This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 18199 genes and 42 clinical features across 180 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 14 clinical features related to at least one genes.
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4 genes correlated to 'Time to Death'.
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GATS|352954 , ZER1|10444 , FAM70B|348013 , UBAC1|10422
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14 genes correlated to 'AGE'.
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NXNL2|158046 , LOC440356|440356 , RARB|5915 , INF2|64423 , C9ORF167|54863 , ...
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1 gene correlated to 'PATHOLOGY.N.STAGE'.
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ART3|419
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1723 genes correlated to 'HISTOLOGICAL.TYPE'.
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TP63|8626 , DNALI1|7802 , GPR109A|338442 , DEPDC6|64798 , PLCH1|23007 , ...
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1 gene correlated to 'NUMBER.OF.LYMPH.NODES'.
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ART3|419
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1 gene correlated to 'RACE'.
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XKR9|389668
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3 genes correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.
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HCG26|352961 , JMJD5|79831 , FAAH2|158584
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1 gene correlated to 'MENOPAUSE_STATUS'.
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SSBP3|23648
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1 gene correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
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ART3|419
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1 gene correlated to 'LYMPH_NODES_EXAMINED'.
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MAGEA10|4109
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1 gene correlated to 'KERATINIZATION_SQUAMOUS_CELL'.
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QKI|9444
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2 genes correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.
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C9ORF171|389799 , SNAPC5|10302
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1 gene correlated to 'CERVIX_SUV_RESULTS'.
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TEX14|56155
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15 genes correlated to 'AGE_AT_DIAGNOSIS'.
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NXNL2|158046 , LOC440356|440356 , C9ORF167|54863 , GPR97|222487 , IGSF9|57549 , ...
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No genes correlated to 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'ETHNICITY', 'TUMOR_STATUS', 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY', 'NEOPLASMHISTOLOGICGRADE', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'TOBACCO_SMOKING_HISTORY', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_THERAPY_TYPE', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'LYMPH_NODE_LOCATION', 'LOCATION_OF_POSITIVE_MARGINS', 'LYMPHOVASCULAR_INVOLVEMENT', 'HYSTERECTOMY_TYPE', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', and 'AJCC_TUMOR_PATHOLOGIC_PT'.
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=4 | shorter survival | N=1 | longer survival | N=3 |
AGE | Spearman correlation test | N=14 | older | N=7 | younger | N=7 |
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | Wilcoxon test | N=1 | class1 | N=1 | class0 | N=0 |
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=1723 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=1 | higher number.of.lymph.nodes | N=0 | lower number.of.lymph.nodes | N=1 |
RACE | Kruskal-Wallis test | N=1 | ||||
ETHNICITY | Wilcoxon test | N=0 | ||||
WEIGHT_KG_AT_DIAGNOSIS | Spearman correlation test | N=3 | higher weight_kg_at_diagnosis | N=3 | lower weight_kg_at_diagnosis | N=0 |
TUMOR_STATUS | Wilcoxon test | N=0 | ||||
TUMOR_SAMPLE_PROCUREMENT_COUNTRY | Kruskal-Wallis test | N=0 | ||||
NEOPLASMHISTOLOGICGRADE | Kruskal-Wallis test | N=0 | ||||
