This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features. The input file " CESC-TP.miRseq_RPKM_log2.txt " is generated in the pipeline miRseq_Preprocess in the stddata run.
Testing the association between 543 miRs and 39 clinical features across 307 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 20 clinical features related to at least one miRs.
-
17 miRs correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
-
HSA-MIR-532 , HSA-MIR-502 , HSA-MIR-101-1 , HSA-MIR-378C , HSA-MIR-150 , ...
-
30 miRs correlated to 'YEARS_TO_BIRTH'.
-
HSA-MIR-424 , HSA-MIR-455 , HSA-MIR-1468 , HSA-MIR-450A-2 , HSA-MIR-31 , ...
-
30 miRs correlated to 'PATHOLOGY_T_STAGE'.
-
HSA-MIR-144 , HSA-MIR-424 , HSA-MIR-486 , HSA-MIR-451 , HSA-MIR-185 , ...
-
12 miRs correlated to 'RADIATION_THERAPY'.
-
HSA-MIR-3917 , HSA-MIR-374A , HSA-MIR-185 , HSA-MIR-500A , HSA-MIR-7-1 , ...
-
30 miRs correlated to 'HISTOLOGICAL_TYPE'.
-
HSA-MIR-205 , HSA-MIR-944 , HSA-MIR-375 , HSA-MIR-194-2 , HSA-MIR-10A , ...
-
5 miRs correlated to 'RACE'.
-
HSA-MIR-24-2 , HSA-MIR-3130-1 , HSA-MIR-2355 , HSA-MIR-454 , HSA-MIR-185
-
30 miRs correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.
-
HSA-MIR-592 , HSA-MIR-548B , HSA-MIR-3130-1 , HSA-MIR-3690 , HSA-MIR-223 , ...
-
15 miRs correlated to 'TUMOR_STATUS'.
-
HSA-MIR-150 , HSA-MIR-378C , HSA-MIR-155 , HSA-MIR-361 , HSA-MIR-451 , ...
-
30 miRs correlated to 'NEOPLASM_HISTOLOGIC_GRADE'.
-
HSA-MIR-486 , HSA-MIR-421 , HSA-MIR-185 , HSA-MIR-144 , HSA-MIR-23B , ...
-
15 miRs correlated to 'TOBACCO_SMOKING_HISTORY'.
-
HSA-MIR-33A , HSA-MIR-4326 , HSA-MIR-27B , HSA-MIR-146B , HSA-MIR-1274B , ...
-
30 miRs correlated to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.
-
HSA-MIR-185 , HSA-MIR-340 , HSA-MIR-758 , HSA-MIR-216A , HSA-MIR-146B , ...
-
3 miRs correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
-
HSA-MIR-1287 , HSA-MIR-19A , HSA-MIR-212
-
1 miR correlated to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.
-
HSA-MIR-26B
-
20 miRs correlated to 'MENOPAUSE_STATUS'.
-
HSA-MIR-424 , HSA-MIR-1468 , HSA-MIR-503 , HSA-MIR-125B-2 , HSA-MIR-1274B , ...
-
22 miRs correlated to 'KERATINIZATION_SQUAMOUS_CELL'.
-
HSA-MIR-152 , HSA-MIR-27A , HSA-MIR-23C , HSA-MIR-191 , HSA-MIR-23A , ...
-
30 miRs correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.
-
HSA-MIR-1274B , HSA-MIR-19A , HSA-MIR-212 , HSA-MIR-660 , HSA-MIR-326 , ...
-
2 miRs correlated to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.
-
HSA-MIR-338 , HSA-MIR-26B
-
13 miRs correlated to 'HEIGHT_CM_AT_DIAGNOSIS'.
-
HSA-MIR-320B-2 , HSA-MIR-320E , HSA-MIR-320D-1 , HSA-MIR-3130-1 , HSA-MIR-548Q , ...
-
30 miRs correlated to 'AGE_AT_DIAGNOSIS'.
-
HSA-MIR-424 , HSA-MIR-455 , HSA-MIR-1468 , HSA-MIR-450A-2 , HSA-MIR-503 , ...
-
12 miRs correlated to 'CLINICAL_STAGE'.
-
HSA-MIR-144 , HSA-MIR-451 , HSA-MIR-486 , HSA-MIR-218-2 , HSA-MIR-185 , ...
