene significantly correlated to 'PATIENT.AGEBEGANSMOKINGINYEARS' by Spearman correlation test

	SpearmanCorr	corrP	Q
GAD1\|2571	0.469	5.977e-06	0.109

Clinical variable #20: 'RADIATION_TOTAL_DOSE'

No gene related to 'RADIATION_TOTAL_DOSE'.

Table S35. Basic characteristics of clinical feature: 'RADIATION_TOTAL_DOSE'


RADIATION_TOTAL_DOSE	Mean (SD)	3643.73 (1700)
	Significant markers	N = 0

Clinical variable #21: 'RADIATION_THERAPY_TYPE'

30 genes related to 'RADIATION_THERAPY_TYPE'.

Table S36. Basic characteristics of clinical feature: 'RADIATION_THERAPY_TYPE'


RADIATION_THERAPY_TYPE	Labels	N
	COMBINATION	20
	EXTERNAL	104
	EXTERNAL BEAM	15
	IMPLANTS	1
	INTERNAL	24

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

Table S37. Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY_TYPE'

	kruskal_wallis_P	Q
?\|390284	1.559e-07	0.00283
JRK\|8629	2.764e-06	0.0251
RPL23P8\|222901	6.589e-06	0.03
PIPSL\|266971	6.608e-06	0.03
LOC644936\|644936	1.266e-05	0.046
HEATR7A\|727957	2.215e-05	0.0671
TMEM120B\|144404	3.712e-05	0.0964
ERH\|2079	5.98e-05	0.122
TAS2R4\|50832	7.07e-05	0.122
LOC341056\|341056	7.373e-05	0.122

Clinical variable #22: 'RADIATION_THERAPY_STATUS'

No gene related to 'RADIATION_THERAPY_STATUS'.

Table S38. Basic characteristics of clinical feature: 'RADIATION_THERAPY_STATUS'


RADIATION_THERAPY_STATUS	Labels	N
	COMPLETED AS PLANNED	29
	TREATMENT NOT COMPLETED	3

	Significant markers	N = 0

Clinical variable #23: 'RADIATION_THERAPY_SITE'

One gene related to 'RADIATION_THERAPY_SITE'.

Table S39. Basic characteristics of clinical feature: 'RADIATION_THERAPY_SITE'


RADIATION_THERAPY_SITE	Labels	N
	DISTANT RECURRENCE	2
	LOCAL RECURRENCE	2
	PRIMARY TUMOR FIELD	38
	REGIONAL SITE	32

	Significant markers	N = 1

List of one gene differentially expressed by 'RADIATION_THERAPY_SITE'

Table S40. Get Full Table List of one gene differentially expressed by 'RADIATION_THERAPY_SITE'

	kruskal_wallis_P	Q
CYB561D1\|284613	8.065e-06	0.147

Clinical variable #24: 'RADIATION_ADJUVANT_UNITS'

No gene related to 'RADIATION_ADJUVANT_UNITS'.

Table S41. Basic characteristics of clinical feature: 'RADIATION_ADJUVANT_UNITS'


RADIATION_ADJUVANT_UNITS	Labels	N
	CGY	57
	GY	5

	Significant markers	N = 0

Clinical variable #25: 'PREGNANCIES_COUNT_TOTAL'

No gene related to 'PREGNANCIES_COUNT_TOTAL'.

Table S42. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'


PREGNANCIES_COUNT_TOTAL	Mean (SD)	3.65 (2.6)
	Significant markers	N = 0

Clinical variable #26: 'PREGNANCIES_COUNT_STILLBIRTH'

No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.

Table S43. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'


PREGNANCIES_COUNT_STILLBIRTH	Mean (SD)	0.07 (0.35)
	Value	N
	0	105
	1	5
	3	1

	Significant markers	N = 0

Clinical variable #27: 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'

No gene related to 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.

Table S44. Basic characteristics of clinical feature: 'PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'


PATIENT_PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT	Mean (SD)	0.55 (0.95)
	Significant markers	N = 0

Clinical variable #28: 'PREGNANCIES_COUNT_LIVE_BIRTH'

30 genes related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.