TOBACCO_SMOKING_YEAR_STOPPED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Spearman correlation test | N=0 | ||||
TOBACCO_SMOKING_HISTORY | Kruskal-Wallis test | N=0 | ||||
PATIENT AGEBEGANSMOKINGINYEARS | Spearman correlation test | N=0 | ||||
RADIATION_THERAPY_TYPE | Kruskal-Wallis test | N=0 | ||||
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=0 | ||||
PATIENT PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Spearman correlation test | N=0 | ||||
PREGNANCIES_COUNT_ECTOPIC | Spearman correlation test | N=0 | ||||
LYMPH_NODE_LOCATION | Kruskal-Wallis test | N=0 | ||||
LOCATION_OF_POSITIVE_MARGINS | Kruskal-Wallis test | N=0 | ||||
MENOPAUSE_STATUS | Kruskal-Wallis test | N=1 | ||||
LYMPHOVASCULAR_INVOLVEMENT | Wilcoxon test | N=0 | ||||
LYMPH_NODES_EXAMINED_HE_COUNT | Spearman correlation test | N=1 | higher lymph_nodes_examined_he_count | N=0 | lower lymph_nodes_examined_he_count | N=1 |
LYMPH_NODES_EXAMINED | Spearman correlation test | N=1 | higher lymph_nodes_examined | N=0 | lower lymph_nodes_examined | N=1 |
KERATINIZATION_SQUAMOUS_CELL | Wilcoxon test | N=1 | non-keratinizing squamous cell carcinoma | N=1 | keratinizing squamous cell carcinoma | N=0 |
INITIAL_PATHOLOGIC_DX_YEAR | Spearman correlation test | N=2 | higher initial_pathologic_dx_year | N=1 | lower initial_pathologic_dx_year | N=1 |
HYSTERECTOMY_TYPE | Kruskal-Wallis test | N=0 | ||||
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Kruskal-Wallis test | N=0 | ||||
HEIGHT_CM_AT_DIAGNOSIS | Spearman correlation test | N=0 | ||||
CORPUS_INVOLVEMENT | Wilcoxon test | N=0 | ||||
CERVIX_SUV_RESULTS | Spearman correlation test | N=1 | higher cervix_suv_results | N=0 | lower cervix_suv_results | N=1 |
AJCC_TUMOR_PATHOLOGIC_PT | Kruskal-Wallis test | N=0 | ||||
AGE_AT_DIAGNOSIS | Spearman correlation test | N=15 | higher age_at_diagnosis | N=8 | lower age_at_diagnosis | N=7 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0-182.9 (median=13.6) |
censored | N = 140 | |
death | N = 33 | |
Significant markers | N = 4 | |
associated with shorter survival | 1 | |
associated with longer survival | 3 |
Table S2. Get Full Table List of 4 genes significantly associated with 'Time to Death' by Cox regression test
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
GATS|352954 | 0.49 | 3.159e-07 | 0.0057 | 0.24 |
ZER1|10444 | 0.13 | 9.559e-07 | 0.017 | 0.273 |
FAM70B|348013 | 1.98 | 4.591e-06 | 0.084 | 0.72 |
UBAC1|10422 | 0.17 | 1.087e-05 | 0.2 | 0.28 |
Table S3. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 47.44 (13) |
Significant markers | N = 14 | |
pos. correlated | 7 | |
neg. correlated | 7 |
Table S4. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
NXNL2|158046 | -0.4475 | 1.502e-09 | 2.73e-05 |
LOC440356|440356 | 0.369 | 1.577e-06 | 0.0287 |
RARB|5915 | 0.3483 | 1.767e-06 | 0.0322 |
INF2|64423 | -0.3477 | 1.849e-06 | 0.0336 |
C9ORF167|54863 | -0.3454 | 2.181e-06 | 0.0397 |
GPR97|222487 | -0.3398 | 3.269e-06 | 0.0595 |
UNC119|9094 | 0.3371 | 3.944e-06 | 0.0717 |
IGSF9|57549 | 0.3343 | 4.797e-06 | 0.0873 |
PGR|5241 | -0.3305 | 6.229e-06 | 0.113 |
RRAGD|58528 | 0.3265 | 8.191e-06 | 0.149 |
Table S5. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 1.31 (0.54) |
N | ||
1 | 100 | |
2 | 37 | |
3 | 2 | |
4 | 1 | |
Significant markers | N = 0 |
Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Labels | N |
class0 | 89 | |
class1 | 42 | |
Significant markers | N = 1 | |
Higher in class1 | 1 | |
Higher in class0 | 0 |
Table S7. Get Full Table List of one gene differentially expressed by 'PATHOLOGY.N.STAGE'
W(pos if higher in 'class1') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
ART3|419 | 677 | 8.549e-06 | 0.156 | 0.7612 |
Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 76 | |
M1 | 3 | |
MX | 65 | |
Significant markers | N = 0 |
Table S9. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
ADENOSQUAMOUS | 2 | |
CERVICAL SQUAMOUS CELL CARCINOMA | 148 | |
ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | 4 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 20 | |
ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | 2 | |
MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE | 4 | |
Significant markers | N = 1723 |
Table S10. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'
ANOVA_P | Q | |
---|---|---|