-
No miRs correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'NUMBER_OF_LYMPH_NODES', 'ETHNICITY', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_STATUS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED_HE_COUNT', 'LYMPH_NODES_EXAMINED', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', and 'CERVIX_SUV_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 miRs that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant miRs | Associated with | Associated with | ||
---|---|---|---|---|---|---|
DAYS_TO_DEATH_OR_LAST_FUP | Cox regression test | N=17 | N=NA | N=NA | ||
YEARS_TO_BIRTH | Spearman correlation test | N=30 | older | N=14 | younger | N=16 |
PATHOLOGY_T_STAGE | Spearman correlation test | N=30 | higher stage | N=10 | lower stage | N=20 |
PATHOLOGY_N_STAGE | Wilcoxon test | N=0 | ||||
PATHOLOGY_M_STAGE | Wilcoxon test | N=0 | ||||
RADIATION_THERAPY | Wilcoxon test | N=12 | yes | N=12 | no | N=0 |
HISTOLOGICAL_TYPE | Kruskal-Wallis test | N=30 | ||||
NUMBER_PACK_YEARS_SMOKED | Spearman correlation test | N=0 | ||||
NUMBER_OF_LYMPH_NODES | Spearman correlation test | N=0 | ||||
RACE | Kruskal-Wallis test | N=5 | ||||
ETHNICITY | Wilcoxon test | N=0 | ||||
WEIGHT_KG_AT_DIAGNOSIS | Spearman correlation test | N=30 | higher weight_kg_at_diagnosis | N=24 | lower weight_kg_at_diagnosis | N=6 |
TUMOR_STATUS | Wilcoxon test | N=15 | with tumor | N=15 | tumor free | N=0 |
NEOPLASM_HISTOLOGIC_GRADE | Kruskal-Wallis test | N=30 | ||||
TOBACCO_SMOKING_YEAR_STOPPED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_HISTORY | Spearman correlation test | N=15 | higher tobacco_smoking_history | N=10 | lower tobacco_smoking_history | N=5 |
AGEBEGANSMOKINGINYEARS | Spearman correlation test | N=0 | ||||
RADIATION_THERAPY_STATUS | Wilcoxon test | N=0 | ||||
PREGNANCIES_COUNT_TOTAL | Spearman correlation test | N=0 | ||||
PREGNANCIES_COUNT_STILLBIRTH | Spearman correlation test | N=0 | ||||
PREGNANCY_SPONTANEOUS_ABORTION_COUNT | Spearman correlation test | N=30 | higher pregnancy_spontaneous_abortion_count | N=12 | lower pregnancy_spontaneous_abortion_count | N=18 |
PREGNANCIES_COUNT_LIVE_BIRTH | Spearman correlation test | N=3 | higher pregnancies_count_live_birth | N=1 | lower pregnancies_count_live_birth | N=2 |
PREGNANCY_THERAPEUTIC_ABORTION_COUNT | Spearman correlation test | N=1 | higher pregnancy_therapeutic_abortion_count | N=0 | lower pregnancy_therapeutic_abortion_count | N=1 |
PREGNANCIES_COUNT_ECTOPIC | Spearman correlation test | N=0 | ||||
POS_LYMPH_NODE_LOCATION | Kruskal-Wallis test | N=0 | ||||
MENOPAUSE_STATUS | Kruskal-Wallis test | N=20 | ||||
LYMPHOVASCULAR_INVOLVEMENT | Wilcoxon test | N=0 | ||||
LYMPH_NODES_EXAMINED_HE_COUNT | Spearman correlation test | N=0 | ||||
LYMPH_NODES_EXAMINED | Spearman correlation test | N=0 | ||||
KERATINIZATION_SQUAMOUS_CELL | Wilcoxon test | N=22 | non-keratinizing squamous cell carcinoma | N=22 | keratinizing squamous cell carcinoma | N=0 |
INITIAL_PATHOLOGIC_DX_YEAR | Spearman correlation test | N=30 | higher initial_pathologic_dx_year | N=8 | lower initial_pathologic_dx_year | N=22 |
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Kruskal-Wallis test | N=2 | ||||
HEIGHT_CM_AT_DIAGNOSIS | Spearman correlation test | N=13 | higher height_cm_at_diagnosis | N=13 | lower height_cm_at_diagnosis | N=0 |
CORPUS_INVOLVEMENT | Wilcoxon test | N=0 | ||||
CHEMO_CONCURRENT_TYPE | Kruskal-Wallis test | N=0 | ||||
CERVIX_SUV_RESULTS | Spearman correlation test | N=0 | ||||
AGE_AT_DIAGNOSIS | Spearman correlation test | N=30 | higher age_at_diagnosis | N=13 | lower age_at_diagnosis | N=17 |
CLINICAL_STAGE | Kruskal-Wallis test | N=12 |
Table S1. Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'
DAYS_TO_DEATH_OR_LAST_FUP | Duration (Months) | 0.1-210.7 (median=23) |
censored | N = 234 | |
death | N = 72 | |
Significant markers | N = 17 | |
associated with shorter survival | NA | |
associated with longer survival | NA |
Table S2. Get Full Table List of top 10 miRs significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.