Table S45. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_LIVE_BIRTH'


PREGNANCIES_COUNT_LIVE_BIRTH	Mean (SD)	2.86 (2.1)
	Significant markers	N = 30
	pos. correlated	5
	neg. correlated	25

List of top 10 genes differentially expressed by 'PREGNANCIES_COUNT_LIVE_BIRTH'

Table S46. Get Full Table List of top 10 genes significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test

	SpearmanCorr	corrP	Q
ENPP3\|5169	-0.2727	3.384e-05	0.217
POU2F1\|5451	-0.2536	3.76e-05	0.217
RPL19P12\|100129424	-0.2494	5.105e-05	0.217
FLJ44635\|392490	-0.2479	5.67e-05	0.217
SDCBP\|6386	-0.2472	5.968e-05	0.217
FANCG\|2189	0.244	7.473e-05	0.227
FAM35B2\|439965	-0.2403	9.715e-05	0.24
ZBTB3\|79842	0.2372	0.0001196	0.24
HSP90B3P\|343477	-0.2362	0.0001286	0.24
CREM\|1390	-0.2327	0.0001624	0.24

Clinical variable #29: 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'

No gene related to 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.

Table S47. Basic characteristics of clinical feature: 'PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'


PATIENT_PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT	Mean (SD)	0.86 (1.8)
	Significant markers	N = 0

Clinical variable #30: 'PREGNANCIES_COUNT_ECTOPIC'

No gene related to 'PREGNANCIES_COUNT_ECTOPIC'.

Table S48. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'


PREGNANCIES_COUNT_ECTOPIC	Mean (SD)	0.11 (0.34)
	Value	N
	0	103
	1	11
	2	1

	Significant markers	N = 0

Clinical variable #31: 'POS_LYMPH_NODE_LOCATION'

No gene related to 'POS_LYMPH_NODE_LOCATION'.

Table S49. Basic characteristics of clinical feature: 'POS_LYMPH_NODE_LOCATION'


POS_LYMPH_NODE_LOCATION	Labels	N
	MACROSCOPIC PARAMETRIAL INVOLVEMENT	2
	MICROSCOPIC PARAMETRIAL INVOLVEMENT	8
	OTHER LOCATION, SPECIFY	39
	POSITIVE BLADDER MARGIN	1
	POSITIVE VAGINAL MARGIN	10

	Significant markers	N = 0

Clinical variable #32: 'MENOPAUSE_STATUS'

30 genes related to 'MENOPAUSE_STATUS'.

Table S50. Basic characteristics of clinical feature: 'MENOPAUSE_STATUS'


MENOPAUSE_STATUS	Labels	N
	INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)	2
	PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)	25
	POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)	81
	PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)	123

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

Table S51. Get Full Table List of top 10 genes differentially expressed by 'MENOPAUSE_STATUS'

	kruskal_wallis_P	Q
RIMBP3\|85376	4.318e-08	0.000785
RIMBP3C\|150221	1.196e-06	0.0109
RARB\|5915	2.301e-06	0.014
PHGDH\|26227	1.013e-05	0.0424
C1ORF52\|148423	1.166e-05	0.0424
DIO2\|1734	1.562e-05	0.0448
RPF1\|80135	1.726e-05	0.0448
SSBP3\|23648	3.232e-05	0.0548
GREB1\|9687	3.298e-05	0.0548
BCAS2\|10286	3.381e-05	0.0548

Clinical variable #33: 'LYMPHOVASCULAR_INVOLVEMENT'

9 genes related to 'LYMPHOVASCULAR_INVOLVEMENT'.

