This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 18197 genes and 45 clinical features across 239 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 16 clinical features related to at least one genes.
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13 genes correlated to 'Time to Death'.
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TM2D1|83941 , GATS|352954 , ZER1|10444 , EGLN1|54583 , PEAR1|375033 , ...
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41 genes correlated to 'AGE'.
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NXNL2|158046 , RHOF|54509 , LANCL1|10314 , RARB|5915 , DBI|1622 , ...
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1 gene correlated to 'PATHOLOGY.N.STAGE'.
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ART3|419
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1908 genes correlated to 'HISTOLOGICAL.TYPE'.
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EPCAM|4072 , TP63|8626 , GPR109A|338442 , BICD2|23299 , GM2A|2760 , ...
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2 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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CD99L2|83692 , ART3|419
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2 genes correlated to 'RACE'.
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XKR9|389668 , RNF112|7732
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5 genes correlated to 'WEIGHT_KG_AT_DIAGNOSIS'.
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HCG26|352961 , AGER|177 , NUBP1|4682 , AKAP5|9495 , BLOC1S1|2647
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4 genes correlated to 'NEOPLASMHISTOLOGICGRADE'.
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ABLIM1|3983 , CDS1|1040 , FUT6|2528 , FUT2|2524
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1 gene correlated to 'TOBACCO_SMOKING_HISTORY'.
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GPR15|2838
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4 genes correlated to 'MENOPAUSE_STATUS'.
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SSBP3|23648 , RARB|5915 , DBI|1622 , PRSS23|11098
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2 genes correlated to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
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CD99L2|83692 , ART3|419
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1 gene correlated to 'KERATINIZATION_SQUAMOUS_CELL'.
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QKI|9444
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1 gene correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.
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C9ORF171|389799
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7 genes correlated to 'CERVIX_SUV_RESULTS'.
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C14ORF33|100129075 , C7ORF11|136647 , ELFN2|114794 , GRK7|131890 , HAMP|57817 , ...
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1 gene correlated to 'AJCC_TUMOR_PATHOLOGIC_PT'.
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FBXL18|80028
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38 genes correlated to 'AGE_AT_DIAGNOSIS'.
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NXNL2|158046 , DBI|1622 , GPR97|222487 , UBASH3B|84959 , PGR|5241 , ...