logrank_P | Q | C_index | |
---|---|---|---|
HSA-MIR-532 | 0.000162 | 0.088 | 0.361 |
HSA-MIR-502 | 0.000376 | 0.1 | 0.331 |
HSA-MIR-101-1 | 0.000957 | 0.15 | 0.356 |
HSA-MIR-378C | 0.00111 | 0.15 | 0.336 |
HSA-MIR-150 | 0.00168 | 0.18 | 0.341 |
HSA-MIR-541 | 0.00234 | 0.21 | 0.653 |
HSA-MIR-876 | 0.00324 | 0.24 | 0.576 |
HSA-MIR-1288 | 0.00393 | 0.24 | 0.421 |
HSA-MIR-361 | 0.00437 | 0.24 | 0.374 |
HSA-MIR-412 | 0.00441 | 0.24 | 0.55 |
Table S3. Basic characteristics of clinical feature: 'YEARS_TO_BIRTH'
YEARS_TO_BIRTH | Mean (SD) | 48.2 (14) |
Significant markers | N = 30 | |
pos. correlated | 14 | |
neg. correlated | 16 |
Table S4. Get Full Table List of top 10 miRs significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-424 | -0.309 | 3.595e-08 | 1.95e-05 |
HSA-MIR-455 | -0.2889 | 2.839e-07 | 7.71e-05 |
HSA-MIR-1468 | 0.2738 | 1.408e-06 | 0.000255 |
HSA-MIR-450A-2 | -0.2293 | 5.302e-05 | 0.00695 |
HSA-MIR-31 | -0.2258 | 6.911e-05 | 0.00695 |
HSA-MIR-503 | -0.2244 | 7.675e-05 | 0.00695 |
HSA-MIR-204 | 0.2301 | 0.0001023 | 0.00793 |
HSA-MIR-653 | 0.2054 | 0.0003501 | 0.0238 |
HSA-MIR-133A-2 | 0.2706 | 0.0006093 | 0.0351 |
HSA-MIR-125B-2 | 0.1943 | 0.0006458 | 0.0351 |
Table S5. Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'
PATHOLOGY_T_STAGE | Mean (SD) | 1.59 (0.81) |
N | ||
T1 | 141 | |
T2 | 72 | |
T3 | 21 | |
T4 | 10 | |
Significant markers | N = 30 | |
pos. correlated | 10 | |
neg. correlated | 20 |
Table S6. Get Full Table List of top 10 miRs significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-144 | 0.3186 | 3.684e-07 | 2e-04 |
HSA-MIR-424 | -0.3037 | 1.339e-06 | 0.000275 |
HSA-MIR-486 | 0.3022 | 1.52e-06 | 0.000275 |
HSA-MIR-451 | 0.2985 | 2.066e-06 | 0.00028 |
HSA-MIR-185 | 0.2832 | 6.989e-06 | 0.000759 |
HSA-MIR-450A-2 | -0.2644 | 2.872e-05 | 0.0026 |
HSA-MIR-1247 | -0.2491 | 8.662e-05 | 0.00672 |
HSA-MIR-181A-1 | 0.2426 | 0.0001291 | 0.00876 |
HSA-MIR-10A | -0.2382 | 0.000173 | 0.0104 |
HSA-MIR-103-1 | 0.2353 | 0.0002087 | 0.0105 |
Table S7. Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'
PATHOLOGY_N_STAGE | Labels | N |
N0 | 135 | |
N1 | 60 | |
Significant markers | N = 0 |
Table S8. Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'
PATHOLOGY_M_STAGE | Labels | N |
class0 | 116 | |
class1 | 10 | |
Significant markers | N = 0 |
Table S9. Basic characteristics of clinical feature: 'RADIATION_THERAPY'
RADIATION_THERAPY | Labels | N |
NO | 55 | |
YES | 129 | |
Significant markers | N = 12 | |
Higher in YES | 12 | |
Higher in NO | 0 |
Table S10. Get Full Table List of top 10 miRs differentially expressed by 'RADIATION_THERAPY'
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-3917 | 2137 | 3.301e-05 | 0.0179 | 0.6941 |
HSA-MIR-374A | 2365 | 0.0003517 | 0.0955 | 0.6667 |
HSA-MIR-185 | 4659 | 0.0007815 | 0.132 | 0.6567 |
HSA-MIR-500A | 2472 | 0.001152 | 0.132 | 0.6516 |
HSA-MIR-7-1 | 2477 | 0.001215 | 0.132 | 0.6509 |
HSA-MIR-181A-1 | 4601 | 0.001453 | 0.132 | 0.6485 |
HSA-MIR-107 | 4498 | 0.004073 | 0.279 | 0.634 |
HSA-MIR-320A | 2598 | 0.004112 | 0.279 | 0.6338 |