Table S52. Basic characteristics of clinical feature: 'LYMPHOVASCULAR_INVOLVEMENT'


LYMPHOVASCULAR_INVOLVEMENT	Labels	N
	ABSENT	70
	PRESENT	78

	Significant markers	N = 9
	Higher in PRESENT	9
	Higher in ABSENT	0

List of 9 genes differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

Table S53. Get Full Table List of 9 genes differentially expressed by 'LYMPHOVASCULAR_INVOLVEMENT'

	W(pos if higher in 'PRESENT')	wilcoxontestP	Q	AUC
TBCE\|6905	c("3848", "1.772e-05")	c("3848", "1.772e-05")	0.251	0.7048
EXOG\|9941	c("1638", "2.765e-05")	c("1638", "2.765e-05")	0.251	0.7
LOC255167\|255167	c("2837", "5.954e-05")	c("2837", "5.954e-05")	0.279	0.7071
LIMD1\|8994	c("1708", "8.738e-05")	c("1708", "8.738e-05")	0.279	0.6872
SUSD4\|55061	c("3741", "0.0001041")	c("3741", "0.0001041")	0.279	0.6852
COX8C\|341947	c("670", "0.0001182")	c("670", "0.0001182")	0.279	0.7976
C3ORF38\|285237	c("1731", "0.0001256")	c("1731", "0.0001256")	0.279	0.683
MRPL30\|51263	c("3725", "0.0001337")	c("3725", "0.0001337")	0.279	0.6822
PHLDB3\|653583	c("3723", "0.000138")	c("3723", "0.000138")	0.279	0.6819

Clinical variable #34: 'LYMPH_NODES_EXAMINED_HE_COUNT'

30 genes related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.

Table S54. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED_HE_COUNT'


LYMPH_NODES_EXAMINED_HE_COUNT	Mean (SD)	1.05 (2.4)
	Significant markers	N = 30
	pos. correlated	20
	neg. correlated	10

List of top 10 genes differentially expressed by 'LYMPH_NODES_EXAMINED_HE_COUNT'

Table S55. Get Full Table List of top 10 genes significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test

	SpearmanCorr	corrP	Q
A2ML1\|144568	0.3287	2.963e-05	0.121
KLRG2\|346689	0.3257	3.55e-05	0.121
CD99L2\|83692	-0.323	3.698e-05	0.121
TMPRSS3\|64699	-0.3205	4.281e-05	0.121
SERPINB12\|89777	0.3899	4.668e-05	0.121
APC2\|10297	0.317	5.518e-05	0.121
METTL8\|79828	0.3156	5.664e-05	0.121
NCAM2\|4685	0.3342	5.793e-05	0.121
FLJ35390\|255031	0.3126	6.74e-05	0.121
PHC2\|1912	-0.3108	7.43e-05	0.121

Clinical variable #35: 'LYMPH_NODES_EXAMINED'

No gene related to 'LYMPH_NODES_EXAMINED'.

Table S56. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'


LYMPH_NODES_EXAMINED	Mean (SD)	22.43 (13)
	Significant markers	N = 0

Clinical variable #36: 'KERATINIZATION_SQUAMOUS_CELL'

30 genes related to 'KERATINIZATION_SQUAMOUS_CELL'.

Table S57. Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'


KERATINIZATION_SQUAMOUS_CELL	Labels	N
	KERATINIZING SQUAMOUS CELL CARCINOMA	54
	NON-KERATINIZING SQUAMOUS CELL CARCINOMA	118

	Significant markers	N = 30
	Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA	30
	Higher in KERATINIZING SQUAMOUS CELL CARCINOMA	0

List of top 10 genes differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

Table S58. Get Full Table List of top 10 genes differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'

	W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA')	wilcoxontestP	Q	AUC
QKI\|9444	1767	2.867e-06	0.0521	0.7227
SYT17\|51760	4463	2.535e-05	0.18	0.7004
MAP7D3\|79649	1922	3.063e-05	0.18	0.6984
SPG7\|6687	4432	3.968e-05	0.18	0.6955
FRAT2\|23401	4394	6.777e-05	0.234	0.6896
C9ORF30\|91283	1993	8.337e-05	0.234	0.6872
SFXN2\|118980	4358	0.000111	0.234	0.6839
CAPS\|828	4355	0.0001156	0.234	0.6835
TAS2R4\|50832	3372	0.0001159	0.234	0.6951
BCL2L2\|599	2055	0.0001915	0.236	0.6775

Clinical variable #37: 'INITIAL_PATHOLOGIC_DX_YEAR'

30 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.

