This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 8 clinical features across 104 patients, 9 significant findings detected with P value < 0.05 and Q value < 0.25.
-
5 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'LYMPH.NODE.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.
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CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'LYMPH.NODE.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.
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Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that correlate to 'GENDER', 'LYMPH.NODE.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
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4 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature CNMF subtypes'. These subtypes do not correlate to any clinical features.
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3 subtypes identified in current cancer cohort by 'MIRseq Mature cHierClus subtypes'. These subtypes correlate to 'LYMPH.NODE.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | ANOVA | Fisher's exact test | ANOVA | Chi-square test | Chi-square test | ANOVA | Chi-square test |
Copy Number Ratio CNMF subtypes |
0.0309 (1.00) |
0.399 (1.00) |
0.0797 (1.00) |
0.787 (1.00) |
0.684 (1.00) |
0.027 (0.998) |
0.231 (1.00) |
|
METHLYATION CNMF |
0.147 (1.00) |
0.0601 (1.00) |
0.219 (1.00) |
0.192 (1.00) |
0.099 (1.00) |
0.000134 (0.00697) |
2.46e-06 (0.000138) |
|
RNAseq CNMF subtypes |
0.0331 (1.00) |
0.00566 (0.266) |
0.0139 (0.544) |
0.433 (1.00) |
0.0124 (0.498) |
0.00147 (0.0705) |
7.89e-05 (0.00418) |
|
RNAseq cHierClus subtypes |
0.0119 (0.486) |
0.495 (1.00) |
0.000483 (0.0246) |
0.578 (1.00) |
0.00843 (0.362) |
1.53e-05 (0.000827) |
1.4e-05 (0.000772) |
|
MIRSEQ CNMF |
0.876 (1.00) |
0.542 (1.00) |
0.00796 (0.358) |
0.51 (1.00) |
0.459 (1.00) |
0.0618 (1.00) |
0.0115 (0.485) |
|
MIRSEQ CHIERARCHICAL |
0.668 (1.00) |
0.768 (1.00) |
0.00802 (0.358) |
0.535 (1.00) |
0.6 (1.00) |
0.071 (1.00) |
0.0293 (1.00) |
|
MIRseq Mature CNMF subtypes |
0.836 (1.00) |
0.471 (1.00) |
0.163 (1.00) |
0.282 (1.00) |
0.121 (1.00) |
0.223 (1.00) |
0.00749 (0.345) |
|
MIRseq Mature cHierClus subtypes |
0.108 (1.00) |
0.225 (1.00) |
0.0202 (0.767) |
0.255 (1.00) |
0.167 (1.00) |
0.00073 (0.0365) |
0.000811 (0.0398) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Number of samples | 20 | 38 | 9 | 20 | 17 |
P value = 0.0309 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 97 | 14 | 0.0 - 182.7 (13.7) |
subtype1 | 20 | 4 | 0.0 - 80.8 (14.1) |
subtype2 | 34 | 3 | 0.2 - 129.9 (21.0) |
subtype3 | 9 | 1 | 0.0 - 50.5 (15.5) |
subtype4 | 19 | 4 | 0.5 - 25.4 (11.1) |
subtype5 | 15 | 2 | 0.6 - 182.7 (32.1) |
P value = 0.399 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 101 | 59.6 (12.4) |
subtype1 | 20 | 58.5 (16.0) |
subtype2 | 38 | 60.7 (12.9) |
subtype3 | 9 | 52.8 (7.7) |
subtype4 | 19 | 59.7 (10.9) |
subtype5 | 15 | 62.7 (8.9) |
P value = 0.0797 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 70 |
subtype1 | 8 | 12 |
subtype2 | 17 | 21 |
subtype3 | 1 | 8 |
subtype4 | 6 | 14 |
subtype5 | 2 | 15 |
P value = 0.787 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 22 | 87.7 (23.3) |
subtype1 | 4 | 92.5 (5.0) |
subtype2 | 7 | 87.1 (21.4) |
subtype3 | 3 | 93.3 (5.8) |
subtype4 | 6 | 78.3 (38.7) |
subtype5 | 2 | 100.0 (0.0) |
P value = 0.684 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 55 | 5 | 36 |
subtype1 | 9 | 2 | 7 |
subtype2 | 21 | 1 | 14 |
subtype3 | 4 | 0 | 4 |
subtype4 | 10 | 2 | 7 |
subtype5 | 11 | 0 | 4 |