HSA-MIR-486 | 4472 | 0.005209 | 0.296 | 0.6303 |
HSA-MIR-28 | 2630 | 0.00556 | 0.296 | 0.6293 |
Table S11. Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'
HISTOLOGICAL_TYPE | Labels | N |
ADENOSQUAMOUS | 6 | |
CERVICAL SQUAMOUS CELL CARCINOMA | 254 | |
ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | 6 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 21 | |
ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | 3 | |
MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE | 17 | |
Significant markers | N = 30 |
Table S12. Get Full Table List of top 10 miRs differentially expressed by 'HISTOLOGICAL_TYPE'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-205 | 4.976e-22 | 2.7e-19 |
HSA-MIR-944 | 5.309e-19 | 1.44e-16 |
HSA-MIR-375 | 5.394e-18 | 9.76e-16 |
HSA-MIR-194-2 | 1.364e-14 | 1.85e-12 |
HSA-MIR-10A | 5.094e-14 | 5.53e-12 |
HSA-MIR-192 | 1.415e-13 | 1.28e-11 |
HSA-MIR-194-1 | 1.771e-13 | 1.37e-11 |
HSA-MIR-203 | 4.71e-13 | 3.2e-11 |
HSA-MIR-1293 | 8.087e-13 | 4.88e-11 |
HSA-MIR-221 | 6.133e-12 | 3.33e-10 |
Table S13. Basic characteristics of clinical feature: 'NUMBER_PACK_YEARS_SMOKED'
NUMBER_PACK_YEARS_SMOKED | Mean (SD) | 17.38 (14) |
Significant markers | N = 0 |
Table S14. Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'
NUMBER_OF_LYMPH_NODES | Mean (SD) | 1.04 (2.4) |
Significant markers | N = 0 |
Table S15. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 8 | |
ASIAN | 20 | |
BLACK OR AFRICAN AMERICAN | 30 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 2 | |
WHITE | 211 | |
Significant markers | N = 5 |
Table S16. Get Full Table List of 5 miRs differentially expressed by 'RACE'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-24-2 | 0.0004318 | 0.211 |
HSA-MIR-3130-1 | 0.001064 | 0.211 |
HSA-MIR-2355 | 0.001539 | 0.211 |
HSA-MIR-454 | 0.001875 | 0.211 |
HSA-MIR-185 | 0.001941 | 0.211 |
Table S17. Basic characteristics of clinical feature: 'ETHNICITY'
ETHNICITY | Labels | N |
HISPANIC OR LATINO | 24 | |
NOT HISPANIC OR LATINO | 171 | |
Significant markers | N = 0 |
Table S18. Basic characteristics of clinical feature: 'WEIGHT_KG_AT_DIAGNOSIS'
WEIGHT_KG_AT_DIAGNOSIS | Mean (SD) | 73.04 (22) |
Significant markers | N = 30 | |
pos. correlated | 24 | |
neg. correlated | 6 |
Table S19. Get Full Table List of top 10 miRs significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-592 | 0.2392 | 6.163e-05 | 0.0335 |
HSA-MIR-548B | 0.214 | 0.0006741 | 0.169 |
HSA-MIR-3130-1 | 0.1938 | 0.001265 | 0.169 |
HSA-MIR-3690 | 0.2066 | 0.002015 | 0.169 |
HSA-MIR-223 | -0.1837 | 0.002105 | 0.169 |
HSA-MIR-639 | 0.205 | 0.002412 | 0.169 |
HSA-MIR-518C | 0.2761 | 0.002478 | 0.169 |
HSA-MIR-618 | -0.2062 | 0.002488 | 0.169 |
HSA-MIR-181C | 0.1749 | 0.003447 | 0.179 |
HSA-MIR-24-1 | 0.1747 | 0.003472 | 0.179 |
Table S20. Basic characteristics of clinical feature: 'TUMOR_STATUS'
TUMOR_STATUS | Labels | N |
TUMOR FREE | 201 | |
WITH TUMOR | 80 | |
Significant markers | N = 15 | |
Higher in WITH TUMOR | 15 | |
Higher in TUMOR FREE | 0 |