Table S59. Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'


INITIAL_PATHOLOGIC_DX_YEAR	Mean (SD)	2008.26 (4.8)
	Significant markers	N = 30
	pos. correlated	9
	neg. correlated	21

List of top 10 genes differentially expressed by 'INITIAL_PATHOLOGIC_DX_YEAR'

Table S60. Get Full Table List of top 10 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test

	SpearmanCorr	corrP	Q
?\|390284	-0.2865	5.603e-07	0.0102
RPPH1\|85495	-0.2518	1.048e-05	0.0869
SNAPC5\|10302	-0.248	1.434e-05	0.0869
C19ORF33\|64073	-0.2418	2.376e-05	0.108
C9ORF171\|389799	0.3285	4.871e-05	0.159
POM121L8P\|29797	0.2976	6.648e-05	0.159
RCL1\|10171	-0.2261	7.991e-05	0.159
RPL36A\|6173	-0.225	8.657e-05	0.159
FAM22G\|441457	0.2262	8.659e-05	0.159
RPL13AP6\|644511	-0.2249	8.769e-05	0.159

Clinical variable #38: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'

No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.

Table S61. Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'


HISTORY_HORMONAL_CONTRACEPTIVES_USE	Labels	N
	CURRENT USER	15
	FORMER USER	52
	NEVER USED	88

	Significant markers	N = 0

Clinical variable #39: 'HEIGHT_CM_AT_DIAGNOSIS'

30 genes related to 'HEIGHT_CM_AT_DIAGNOSIS'.

Table S62. Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'


HEIGHT_CM_AT_DIAGNOSIS	Mean (SD)	161.08 (7.1)
	Significant markers	N = 30
	pos. correlated	20
	neg. correlated	10

List of top 10 genes differentially expressed by 'HEIGHT_CM_AT_DIAGNOSIS'

Table S63. Get Full Table List of top 10 genes significantly correlated to 'HEIGHT_CM_AT_DIAGNOSIS' by Spearman correlation test

	SpearmanCorr	corrP	Q
RRAD\|6236	0.27	1.048e-05	0.0936
FOSB\|2354	0.2632	1.783e-05	0.0936
C19ORF33\|64073	0.2612	2.068e-05	0.0936
ZNF107\|51427	-0.2572	2.785e-05	0.0936
?\|390284	0.2578	2.878e-05	0.0936
DUSP1\|1843	0.2558	3.088e-05	0.0936
LOC541471\|541471	0.2523	3.999e-05	0.104
ANP32C\|23520	0.2516	5.342e-05	0.121
SPAG7\|9552	0.2447	6.881e-05	0.139
PLK3\|1263	0.2422	8.232e-05	0.15

Clinical variable #40: 'CORPUS_INVOLVEMENT'

No gene related to 'CORPUS_INVOLVEMENT'.

Table S64. Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'


CORPUS_INVOLVEMENT	Labels	N
	ABSENT	99
	PRESENT	18

	Significant markers	N = 0

Clinical variable #41: 'CHEMO_CONCURRENT_TYPE'

No gene related to 'CHEMO_CONCURRENT_TYPE'.

Table S65. Basic characteristics of clinical feature: 'CHEMO_CONCURRENT_TYPE'


CHEMO_CONCURRENT_TYPE	Labels	N
	CARBOPLATIN	3
	CISPLATIN	18
	OTHER	1

	Significant markers	N = 0

Clinical variable #42: 'CERVIX_SUV_RESULTS'

One gene related to 'CERVIX_SUV_RESULTS'.

Table S66. Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'


CERVIX_SUV_RESULTS	Mean (SD)	13.22 (7.2)
	Significant markers	N = 1
	pos. correlated	1
	neg. correlated	0

List of one gene differentially expressed by 'CERVIX_SUV_RESULTS'

Table S67. Get Full Table List of one gene significantly correlated to 'CERVIX_SUV_RESULTS' by Spearman correlation test

	SpearmanCorr	corrP	Q
HDHD1A\|8226	0.848	0	0

Clinical variable #43: 'AJCC_TUMOR_PATHOLOGIC_PT'

30 genes related to 'AJCC_TUMOR_PATHOLOGIC_PT'.