TP63|8626 | 1.795e-14 | 3.27e-10 |
DNALI1|7802 | 3.577e-14 | 6.51e-10 |
GPR109A|338442 | 4.05e-14 | 7.37e-10 |
DEPDC6|64798 | 4.085e-14 | 7.43e-10 |
PLCH1|23007 | 5.288e-14 | 9.62e-10 |
BICD2|23299 | 5.591e-14 | 1.02e-09 |
GOLM1|51280 | 7.837e-14 | 1.43e-09 |
CABLES1|91768 | 9.298e-14 | 1.69e-09 |
SLC6A20|54716 | 1.092e-13 | 1.99e-09 |
PKP1|5317 | 1.244e-13 | 2.26e-09 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S11. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 30 | |
YES | 150 | |
Significant markers | N = 0 |
Table S12. Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'
NUMBERPACKYEARSSMOKED | Mean (SD) | 18.59 (12) |
Significant markers | N = 0 |
Table S13. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1.07 (2.6) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
Table S14. Get Full Table List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
ART3|419 | -0.4404 | 5.081e-06 | 0.0925 |
Table S15. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 6 | |
ASIAN | 15 | |
BLACK OR AFRICAN AMERICAN | 18 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 1 | |
WHITE | 135 | |
Significant markers | N = 1 |
Table S16. Get Full Table List of one gene differentially expressed by 'RACE'
ANOVA_P | Q | |
---|---|---|
XKR9|389668 | 4.026e-06 | 0.0733 |
Table S17. Basic characteristics of clinical feature: 'ETHNICITY'
ETHNICITY | Labels | N |
HISPANIC OR LATINO | 12 | |
NOT HISPANIC OR LATINO | 129 | |
Significant markers | N = 0 |
Table S18. Basic characteristics of clinical feature: 'WEIGHT_KG_AT_DIAGNOSIS'
WEIGHT_KG_AT_DIAGNOSIS | Mean (SD) | 75.31 (21) |
Significant markers | N = 3 | |
pos. correlated | 3 | |
neg. correlated | 0 |
Table S19. Get Full Table List of 3 genes significantly correlated to 'WEIGHT_KG_AT_DIAGNOSIS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
HCG26|352961 | 0.3621 | 1.631e-06 | 0.0297 |
JMJD5|79831 | 0.3366 | 9.217e-06 | 0.168 |
FAAH2|158584 | 0.331 | 1.328e-05 | 0.242 |
Table S20. Basic characteristics of clinical feature: 'TUMOR_STATUS'
TUMOR_STATUS | Labels | N |
TUMOR FREE | 50 | |
WITH TUMOR | 20 | |
Significant markers | N = 0 |
No gene related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.
Table S21. Basic characteristics of clinical feature: 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'
TUMOR_SAMPLE_PROCUREMENT_COUNTRY | Labels | N |
NIGERIA | 1 | |
RUSSIA | 11 | |
UKRAINE | 6 | |
UNITED STATES | 150 | |
VIETNAM | 12 | |
Significant markers | N = 0 |
Table S22. Basic characteristics of clinical feature: 'NEOPLASMHISTOLOGICGRADE'
NEOPLASMHISTOLOGICGRADE | Labels | N |
G1 | 14 | |
G2 | 85 | |
G3 | 74 | |
G4 | 1 | |
GX | 5 | |
Significant markers | N = 0 |
No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.
Table S23. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_YEAR_STOPPED'
TOBACCO_SMOKING_YEAR_STOPPED | Mean (SD) | 1997.72 (12) |
Significant markers | N = 0 |
No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
Table S24. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Mean (SD) | 18.59 (12) |
Significant markers | N = 0 |
Table S25. Basic characteristics of clinical feature: 'TOBACCO_SMOKING_HISTORY'
TOBACCO_SMOKING_HISTORY | Labels | N |
CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | 23 | |
CURRENT REFORMED SMOKER FOR > 15 YEARS | 8 | |
CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED | 1 | |
CURRENT SMOKER | 36 | |
LIFELONG NON-SMOKER | 83 | |
Significant markers | N = 0 |
No gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.
Table S26. Basic characteristics of clinical feature: 'PATIENT.AGEBEGANSMOKINGINYEARS'
PATIENT.AGEBEGANSMOKINGINYEARS | Mean (SD) | 20.52 (6.3) |
Significant markers | N = 0 |
Table S27. Basic characteristics of clinical feature: 'RADIATION_THERAPY_TYPE'
RADIATION_THERAPY_TYPE | Labels | N |
COMBINATION | 17 | |
EXTERNAL | 37 | |
EXTERNAL BEAM | 14 | |
INTERNAL | 5 | |
Significant markers | N = 0 |
Table S28. Basic characteristics of clinical feature: 'RADIATION_ADJUVANT_UNITS'
RADIATION_ADJUVANT_UNITS | Labels | N |
CGY | 12 | |
GY | 3 | |
Significant markers | N = 0 |
Table S29. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_TOTAL'
PREGNANCIES_COUNT_TOTAL | Mean (SD) | 3.46 (2.5) |
Significant markers | N = 0 |
No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.