Table S21. Get Full Table List of top 10 miRs differentially expressed by 'TUMOR_STATUS'
W(pos if higher in 'WITH TUMOR') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-150 | 5892 | 0.0004768 | 0.0902 | 0.6336 |
HSA-MIR-378C | 5882 | 0.0005414 | 0.0902 | 0.6324 |
HSA-MIR-155 | 5951 | 0.0006801 | 0.0902 | 0.6299 |
HSA-MIR-361 | 5965 | 0.0007389 | 0.0902 | 0.629 |
HSA-MIR-451 | 10063 | 0.001001 | 0.0902 | 0.6258 |
HSA-MIR-144 | 10052 | 0.001067 | 0.0902 | 0.6251 |
HSA-MIR-142 | 6043 | 0.001163 | 0.0902 | 0.6242 |
HSA-MIR-556 | 6652 | 0.001996 | 0.135 | 0.6323 |
HSA-MIR-301B | 8985 | 0.002469 | 0.149 | 0.6195 |
HSA-MIR-486 | 9850 | 0.003244 | 0.176 | 0.6126 |
Table S22. Basic characteristics of clinical feature: 'NEOPLASM_HISTOLOGIC_GRADE'
NEOPLASM_HISTOLOGIC_GRADE | Labels | N |
G1 | 18 | |
G2 | 136 | |
G3 | 120 | |
G4 | 1 | |
GX | 24 | |
Significant markers | N = 30 |
Table S23. Get Full Table List of top 10 miRs differentially expressed by 'NEOPLASM_HISTOLOGIC_GRADE'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-486 | 0.0002665 | 0.0552 |
HSA-MIR-421 | 0.0002798 | 0.0552 |
HSA-MIR-185 | 0.0003936 | 0.0552 |
HSA-MIR-144 | 0.0004068 | 0.0552 |
HSA-MIR-23B | 0.0006318 | 0.0686 |
HSA-MIR-19A | 0.000839 | 0.0759 |
HSA-MIR-496 | 0.001091 | 0.0847 |
HSA-MIR-346 | 0.001686 | 0.0913 |
HSA-MIR-17 | 0.001834 | 0.0913 |
HSA-MIR-216B | 0.001901 | 0.0913 |
No miR related to 'TOBACCO_SMOKING_YEAR_STOPPED'.
Table S24. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_YEAR_STOPPED'
TOBACCO_SMOKING_YEAR_STOPPED | Mean (SD) | 1999.7 (14) |
Significant markers | N = 0 |
No miR related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
Table S25. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Mean (SD) | 17.38 (14) |
Significant markers | N = 0 |
Table S26. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_HISTORY'
TOBACCO_SMOKING_HISTORY | Mean (SD) | 1.83 (1.1) |
Value | N | |
1 | 146 | |
2 | 64 | |
3 | 9 | |
4 | 40 | |
5 | 4 | |
Significant markers | N = 15 | |
pos. correlated | 10 | |
neg. correlated | 5 |
Table S27. Get Full Table List of top 10 miRs significantly correlated to 'TOBACCO_SMOKING_HISTORY' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-33A | 0.258 | 2.267e-05 | 0.0123 |
HSA-MIR-4326 | -0.2464 | 0.0001268 | 0.0344 |
HSA-MIR-27B | 0.2184 | 0.0003584 | 0.0649 |
HSA-MIR-146B | -0.2103 | 0.0005973 | 0.0659 |
HSA-MIR-1274B | 0.2108 | 0.0006071 | 0.0659 |
HSA-MIR-26A-2 | 0.1943 | 0.001548 | 0.12 |
HSA-MIR-27A | 0.1935 | 0.001615 | 0.12 |
HSA-MIR-501 | -0.1919 | 0.001768 | 0.12 |
HSA-MIR-1537 | -0.2243 | 0.002762 | 0.167 |
HSA-MIR-3609 | -0.2633 | 0.003966 | 0.215 |
Table S28. Basic characteristics of clinical feature: 'AGEBEGANSMOKINGINYEARS'
AGEBEGANSMOKINGINYEARS | Mean (SD) | 21.14 (7.7) |
Significant markers | N = 0 |
Table S29. 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 |
Table S30. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'
PREGNANCIES_COUNT_TOTAL | Mean (SD) | 3.61 (2.6) |
Significant markers | N = 0 |
No miR related to 'PREGNANCIES_COUNT_STILLBIRTH'.