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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', 'TOBACCO_SMOKING_YEAR_STOPPED', 'TOBACCO_SMOKING_PACK_YEARS_SMOKED', 'PATIENT.AGEBEGANSMOKINGINYEARS', 'RADIATION_TOTAL_DOSE', 'RADIATION_THERAPY_TYPE', 'RADIATION_THERAPY_STATUS', 'RADIATION_THERAPY_SITE', 'RADIATION_ADJUVANT_UNITS', 'PREGNANCIES_COUNT_TOTAL', 'PREGNANCIES_COUNT_STILLBIRTH', 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT', 'PREGNANCIES_COUNT_LIVE_BIRTH', 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT', 'PREGNANCIES_COUNT_ECTOPIC', 'POS_LYMPH_NODE_LOCATION', 'LYMPHOVASCULAR_INVOLVEMENT', 'LYMPH_NODES_EXAMINED', 'HISTORY_HORMONAL_CONTRACEPTIVES_USE', 'HEIGHT_CM_AT_DIAGNOSIS', 'CORPUS_INVOLVEMENT', 'CHEMO_CONCURRENT_TYPE', and 'STAGE_EVENT.CLINICAL_STAGE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=13 | shorter survival | N=5 | longer survival | N=8 |
AGE | Spearman correlation test | N=41 | older | N=15 | younger | N=26 |
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=1908 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=2 | higher number.of.lymph.nodes | N=0 | lower number.of.lymph.nodes | N=2 |
RACE | Kruskal-Wallis test | N=2 | ||||
ETHNICITY | Wilcoxon test | N=0 | ||||
WEIGHT_KG_AT_DIAGNOSIS | Spearman correlation test | N=5 | higher weight_kg_at_diagnosis | N=5 | 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=4 | ||||
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=1 | ||||
PATIENT AGEBEGANSMOKINGINYEARS | Spearman correlation test | N=0 | ||||
RADIATION_TOTAL_DOSE | Spearman correlation test | N=0 | ||||
RADIATION_THERAPY_TYPE | Kruskal-Wallis test | N=0 | ||||
RADIATION_THERAPY_STATUS | Wilcoxon test | N=0 | ||||
RADIATION_THERAPY_SITE | 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 | ||||
POS_LYMPH_NODE_LOCATION | Kruskal-Wallis test | N=0 | ||||
MENOPAUSE_STATUS | Kruskal-Wallis test | N=4 | ||||
LYMPHOVASCULAR_INVOLVEMENT | Wilcoxon test | N=0 | ||||
LYMPH_NODES_EXAMINED_HE_COUNT | Spearman correlation test | N=2 | higher lymph_nodes_examined_he_count | N=0 | lower lymph_nodes_examined_he_count | N=2 |
LYMPH_NODES_EXAMINED | Spearman correlation test | N=0 | ||||
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=1 | higher initial_pathologic_dx_year | N=1 | lower initial_pathologic_dx_year | 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 | ||||
CHEMO_CONCURRENT_TYPE | Kruskal-Wallis test | N=0 | ||||
CERVIX_SUV_RESULTS | Spearman correlation test | N=7 | higher cervix_suv_results | N=4 | lower cervix_suv_results | N=3 |
AJCC_TUMOR_PATHOLOGIC_PT | Kruskal-Wallis test | N=1 | ||||
AGE_AT_DIAGNOSIS | Spearman correlation test | N=38 | higher age_at_diagnosis | N=13 | lower age_at_diagnosis | N=25 |
STAGE_EVENT CLINICAL_STAGE | Kruskal-Wallis test | N=0 |
Time to Death | Duration (Months) | 0-195.8 (median=15.9) |
censored | N = 183 | |
death | N = 51 | |
Significant markers | N = 13 | |
associated with shorter survival | 5 | |
associated with longer survival | 8 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
TM2D1|83941 | 2.4 | 3.406e-08 | 0.00062 | 0.623 |
GATS|352954 | 0.53 | 7.138e-08 | 0.0013 | 0.26 |
ZER1|10444 | 0.17 | 4.925e-07 | 0.009 | 0.31 |
EGLN1|54583 | 2.8 | 6.313e-07 | 0.011 | 0.708 |
PEAR1|375033 | 1.62 | 1.485e-06 | 0.027 | 0.715 |
UBAC1|10422 | 0.24 | 4.825e-06 | 0.088 | 0.326 |
RIBC2|26150 | 0.74 | 6.89e-06 | 0.13 | 0.303 |
FAM95B1|100133036 | 0.75 | 1.065e-05 | 0.19 | 0.309 |
MATN3|4148 | 1.28 | 1.125e-05 | 0.2 | 0.693 |
ITGA5|3678 | 1.5 | 1.158e-05 | 0.21 | 0.678 |
AGE | Mean (SD) | 47.19 (13) |
Significant markers | N = 41 | |
pos. correlated | 15 | |
neg. correlated | 26 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NXNL2|158046 | -0.4105 | 2.865e-10 | 5.21e-06 |
RHOF|54509 | -0.3212 | 4.866e-07 | 0.00885 |
LANCL1|10314 | 0.3201 | 5.352e-07 | 0.00974 |
RARB|5915 | 0.3195 | 5.607e-07 | 0.0102 |
DBI|1622 | 0.3157 | 7.811e-07 | 0.0142 |
LHFPL1|340596 | 0.3642 | 9.04e-07 | 0.0164 |
GPR97|222487 | -0.3136 | 9.267e-07 | 0.0169 |