Table S30. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_STILLBIRTH'
PREGNANCIES_COUNT_STILLBIRTH | Mean (SD) | 0.08 (0.37) |
Value | N | |
0 | 90 | |
1 | 5 | |
3 | 1 | |
Significant markers | N = 0 |
No gene related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.
Table S31. Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Mean (SD) | 0.31 (0.56) |
Value | N | |
0 | 78 | |
1 | 27 | |
2 | 2 | |
3 | 1 | |
Significant markers | N = 0 |
No gene related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
Table S32. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_LIVE_BIRTH'
PREGNANCIES_COUNT_LIVE_BIRTH | Mean (SD) | 2.39 (1.7) |
Significant markers | N = 0 |
No gene related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.
Table S33. Basic characteristics of clinical feature: 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Mean (SD) | 0.92 (1.9) |
Significant markers | N = 0 |
Table S34. Basic characteristics of clinical feature: 'PREGNANCIES_COUNT_ECTOPIC'
PREGNANCIES_COUNT_ECTOPIC | Mean (SD) | 0.1 (0.34) |
Value | N | |
0 | 88 | |
1 | 8 | |
2 | 1 | |
Significant markers | N = 0 |
Table S35. Basic characteristics of clinical feature: 'LYMPH_NODE_LOCATION'
LYMPH_NODE_LOCATION | Labels | N |
2003 | 1 | |
2010 | 1 | |
COMMON ILIAC | 1 | |
PELVIC (EXTERNAL ILIAC, INTERNAL ILIAC, OBTURATOR) | 39 | |
Significant markers | N = 0 |
No gene related to 'LOCATION_OF_POSITIVE_MARGINS'.
Table S36. Basic characteristics of clinical feature: 'LOCATION_OF_POSITIVE_MARGINS'
LOCATION_OF_POSITIVE_MARGINS | Labels | N |
MACROSCOPIC PARAMETRIAL INVOLVEMENT | 2 | |
MICROSCOPIC PARAMETRIAL INVOLVEMENT | 6 | |
OTHER LOCATION, SPECIFY | 12 | |
POSITIVE BLADDER MARGIN | 1 | |
POSITIVE VAGINAL MARGIN | 5 | |
Significant markers | N = 0 |
Table S37. 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) | 10 | |
POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) | 53 | |
PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) | 81 | |
Significant markers | N = 1 |
Table S38. Get Full Table List of one gene differentially expressed by 'MENOPAUSE_STATUS'
ANOVA_P | Q | |
---|---|---|
SSBP3|23648 | 2.204e-06 | 0.0401 |
No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.
Table S39. Basic characteristics of clinical feature: 'LYMPHOVASCULAR_INVOLVEMENT'
LYMPHOVASCULAR_INVOLVEMENT | Labels | N |
ABSENT | 54 | |
PRESENT | 62 | |
Significant markers | N = 0 |
One gene related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
Table S40. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED_HE_COUNT'
LYMPH_NODES_EXAMINED_HE_COUNT | Mean (SD) | 1.07 (2.6) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
Table S41. Get Full Table List of one gene significantly correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
ART3|419 | -0.4404 | 5.081e-06 | 0.0925 |
Table S42. Basic characteristics of clinical feature: 'LYMPH_NODES_EXAMINED'
LYMPH_NODES_EXAMINED | Mean (SD) | 22.28 (13) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
Table S43. Get Full Table List of one gene significantly correlated to 'LYMPH_NODES_EXAMINED' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
MAGEA10|4109 | -0.5824 | 1.621e-06 | 0.0295 |
One gene related to 'KERATINIZATION_SQUAMOUS_CELL'.