Table S68. Basic characteristics of clinical feature: 'AJCC_TUMOR_PATHOLOGIC_PT'


AJCC_TUMOR_PATHOLOGIC_PT	Labels	N
	T1A1	1
	T1B	36
	T1B1	71
	T1B2	31
	T2	6
	T2A	10
	T2A1	7
	T2A2	10
	T2B	36
	T3	1
	T3A	2
	T3B	17
	T4	10
	TIS	1
	TX	17

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

Table S69. Get Full Table List of top 10 genes differentially expressed by 'AJCC_TUMOR_PATHOLOGIC_PT'

	kruskal_wallis_P	Q
FBXL18\|80028	5.192e-11	9.44e-07
TRIM25\|7706	1.987e-07	0.00122
ZC3HAV1\|56829	2.012e-07	0.00122
CYB561D1\|284613	2.982e-07	0.00136
TNFRSF10D\|8793	2.801e-06	0.00912
PPFIA4\|8497	3.213e-06	0.00912
TSC22D3\|1831	3.51e-06	0.00912
FAM107A\|11170	4.729e-06	0.0106
UNC119B\|84747	5.267e-06	0.0106
FOXK1\|221937	6.509e-06	0.0111

Clinical variable #44: 'AGE_AT_DIAGNOSIS'

30 genes related to 'AGE_AT_DIAGNOSIS'.

Table S70. Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'


AGE_AT_DIAGNOSIS	Mean (SD)	48.17 (14)
	Significant markers	N = 30
	pos. correlated	13
	neg. correlated	17

List of top 10 genes differentially expressed by 'AGE_AT_DIAGNOSIS'

Table S71. Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test

	SpearmanCorr	corrP	Q
NXNL2\|158046	-0.3793	6.586e-11	1.2e-06
PGR\|5241	-0.3137	2.845e-08	0.000199
RHOF\|54509	-0.3118	3.279e-08	0.000199
CORO6\|84940	-0.3073	5.29e-08	0.000241
GPR97\|222487	-0.3037	7.651e-08	0.000256
LANCL1\|10314	0.3024	8.77e-08	0.000256
IL24\|11009	-0.3047	9.85e-08	0.000256
RRAGD\|58528	0.2984	1.32e-07	0.000267
CSF3\|1440	-0.3026	1.34e-07	0.000267
DIO2\|1734	-0.2972	1.486e-07	0.000267

Clinical variable #45: 'STAGE_EVENT.CLINICAL_STAGE'

30 genes related to 'STAGE_EVENT.CLINICAL_STAGE'.

Table S72. Basic characteristics of clinical feature: 'STAGE_EVENT.CLINICAL_STAGE'


STAGE_EVENT.CLINICAL_STAGE	Labels	N
	STAGE I	5
	STAGE IA	1
	STAGE IA1	1
	STAGE IA2	1
	STAGE IB	37
	STAGE IB1	77
	STAGE IB2	38
	STAGE II	5
	STAGE IIA	9
	STAGE IIA1	5
	STAGE IIA2	7
	STAGE IIB	42
	STAGE III	1
	STAGE IIIA	2
	STAGE IIIB	42
	STAGE IVA	9
	STAGE IVB	12

	Significant markers	N = 30

List of top 10 genes differentially expressed by 'STAGE_EVENT.CLINICAL_STAGE'

Table S73. Get Full Table List of top 10 genes differentially expressed by 'STAGE_EVENT.CLINICAL_STAGE'

	kruskal_wallis_P	Q
TRIM25\|7706	1.851e-09	3.37e-05
FBXL18\|80028	3.576e-08	0.000325
RGS1\|5996	8.081e-08	0.000405
ZC3HAV1\|56829	8.911e-08	0.000405
PPFIA4\|8497	7.679e-07	0.00279
ZBTB3\|79842	3.207e-06	0.00972
CYB561D1\|284613	4.742e-06	0.0123
DNAJC5\|80331	1.868e-05	0.0425
LRRC70\|100130733	2.28e-05	0.0461
TSC22D3\|1831	3.124e-05	0.0568

Methods & Data

Input

Expresson data file = CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Clinical data file = CESC-TP.merged_data.txt
Number of patients = 301
Number of genes = 18187
Number of clinical features = 45

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