Table S31. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'
PREGNANCIES_COUNT_STILLBIRTH | Mean (SD) | 0.07 (0.35) |
Value | N | |
0 | 106 | |
1 | 5 | |
3 | 1 | |
Significant markers | N = 0 |
30 miRs related to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'.
Table S32. Basic characteristics of clinical feature: 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT'
PREGNANCY_SPONTANEOUS_ABORTION_COUNT | Mean (SD) | 0.54 (0.95) |
Significant markers | N = 30 | |
pos. correlated | 12 | |
neg. correlated | 18 |
Table S33. Get Full Table List of top 10 miRs significantly correlated to 'PREGNANCY_SPONTANEOUS_ABORTION_COUNT' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-185 | 0.3532 | 1.146e-05 | 0.00622 |
HSA-MIR-340 | 0.2844 | 0.000482 | 0.0663 |
HSA-MIR-758 | -0.2834 | 0.0005043 | 0.0663 |
HSA-MIR-216A | -0.3877 | 0.0005891 | 0.0663 |
HSA-MIR-146B | 0.2794 | 0.0006106 | 0.0663 |
HSA-MIR-19A | 0.2663 | 0.001114 | 0.0746 |
HSA-MIR-539 | -0.2671 | 0.001163 | 0.0746 |
HSA-MIR-379 | -0.2593 | 0.001514 | 0.0746 |
HSA-MIR-3912 | 0.2628 | 0.001778 | 0.0746 |
HSA-MIR-15A | 0.2549 | 0.001835 | 0.0746 |
3 miRs related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
Table S34. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_LIVE_BIRTH'
PREGNANCIES_COUNT_LIVE_BIRTH | Mean (SD) | 2.84 (2) |
Significant markers | N = 3 | |
pos. correlated | 1 | |
neg. correlated | 2 |
Table S35. Get Full Table List of 3 miRs significantly correlated to 'PREGNANCIES_COUNT_LIVE_BIRTH' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-1287 | -0.2378 | 0.0001016 | 0.0551 |
HSA-MIR-19A | 0.198 | 0.001274 | 0.28 |
HSA-MIR-212 | -0.1946 | 0.001549 | 0.28 |
One miR related to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'.
Table S36. Basic characteristics of clinical feature: 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT'
PREGNANCY_THERAPEUTIC_ABORTION_COUNT | Mean (SD) | 0.85 (1.8) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
Table S37. Get Full Table List of one miR significantly correlated to 'PREGNANCY_THERAPEUTIC_ABORTION_COUNT' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-26B | -0.3242 | 0.0002692 | 0.146 |
Table S38. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'
PREGNANCIES_COUNT_ECTOPIC | Mean (SD) | 0.11 (0.34) |
Value | N | |
0 | 104 | |
1 | 11 | |
2 | 1 | |
Significant markers | N = 0 |
Table S39. 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 | 40 | |
POSITIVE BLADDER MARGIN | 1 | |
POSITIVE VAGINAL MARGIN | 12 | |
Significant markers | N = 0 |
Table S40. Basic characteristics of clinical feature: 'MENOPAUSE_STATUS'
MENOPAUSE_STATUS | Labels | N |
INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) | 3 | |
PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) | 25 | |
POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) | 84 | |
PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) | 125 | |
Significant markers | N = 20 |
Table S41. Get Full Table List of top 10 miRs differentially expressed by 'MENOPAUSE_STATUS'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-424 | 6.108e-05 | 0.0332 |
HSA-MIR-1468 | 0.0001562 | 0.0356 |
HSA-MIR-503 | 0.0001968 | 0.0356 |
HSA-MIR-125B-2 | 0.0002751 | 0.0373 |
HSA-MIR-1274B | 0.0004469 | 0.0485 |
HSA-MIR-99A | 0.0007493 | 0.0678 |
HSA-LET-7C | 0.0008864 | 0.0688 |
HSA-MIR-455 | 0.001289 | 0.0875 |
HSA-MIR-3199-1 | 0.004019 | 0.221 |
HSA-MIR-4326 | 0.004448 | 0.221 |
Table S42. Basic characteristics of clinical feature: 'LYMPHOVASCULAR_INVOLVEMENT'
LYMPHOVASCULAR_INVOLVEMENT | Labels | N |
ABSENT | 72 | |
PRESENT | 80 | |
Significant markers | N = 0 |
No miR related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
Table S43. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED_HE_COUNT'
LYMPH_NODES_EXAMINED_HE_COUNT | Mean (SD) | 1.04 (2.4) |
Significant markers | N = 0 |
Table S44. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'
LYMPH_NODES_EXAMINED | Mean (SD) | 22.28 (13) |
Significant markers | N = 0 |
22 miRs related to 'KERATINIZATION_SQUAMOUS_CELL'.