Table S44. Basic characteristics of clinical feature: 'KERATINIZATION_SQUAMOUS_CELL'
KERATINIZATION_SQUAMOUS_CELL | Labels | N |
KERATINIZING SQUAMOUS CELL CARCINOMA | 39 | |
NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 81 | |
Significant markers | N = 1 | |
Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 1 | |
Higher in KERATINIZING SQUAMOUS CELL CARCINOMA | 0 |
Table S45. Get Full Table List of one gene differentially expressed by 'KERATINIZATION_SQUAMOUS_CELL'
W(pos if higher in 'NON-KERATINIZING SQUAMOUS CELL CARCINOMA') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
QKI|9444 | 792 | 1.036e-05 | 0.188 | 0.7493 |
2 genes related to 'INITIAL_PATHOLOGIC_DX_YEAR'.
Table S46. Basic characteristics of clinical feature: 'INITIAL_PATHOLOGIC_DX_YEAR'
INITIAL_PATHOLOGIC_DX_YEAR | Mean (SD) | 2007.5 (5.1) |
Significant markers | N = 2 | |
pos. correlated | 1 | |
neg. correlated | 1 |
Table S47. Get Full Table List of 2 genes significantly correlated to 'INITIAL_PATHOLOGIC_DX_YEAR' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
C9ORF171|389799 | 0.4376 | 1.034e-05 | 0.188 |
SNAPC5|10302 | -0.3158 | 1.576e-05 | 0.287 |
Table S48. Basic characteristics of clinical feature: 'HYSTERECTOMY_TYPE'
HYSTERECTOMY_TYPE | Labels | N |
OTHER | 3 | |
RADICAL HYSTERECTOMY | 117 | |
SIMPLE HYSTERECTOMY | 5 | |
Significant markers | N = 0 |
No gene 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 | 8 | |
FORMER USER | 40 | |
NEVER USED | 43 | |
Significant markers | N = 0 |
Table S50. Basic characteristics of clinical feature: 'HEIGHT_CM_AT_DIAGNOSIS'
HEIGHT_CM_AT_DIAGNOSIS | Mean (SD) | 162.05 (6.9) |
Significant markers | N = 0 |
Table S51. Basic characteristics of clinical feature: 'CORPUS_INVOLVEMENT'
CORPUS_INVOLVEMENT | Labels | N |
ABSENT | 78 | |
PRESENT | 14 | |
Significant markers | N = 0 |
Table S52. Basic characteristics of clinical feature: 'CERVIX_SUV_RESULTS'
CERVIX_SUV_RESULTS | Mean (SD) | 11.37 (4.1) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
Table S53. Get Full Table List of one gene significantly correlated to 'CERVIX_SUV_RESULTS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
TEX14|56155 | -1 | 5.511e-06 | 0.099 |
Table S54. Basic characteristics of clinical feature: 'AJCC_TUMOR_PATHOLOGIC_PT'
AJCC_TUMOR_PATHOLOGIC_PT | Labels | N |
T1A | 2 | |
T1A1 | 1 | |
T1B | 23 | |
T1B1 | 52 | |
T1B2 | 22 | |
T2 | 3 | |
T2A | 6 | |
T2A1 | 6 | |
T2A2 | 9 | |
T2B | 13 | |
T3B | 2 | |
T4 | 1 | |
TX | 7 | |
Significant markers | N = 0 |
Table S55. Basic characteristics of clinical feature: 'AGE_AT_DIAGNOSIS'
AGE_AT_DIAGNOSIS | Mean (SD) | 47.52 (13) |
Significant markers | N = 15 | |
pos. correlated | 8 | |
neg. correlated | 7 |
Table S56. Get Full Table List of top 10 genes significantly correlated to 'AGE_AT_DIAGNOSIS' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
NXNL2|158046 | -0.4475 | 1.502e-09 | 2.73e-05 |
LOC440356|440356 | 0.3769 | 8.324e-07 | 0.0151 |
C9ORF167|54863 | -0.3487 | 1.615e-06 | 0.0294 |
GPR97|222487 | -0.3467 | 1.863e-06 | 0.0339 |
IGSF9|57549 | 0.3398 | 3.053e-06 | 0.0555 |
UNC119|9094 | 0.3391 | 3.225e-06 | 0.0587 |
PGR|5241 | -0.337 | 3.742e-06 | 0.0681 |
RARB|5915 | 0.3367 | 3.798e-06 | 0.0691 |
INF2|64423 | -0.3336 | 4.732e-06 | 0.0861 |
RRAGD|58528 | 0.3293 | 6.365e-06 | 0.116 |
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Expresson data file = CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = CESC-TP.merged_data.txt
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Number of patients = 180
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Number of genes = 18199
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Number of clinical features = 42
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
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-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
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
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.