P value = 0.027 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 12 | 4 | 68 |
subtype1 | 5 | 6 | 1 | 8 |
subtype2 | 5 | 2 | 1 | 30 |
subtype3 | 1 | 0 | 0 | 8 |
subtype4 | 7 | 3 | 2 | 8 |
subtype5 | 2 | 1 | 0 | 14 |
P value = 0.231 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 53 | 7 | 24 | 9 |
subtype1 | 7 | 1 | 7 | 3 |
subtype2 | 23 | 4 | 7 | 1 |
subtype3 | 5 | 0 | 1 | 0 |
subtype4 | 7 | 1 | 7 | 4 |
subtype5 | 11 | 1 | 2 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 21 | 40 | 27 |
P value = 0.147 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 81 | 12 | 0.0 - 182.7 (14.6) |
subtype1 | 19 | 4 | 0.0 - 80.8 (26.0) |
subtype2 | 36 | 2 | 0.0 - 129.9 (14.4) |
subtype3 | 26 | 6 | 0.2 - 182.7 (13.3) |
P value = 0.0601 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 85 | 60.0 (12.6) |
subtype1 | 20 | 65.7 (10.9) |
subtype2 | 39 | 57.6 (10.0) |
subtype3 | 26 | 59.2 (15.9) |
P value = 0.219 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 30 | 58 |
subtype1 | 8 | 13 |
subtype2 | 10 | 30 |
subtype3 | 12 | 15 |
P value = 0.192 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 91.9 (12.9) |
subtype1 | 5 | 80.0 (22.4) |
subtype2 | 14 | 95.7 (5.1) |
subtype3 | 2 | 95.0 (7.1) |
P value = 0.099 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 45 | 4 | 36 |
subtype1 | 12 | 1 | 7 |
subtype2 | 17 | 0 | 21 |
subtype3 | 16 | 3 | 8 |
P value = 0.000134 (Chi-square test), Q value = 0.007
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 10 | 4 | 54 |
subtype1 | 3 | 2 | 1 | 15 |
subtype2 | 8 | 0 | 0 | 32 |
subtype3 | 9 | 8 | 3 | 7 |
P value = 2.46e-06 (Chi-square test), Q value = 0.00014
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 48 | 5 | 23 | 8 |
subtype1 | 14 | 1 | 3 | 2 |
subtype2 | 30 | 3 | 4 | 0 |
subtype3 | 4 | 1 | 16 | 6 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 26 | 24 | 25 |
P value = 0.0331 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 72 | 13 | 0.5 - 182.7 (15.1) |
subtype1 | 24 | 3 | 0.5 - 54.9 (13.1) |
subtype2 | 23 | 8 | 0.9 - 93.3 (13.2) |
subtype3 | 25 | 2 | 6.4 - 182.7 (26.0) |
P value = 0.00566 (ANOVA), Q value = 0.27
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 72 | 59.7 (13.1) |
subtype1 | 24 | 56.5 (12.1) |
subtype2 | 23 | 55.8 (14.2) |
subtype3 | 25 | 66.3 (10.5) |
P value = 0.0139 (Fisher's exact test), Q value = 0.54
nPatients | FEMALE | MALE |
---|---|---|
ALL | 23 | 52 |
subtype1 | 5 | 21 |
subtype2 | 13 | 11 |
subtype3 | 5 | 20 |
P value = 0.433 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 12 | 86.7 (27.7) |
subtype1 | 7 | 94.3 (5.3) |
subtype2 | 3 | 63.3 (55.1) |
subtype3 | 2 | 95.0 (7.1) |
P value = 0.0124 (Chi-square test), Q value = 0.5
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 47 | 5 | 17 |
subtype1 | 15 | 0 | 7 |
subtype2 | 12 | 5 | 6 |
subtype3 | 20 | 0 | 4 |
P value = 0.00147 (Chi-square test), Q value = 0.07
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 15 | 12 | 3 | 45 |
subtype1 | 2 | 0 | 0 | 24 |
subtype2 | 6 | 8 | 2 | 8 |
subtype3 | 7 | 4 | 1 | 13 |
P value = 7.89e-05 (Chi-square test), Q value = 0.0042
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 35 | 3 | 21 | 8 |
subtype1 | 19 | 0 | 2 | 0 |
subtype2 | 4 | 1 | 10 | 7 |
subtype3 | 12 | 2 | 9 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 18 | 36 | 21 |
P value = 0.0119 (logrank test), Q value = 0.49
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 72 | 13 | 0.5 - 182.7 (15.1) |
subtype1 | 17 | 6 | 2.8 - 80.8 (10.8) |
subtype2 | 34 | 3 | 0.5 - 182.7 (13.8) |
subtype3 | 21 | 4 | 0.9 - 123.6 (25.1) |
P value = 0.495 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 72 | 59.7 (13.1) |