Table S45. Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'
KERATINIZATION_SQUAMOUS_CELL | Labels | N |
KERATINIZING SQUAMOUS CELL CARCINOMA | 55 | |
NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 120 | |
Significant markers | N = 22 | |
Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 22 | |
Higher in KERATINIZING SQUAMOUS CELL CARCINOMA | 0 |
Table S46. Get Full Table List of top 10 miRs differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'
W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HSA-MIR-152 | 2035 | 4.819e-05 | 0.0262 | 0.6917 |
HSA-MIR-27A | 2128 | 0.0001663 | 0.0452 | 0.6776 |
HSA-MIR-23C | 1565 | 0.0005318 | 0.0963 | 0.6767 |
HSA-MIR-191 | 4311 | 0.001163 | 0.132 | 0.6532 |
HSA-MIR-23A | 2304 | 0.001376 | 0.132 | 0.6509 |
HSA-MIR-944 | 2292 | 0.001514 | 0.132 | 0.6498 |
HSA-MIR-193A | 2323 | 0.001698 | 0.132 | 0.648 |
HSA-MIR-30C-2 | 4241 | 0.002504 | 0.17 | 0.6426 |
HSA-MIR-24-2 | 2384 | 0.003255 | 0.196 | 0.6388 |
HSA-MIR-93 | 4192 | 0.004165 | 0.226 | 0.6352 |
30 miRs related to 'INITIAL_PATHOLOGIC_DX_YEAR'.
Table S47. Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'
INITIAL_PATHOLOGIC_DX_YEAR | Mean (SD) | 2008.32 (4.8) |
Significant markers | N = 30 | |
pos. correlated | 8 | |
neg. correlated | 22 |
Table S48. Get Full Table List of top 10 miRs significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-1274B | -0.416 | 4.124e-14 | 2.24e-11 |
HSA-MIR-19A | 0.3764 | 1.061e-11 | 2.49e-09 |
HSA-MIR-212 | -0.3741 | 1.443e-11 | 2.49e-09 |
HSA-MIR-660 | 0.3723 | 1.836e-11 | 2.49e-09 |
HSA-MIR-326 | -0.344 | 8.713e-10 | 9.46e-08 |
HSA-MIR-24-2 | -0.3371 | 1.536e-09 | 1.39e-07 |
HSA-MIR-15A | 0.3332 | 2.432e-09 | 1.89e-07 |
HSA-MIR-19B-2 | 0.3298 | 3.6e-09 | 2.44e-07 |
HSA-MIR-3130-1 | -0.3295 | 4.989e-09 | 3.01e-07 |
HSA-MIR-143 | -0.3232 | 7.638e-09 | 4.15e-07 |
2 miRs related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.