HSFX2|100130086 | 0.3122 | 1.046e-06 | 0.019 |
UBASH3B|84959 | -0.3097 | 1.287e-06 | 0.0234 |
PGR|5241 | -0.3065 | 1.768e-06 | 0.0321 |
PATHOLOGY.T.STAGE | Mean (SD) | 1.4 (0.66) |
N | ||
1 | 123 | |
2 | 47 | |
3 | 8 | |
4 | 3 | |
Significant markers | N = 0 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 112 | |
class1 | 49 | |
Significant markers | N = 1 | |
Higher in class1 | 1 | |
Higher in class0 | 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 96 | |
M1 | 8 | |
MX | 88 | |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
ADENOSQUAMOUS | 4 | |
CERVICAL SQUAMOUS CELL CARCINOMA | 200 | |
ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | 5 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 22 | |
ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | 2 | |
MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE | 6 | |
Significant markers | N = 1908 |
ANOVA_P | Q | |
---|---|---|
EPCAM|4072 | 4.376e-17 | 7.96e-13 |
TP63|8626 | 4.516e-17 | 8.22e-13 |
GPR109A|338442 | 5.078e-17 | 9.24e-13 |
BICD2|23299 | 7.959e-17 | 1.45e-12 |
GM2A|2760 | 1.345e-16 | 2.45e-12 |
DDAH1|23576 | 1.851e-16 | 3.37e-12 |
GPR109B|8843 | 2.906e-16 | 5.29e-12 |
C3ORF54|389119 | 3.508e-16 | 6.38e-12 |
CLDN3|1365 | 3.865e-16 | 7.03e-12 |
PPP1R9A|55607 | 4.769e-16 | 8.67e-12 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 33 | |
YES | 206 | |
Significant markers | N = 0 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 18.37 (13) |
Significant markers | N = 0 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 1 (2.4) |
Significant markers | N = 2 | |
pos. correlated | 0 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
CD99L2|83692 | -0.3622 | 1.18e-05 | 0.215 |
ART3|419 | -0.383 | 1.334e-05 | 0.243 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 7 | |
ASIAN | 18 | |
BLACK OR AFRICAN AMERICAN | 26 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 1 | |
WHITE | 170 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
XKR9|389668 | 1.445e-06 | 0.0263 |
RNF112|7732 | 1.005e-05 | 0.183 |
ETHNICITY | Labels | N |
HISPANIC OR LATINO | 17 | |
NOT HISPANIC OR LATINO | 151 | |
Significant markers | N = 0 |
WEIGHT_KG_AT_DIAGNOSIS | Mean (SD) | 74.9 (22) |
Significant markers | N = 5 | |
pos. correlated | 5 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HCG26|352961 | 0.3222 | 1.24e-06 | 0.0226 |
AGER|177 | 0.3196 | 1.53e-06 | 0.0278 |
NUBP1|4682 | 0.3091 | 3.46e-06 | 0.063 |
AKAP5|9495 | 0.2986 | 7.635e-06 | 0.139 |
BLOC1S1|2647 | 0.2917 | 1.26e-05 | 0.229 |
TUMOR_STATUS | Labels | N |
TUMOR FREE | 74 | |
WITH TUMOR | 26 | |
Significant markers | N = 0 |
No gene related to 'TUMOR_SAMPLE_PROCUREMENT_COUNTRY'.
TUMOR_SAMPLE_PROCUREMENT_COUNTRY | Labels | N |
BRAZIL | 20 | |
CANADA | 5 | |
NIGERIA | 1 | |
RUSSIA | 11 | |
UKRAINE | 7 | |
UNITED STATES | 181 | |
VIETNAM | 14 | |
Significant markers | N = 0 |
NEOPLASMHISTOLOGICGRADE | Labels | N |
G1 | 15 | |
G2 | 110 | |
G3 | 96 | |
G4 | 1 | |
GX | 14 | |
Significant markers | N = 4 |
No gene related to 'TOBACCO_SMOKING_YEAR_STOPPED'.
TOBACCO_SMOKING_YEAR_STOPPED | Mean (SD) | 2000.41 (11) |
Significant markers | N = 0 |
No gene related to 'TOBACCO_SMOKING_PACK_YEARS_SMOKED'.
TOBACCO_SMOKING_PACK_YEARS_SMOKED | Mean (SD) | 18.37 (13) |
Significant markers | N = 0 |
TOBACCO_SMOKING_HISTORY | Labels | N |
CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | 33 | |
CURRENT REFORMED SMOKER FOR > 15 YEARS | 8 | |
CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED | 3 | |
CURRENT SMOKER | 52 | |
LIFELONG NON-SMOKER | 106 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
GPR15|2838 | 7.275e-07 | 0.0132 |
No gene related to 'PATIENT.AGEBEGANSMOKINGINYEARS'.