subtype1 | 17 | 57.3 (15.0) |
subtype2 | 34 | 59.3 (11.7) |
subtype3 | 21 | 62.3 (13.7) |
P value = 0.000483 (Fisher's exact test), Q value = 0.025
nPatients | FEMALE | MALE |
---|---|---|
ALL | 23 | 52 |
subtype1 | 11 | 7 |
subtype2 | 4 | 32 |
subtype3 | 8 | 13 |
P value = 0.578 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 12 | 86.7 (27.7) |
subtype1 | 3 | 93.3 (5.8) |
subtype2 | 7 | 95.7 (5.3) |
subtype3 | 2 | 45.0 (63.6) |
P value = 0.00843 (Chi-square test), Q value = 0.36
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 47 | 5 | 17 |
subtype1 | 9 | 4 | 4 |
subtype2 | 20 | 0 | 11 |
subtype3 | 18 | 1 | 2 |
P value = 1.53e-05 (Chi-square test), Q value = 0.00083
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 15 | 12 | 3 | 45 |
subtype1 | 1 | 6 | 2 | 9 |
subtype2 | 4 | 1 | 0 | 31 |
subtype3 | 10 | 5 | 1 | 5 |
P value = 1.4e-05 (Chi-square test), Q value = 0.00077
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 35 | 3 | 21 | 8 |
subtype1 | 6 | 1 | 3 | 6 |
subtype2 | 24 | 1 | 4 | 1 |
subtype3 | 5 | 1 | 14 | 1 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 28 | 37 | 22 | 17 |
P value = 0.876 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 97 | 14 | 0.0 - 182.7 (13.7) |
subtype1 | 23 | 2 | 0.0 - 96.9 (5.8) |
subtype2 | 35 | 6 | 0.2 - 182.7 (19.2) |
subtype3 | 22 | 2 | 3.6 - 63.7 (19.9) |
subtype4 | 17 | 4 | 0.5 - 123.6 (21.6) |
P value = 0.542 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 101 | 59.6 (12.4) |
subtype1 | 25 | 60.6 (10.1) |
subtype2 | 37 | 57.5 (14.3) |
subtype3 | 22 | 62.2 (11.7) |
subtype4 | 17 | 59.5 (12.1) |
P value = 0.00796 (Fisher's exact test), Q value = 0.36
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 70 |
subtype1 | 7 | 21 |
subtype2 | 16 | 21 |
subtype3 | 2 | 20 |
subtype4 | 9 | 8 |
P value = 0.51 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 22 | 87.7 (23.3) |
subtype1 | 4 | 95.0 (5.8) |
subtype2 | 12 | 81.7 (30.4) |
subtype3 | 4 | 95.0 (5.8) |
subtype4 | 2 | 95.0 (7.1) |
P value = 0.459 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 55 | 5 | 36 |
subtype1 | 13 | 0 | 9 |
subtype2 | 19 | 3 | 15 |
subtype3 | 13 | 0 | 8 |
subtype4 | 10 | 2 | 4 |
P value = 0.0618 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 12 | 4 | 68 |
subtype1 | 3 | 0 | 0 | 25 |
subtype2 | 6 | 6 | 3 | 22 |
subtype3 | 5 | 3 | 0 | 14 |
subtype4 | 6 | 3 | 1 | 7 |
P value = 0.0115 (Chi-square test), Q value = 0.49
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 53 | 7 | 24 | 9 |
subtype1 | 17 | 1 | 3 | 0 |
subtype2 | 20 | 3 | 6 | 7 |
subtype3 | 11 | 3 | 7 | 0 |
subtype4 | 5 | 0 | 8 | 2 |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 37 | 29 | 10 | 28 |
P value = 0.668 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 97 | 14 | 0.0 - 182.7 (13.7) |
subtype1 | 33 | 5 | 0.2 - 129.9 (15.5) |
subtype2 | 29 | 6 | 0.9 - 86.7 (14.6) |
subtype3 | 9 | 1 | 3.8 - 182.7 (32.1) |
subtype4 | 26 | 2 | 0.0 - 123.6 (6.6) |
P value = 0.768 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 101 | 59.6 (12.4) |
subtype1 | 36 | 58.4 (14.0) |
subtype2 | 29 | 61.0 (13.6) |
subtype3 | 9 | 62.2 (10.0) |
subtype4 | 27 | 59.1 (9.6) |
P value = 0.00802 (Fisher's exact test), Q value = 0.36
nPatients | FEMALE | MALE |
---|---|---|
ALL | 34 | 70 |
subtype1 | 18 | 19 |
subtype2 | 6 | 23 |
subtype3 | 0 | 10 |
subtype4 | 10 | 18 |
P value = 0.535 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 22 | 87.7 (23.3) |
subtype1 | 11 | 89.1 (17.0) |
subtype2 | 6 | 78.3 (38.7) |
subtype3 | 1 | 100.0 (NA) |
subtype4 | 4 | 95.0 (5.8) |
P value = 0.6 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 55 | 5 | 36 |