Table S49. Basic characteristics of clinical feature: 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Labels | N |
CURRENT USER | 15 | |
FORMER USER | 54 | |
NEVER USED | 90 | |
Significant markers | N = 2 |
Table S50. Get Full Table List of 2 miRs differentially expressed by 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-338 | 0.0006624 | 0.226 |
HSA-MIR-26B | 0.0008337 | 0.226 |
Table S51. Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'
HEIGHT_CM_AT_DIAGNOSIS | Mean (SD) | 160.95 (7.3) |
Significant markers | N = 13 | |
pos. correlated | 13 | |
neg. correlated | 0 |
Table S52. Get Full Table List of top 10 miRs significantly correlated to 'HEIGHT_CM_AT_DIAGNOSIS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-320B-2 | 0.2564 | 2.483e-05 | 0.0135 |
HSA-MIR-320E | 0.3409 | 0.0002348 | 0.0487 |
HSA-MIR-320D-1 | 0.2484 | 0.0002691 | 0.0487 |
HSA-MIR-3130-1 | 0.209 | 0.0006967 | 0.0836 |
HSA-MIR-548Q | 0.2505 | 0.0007697 | 0.0836 |
HSA-MIR-1274B | 0.2014 | 0.001047 | 0.0948 |
HSA-MIR-23C | 0.214 | 0.001405 | 0.096 |
HSA-MIR-320C-1 | 0.2034 | 0.001435 | 0.096 |
HSA-MIR-1910 | 0.2279 | 0.001655 | 0.096 |
HSA-MIR-551A | 0.2311 | 0.001908 | 0.096 |
Table S53. Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'
CORPUS_INVOLVEMENT | Labels | N |
ABSENT | 99 | |
PRESENT | 19 | |
Significant markers | N = 0 |
Table S54. Basic characteristics of clinical feature: 'CHEMO_CONCURRENT_TYPE'
CHEMO_CONCURRENT_TYPE | Labels | N |
CARBOPLATIN | 7 | |
CISPLATIN | 104 | |
OTHER | 2 | |
Significant markers | N = 0 |
Table S55. Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'
CERVIX_SUV_RESULTS | Mean (SD) | 13.22 (7.2) |
Significant markers | N = 0 |
Table S56. Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'
AGE_AT_DIAGNOSIS | Mean (SD) | 48.27 (14) |
Significant markers | N = 30 | |
pos. correlated | 13 | |
neg. correlated | 17 |
Table S57. Get Full Table List of top 10 miRs significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HSA-MIR-424 | -0.3117 | 2.41e-08 | 1.31e-05 |
HSA-MIR-455 | -0.2826 | 4.797e-07 | 0.00013 |
HSA-MIR-1468 | 0.272 | 1.533e-06 | 0.000277 |
HSA-MIR-450A-2 | -0.2298 | 4.809e-05 | 0.00576 |
HSA-MIR-503 | -0.2285 | 5.307e-05 | 0.00576 |
HSA-MIR-204 | 0.2351 | 6.686e-05 | 0.00605 |
HSA-MIR-31 | -0.2146 | 0.0001513 | 0.0117 |
HSA-MIR-653 | 0.2112 | 0.0002244 | 0.0152 |
HSA-MIR-133A-2 | 0.2706 | 0.0005853 | 0.0353 |
HSA-MIR-450A-1 | -0.1912 | 0.000792 | 0.043 |
Table S58. Basic characteristics of clinical feature: 'CLINICAL_STAGE'
CLINICAL_STAGE | Labels | N |
STAGE I | 5 | |
STAGE IA | 1 | |
STAGE IA1 | 1 | |
STAGE IA2 | 1 | |
STAGE IB | 38 | |
STAGE IB1 | 78 | |
STAGE IB2 | 39 | |
STAGE II | 5 | |
STAGE IIA | 9 | |
STAGE IIA1 | 5 | |
STAGE IIA2 | 7 | |
STAGE IIB | 44 | |
STAGE III | 1 | |
STAGE IIIA | 3 | |
STAGE IIIB | 42 | |
STAGE IVA | 9 | |
STAGE IVB | 12 | |
Significant markers | N = 12 |
Table S59. Get Full Table List of top 10 miRs differentially expressed by 'CLINICAL_STAGE'
kruskal_wallis_P | Q | |
---|---|---|
HSA-MIR-144 | 2.675e-05 | 0.0103 |
HSA-MIR-451 | 3.908e-05 | 0.0103 |
HSA-MIR-486 | 5.686e-05 | 0.0103 |
HSA-MIR-218-2 | 0.001166 | 0.109 |
HSA-MIR-185 | 0.001183 | 0.109 |
HSA-MIR-3610 | 0.001204 | 0.109 |
HSA-MIR-424 | 0.001617 | 0.125 |
HSA-MIR-140 | 0.003077 | 0.206 |
HSA-MIR-193A | 0.003537 | 0.206 |
HSA-MIR-375 | 0.003792 | 0.206 |
-
Expresson data file = CESC-TP.miRseq_RPKM_log2.txt
-
Clinical data file = CESC-TP.merged_data.txt
-
Number of patients = 307
-
Number of miRs = 543
-
Number of clinical features = 39
-
Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.
-
There are also useful links about clinical features.
-
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.
For survival clinical features, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival 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
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.
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.
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.