PATIENT.AGEBEGANSMOKINGINYEARS | Mean (SD) | 21.48 (7.9) |
Significant markers | N = 0 |
RADIATION_TOTAL_DOSE | Mean (SD) | 3950.73 (1600) |
Significant markers | N = 0 |
RADIATION_THERAPY_TYPE | Labels | N |
COMBINATION | 19 | |
EXTERNAL | 72 | |
EXTERNAL BEAM | 15 | |
INTERNAL | 11 | |
Significant markers | N = 0 |
RADIATION_THERAPY_STATUS | Labels | N |
COMPLETED AS PLANNED | 28 | |
TREATMENT NOT COMPLETED | 3 | |
Significant markers | N = 0 |
RADIATION_THERAPY_SITE | Labels | N |
DISTANT RECURRENCE | 2 | |
LOCAL RECURRENCE | 2 | |
PRIMARY TUMOR FIELD | 28 | |
REGIONAL SITE | 13 | |
Significant markers | N = 0 |
RADIATION_ADJUVANT_UNITS | Labels | N |
CGY | 31 | |
GY | 3 | |
Significant markers | N = 0 |
PREGNANCIES_COUNT_TOTAL | Mean (SD) | 3.55 (2.5) |
Significant markers | N = 0 |
No gene related to 'PREGNANCIES_COUNT_STILLBIRTH'.
PREGNANCIES_COUNT_STILLBIRTH | Mean (SD) | 0.08 (0.36) |
Value | N | |
0 | 98 | |
1 | 5 | |
3 | 1 | |
Significant markers | N = 0 |
No gene related to 'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT'.
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT | Mean (SD) | 0.46 (0.83) |
Significant markers | N = 0 |
No gene related to 'PREGNANCIES_COUNT_LIVE_BIRTH'.
PREGNANCIES_COUNT_LIVE_BIRTH | Mean (SD) | 2.59 (1.8) |
Significant markers | N = 0 |
No gene related to 'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT'.
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT | Mean (SD) | 0.89 (1.9) |
Significant markers | N = 0 |
PREGNANCIES_COUNT_ECTOPIC | Mean (SD) | 0.1 (0.34) |
Value | N | |
0 | 96 | |
1 | 9 | |
2 | 1 | |
Significant markers | N = 0 |
POS_LYMPH_NODE_LOCATION | Labels | N |
MACROSCOPIC PARAMETRIAL INVOLVEMENT | 2 | |
MICROSCOPIC PARAMETRIAL INVOLVEMENT | 6 | |
OTHER LOCATION, SPECIFY | 32 | |
POSITIVE BLADDER MARGIN | 1 | |
POSITIVE VAGINAL MARGIN | 8 | |
Significant markers | N = 0 |
MENOPAUSE_STATUS | Labels | N |
INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) | 2 | |
PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) | 15 | |
POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) | 65 | |
PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT) | 105 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
SSBP3|23648 | 2.565e-06 | 0.0467 |
RARB|5915 | 6.525e-06 | 0.119 |
DBI|1622 | 8.399e-06 | 0.153 |
PRSS23|11098 | 1.112e-05 | 0.202 |
No gene related to 'LYMPHOVASCULAR_INVOLVEMENT'.
LYMPHOVASCULAR_INVOLVEMENT | Labels | N |
ABSENT | 67 | |
PRESENT | 71 | |
Significant markers | N = 0 |
2 genes related to 'LYMPH_NODES_EXAMINED_HE_COUNT'.
LYMPH_NODES_EXAMINED_HE_COUNT | Mean (SD) | 1 (2.4) |
Significant markers | N = 2 | |
pos. correlated | 0 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
CD99L2|83692 | -0.3622 | 1.18e-05 | 0.215 |
ART3|419 | -0.383 | 1.334e-05 | 0.243 |
LYMPH_NODES_EXAMINED | Mean (SD) | 21.77 (12) |
Significant markers | N = 0 |
One gene related to 'KERATINIZATION_SQUAMOUS_CELL'.
KERATINIZATION_SQUAMOUS_CELL | Labels | N |
KERATINIZING SQUAMOUS CELL CARCINOMA | 48 | |
NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 94 | |
Significant markers | N = 1 | |
Higher in NON-KERATINIZING SQUAMOUS CELL CARCINOMA | 1 | |
Higher in KERATINIZING SQUAMOUS CELL CARCINOMA | 0 |
One gene related to 'INITIAL_PATHOLOGIC_DX_YEAR'.