subtype1 | 18 | 3 | 16 |
subtype2 | 19 | 2 | 8 |
subtype3 | 6 | 0 | 3 |
subtype4 | 12 | 0 | 9 |
P value = 0.071 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 12 | 4 | 68 |
subtype1 | 6 | 5 | 3 | 23 |
subtype2 | 9 | 6 | 1 | 13 |
subtype3 | 1 | 1 | 0 | 8 |
subtype4 | 4 | 0 | 0 | 24 |
P value = 0.0293 (Chi-square test), Q value = 1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 53 | 7 | 24 | 9 |
subtype1 | 20 | 3 | 7 | 6 |
subtype2 | 11 | 2 | 14 | 2 |
subtype3 | 8 | 0 | 0 | 1 |
subtype4 | 14 | 2 | 3 | 0 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 30 | 35 | 23 |
P value = 0.836 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 81 | 12 | 0.0 - 182.7 (14.6) |
subtype1 | 29 | 4 | 0.0 - 123.6 (26.0) |
subtype2 | 33 | 6 | 0.2 - 182.7 (20.1) |
subtype3 | 19 | 2 | 0.0 - 51.2 (12.7) |
P value = 0.471 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 85 | 60.0 (12.6) |
subtype1 | 29 | 62.3 (12.2) |
subtype2 | 35 | 58.7 (14.5) |
subtype3 | 21 | 58.9 (9.5) |
P value = 0.163 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 30 | 58 |
subtype1 | 7 | 23 |
subtype2 | 16 | 19 |
subtype3 | 7 | 16 |
P value = 0.282 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 91.9 (12.9) |
subtype1 | 4 | 95.0 (5.8) |
subtype2 | 9 | 86.7 (18.0) |
subtype3 | 8 | 96.2 (5.2) |
P value = 0.121 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 45 | 4 | 36 |
subtype1 | 20 | 0 | 8 |
subtype2 | 16 | 3 | 16 |
subtype3 | 9 | 1 | 12 |
P value = 0.223 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 10 | 4 | 54 |
subtype1 | 10 | 3 | 1 | 16 |
subtype2 | 6 | 6 | 3 | 20 |
subtype3 | 4 | 1 | 0 | 18 |
P value = 0.00749 (Chi-square test), Q value = 0.34
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 48 | 5 | 23 | 8 |
subtype1 | 12 | 2 | 14 | 0 |
subtype2 | 20 | 2 | 6 | 7 |
subtype3 | 16 | 1 | 3 | 1 |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 37 | 15 | 36 |
P value = 0.108 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 81 | 12 | 0.0 - 182.7 (14.6) |
subtype1 | 33 | 1 | 0.0 - 123.6 (13.6) |
subtype2 | 15 | 5 | 0.9 - 86.7 (21.6) |
subtype3 | 33 | 6 | 0.2 - 182.7 (20.1) |
P value = 0.225 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 85 | 60.0 (12.6) |
subtype1 | 35 | 59.7 (9.6) |
subtype2 | 15 | 64.9 (14.1) |
subtype3 | 35 | 58.2 (14.3) |
P value = 0.0202 (Fisher's exact test), Q value = 0.77
nPatients | FEMALE | MALE |
---|---|---|
ALL | 30 | 58 |
subtype1 | 7 | 30 |
subtype2 | 5 | 10 |
subtype3 | 18 | 18 |
P value = 0.255 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 91.9 (12.9) |
subtype1 | 9 | 95.6 (5.3) |
subtype2 | 1 | 90.0 (NA) |
subtype3 | 11 | 89.1 (17.0) |
P value = 0.167 (Chi-square test), Q value = 1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 45 | 4 | 36 |
subtype1 | 17 | 0 | 17 |
subtype2 | 11 | 1 | 3 |
subtype3 | 17 | 3 | 16 |
P value = 0.00073 (Chi-square test), Q value = 0.036
nPatients | N0 | N1 | N2 | NX |
---|---|---|---|---|
ALL | 20 | 10 | 4 | 54 |
subtype1 | 6 | 0 | 0 | 31 |
subtype2 | 7 | 4 | 1 | 3 |
subtype3 | 7 | 6 | 3 | 20 |
P value = 0.000811 (Chi-square test), Q value = 0.04
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 48 | 5 | 23 | 8 |
subtype1 | 25 | 2 | 6 | 0 |
subtype2 | 3 | 1 | 10 | 1 |
subtype3 | 20 | 2 | 7 | 7 |
-
Cluster data file = KIRP-TP.mergedcluster.txt
-
Clinical data file = KIRP-TP.clin.merged.picked.txt
-
Number of patients = 104
-
Number of clustering approaches = 8
-
Number of selected clinical features = 8
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary clinical features, two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.