INITIAL_PATHOLOGIC_DX_YEAR | Mean (SD) | 2007.73 (5) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
C9ORF171|389799 | 0.3893 | 9.346e-06 | 0.17 |
No gene related to 'HISTORY_HORMONAL_CONTRACEPTIVES_USE'.
HISTORY_HORMONAL_CONTRACEPTIVES_USE | Labels | N |
CURRENT USER | 10 | |
FORMER USER | 47 | |
NEVER USED | 56 | |
Significant markers | N = 0 |
HEIGHT_CM_AT_DIAGNOSIS | Mean (SD) | 161.78 (6.7) |
Significant markers | N = 0 |
CORPUS_INVOLVEMENT | Labels | N |
ABSENT | 93 | |
PRESENT | 16 | |
Significant markers | N = 0 |
CHEMO_CONCURRENT_TYPE | Labels | N |
CARBOPLATIN | 2 | |
CISPLATIN | 17 | |
OTHER | 1 | |
Significant markers | N = 0 |
CERVIX_SUV_RESULTS | Mean (SD) | 12.43 (5.5) |
Significant markers | N = 7 | |
pos. correlated | 4 | |
neg. correlated | 3 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
C14ORF33|100129075 | 0.9066 | 0 | 0 |
C7ORF11|136647 | 0.956 | 0 | 0 |
ELFN2|114794 | 0.9231 | 0 | 0 |
GRK7|131890 | -0.9273 | 0 | 0 |
HAMP|57817 | -0.8956 | 0 | 0 |
MBD4|8930 | -0.9341 | 0 | 0 |
PTPRR|5801 | 0.9161 | 0 | 0 |
AJCC_TUMOR_PATHOLOGIC_PT | Labels | N |
T1A | 1 | |
T1A1 | 1 | |
T1B | 32 | |
T1B1 | 64 | |
T1B2 | 25 | |
T2 | 4 | |
T2A | 8 | |
T2A1 | 7 | |
T2A2 | 10 | |
T2B | 18 | |
T3 | 1 | |
T3B | 7 | |
T4 | 3 | |
TIS | 1 | |
TX | 15 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
FBXL18|80028 | 3.373e-06 | 0.0614 |
AGE_AT_DIAGNOSIS | Mean (SD) | 47.32 (13) |
Significant markers | N = 38 | |
pos. correlated | 13 | |
neg. correlated | 25 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
NXNL2|158046 | -0.4092 | 2.741e-10 | 4.99e-06 |
DBI|1622 | 0.3213 | 3.857e-07 | 0.00702 |
GPR97|222487 | -0.3188 | 4.774e-07 | 0.00869 |
UBASH3B|84959 | -0.3118 | 8.731e-07 | 0.0159 |
PGR|5241 | -0.3122 | 8.871e-07 | 0.0161 |
RHOF|54509 | -0.3113 | 9.101e-07 | 0.0166 |
LOC440356|440356 | 0.3281 | 9.75e-07 | 0.0177 |
C20ORF151|140893 | 0.3077 | 1.239e-06 | 0.0225 |
RARB|5915 | 0.3075 | 1.253e-06 | 0.0228 |
LHFPL1|340596 | 0.3564 | 1.293e-06 | 0.0235 |
No gene related to 'STAGE_EVENT.CLINICAL_STAGE'.
STAGE_EVENT.CLINICAL_STAGE | Labels | N |
STAGE I | 4 | |
STAGE IA | 2 | |
STAGE IA1 | 1 | |
STAGE IA2 | 1 | |
STAGE IB | 34 | |
STAGE IB1 | 67 | |
STAGE IB2 | 34 | |
STAGE II | 4 | |
STAGE IIA | 6 | |
STAGE IIA1 | 5 | |
STAGE IIA2 | 7 | |
STAGE IIB | 23 | |
STAGE III | 1 | |
STAGE IIIB | 33 | |
STAGE IVA | 4 | |
STAGE IVB | 7 | |
Significant markers | N = 0 |
-
Expresson data file = CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Clinical data file = CESC-TP.merged_data.txt
-
Number of patients = 239
-
Number of genes = 18197
-
Number of clinical features = 45
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.