This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.
Testing the association between 160 genes and 11 clinical features across 212 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 7 clinical features related to at least one genes.
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4 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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ARID1A|ARID1A-M-V , RPS6|S6_PS240_S244-R-V , MAPK1 MAPK3|MAPK_PT202_Y204-R-V , CHGA|CHROMOGRANIN-A-N-TERM-R-E
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9 genes correlated to 'PATHOLOGY.T.STAGE'.
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ARID1A|ARID1A-M-V , MAPK1 MAPK3|MAPK_PT202_Y204-R-V , RPS6|S6_PS240_S244-R-V , RPS6|S6_PS235_S236-R-V , AKT1 AKT2 AKT3|AKT_PS473-R-V , ...
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8 genes correlated to 'PATHOLOGY.N.STAGE'.
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SRC|SRC_PY416-R-C , ANXA1|ANNEXIN_I-R-V , YAP1|YAP_PS127-R-C , MAPK9|JNK2-R-C , PRKCA |PKC-ALPHA_PS657-R-V , ...
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6 genes correlated to 'GENDER'.
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YAP1|YAP_PS127-R-C , MAPK14|P38_PT180_Y182-R-V , MAPK1 MAPK3|MAPK_PT202_Y204-R-V , RPS6|S6_PS235_S236-R-V , BAD|BAD_PS112-R-V , ...
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2 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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BCL2|BCL-2-M-V , COL6A1|COLLAGEN_VI-R-V
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2 genes correlated to 'NUMBERPACKYEARSSMOKED'.
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TP63|P63-R-E , CHEK2|CHK2-M-C
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8 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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ANXA1|ANNEXIN_I-R-V , SRC|SRC_PY416-R-C , YAP1|YAP_PS127-R-C , PRKCA |PKC-ALPHA_PS657-R-V , FN1|FIBRONECTIN-R-C , ...
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No genes correlated to 'Time to Death', 'AGE', 'RACE', and 'ETHNICITY'.
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=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=4 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=9 | higher stage | N=3 | lower stage | N=6 |
PATHOLOGY N STAGE | Spearman correlation test | N=8 | higher stage | N=3 | lower stage | N=5 |
GENDER | Wilcoxon test | N=6 | male | N=6 | female | N=0 |
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=2 | yes | N=2 | no | N=0 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=2 | higher numberpackyearssmoked | N=2 | lower numberpackyearssmoked | N=0 |
NUMBER OF LYMPH NODES | Spearman correlation test | N=8 | higher number.of.lymph.nodes | N=4 | lower number.of.lymph.nodes | N=4 |
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Years) | 45-3837 (median=1207) |
censored | N = 92 | |
death | N = 77 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.12 (12) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 9 | |
STAGE II | 39 | |
STAGE III | 31 | |
STAGE IVA | 117 | |
STAGE IVB | 4 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
ARID1A|ARID1A-M-V | 5.173e-06 | 0.000828 |
RPS6|S6_PS240_S244-R-V | 0.0006838 | 0.109 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | 0.0009772 | 0.154 |
CHGA|CHROMOGRANIN-A-N-TERM-R-E | 0.001507 | 0.237 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.97 (0.97) |
N | ||
1 | 13 | |
2 | 59 | |
3 | 53 | |
4 | 79 | |
Significant markers | N = 9 | |
pos. correlated | 3 | |
neg. correlated | 6 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ARID1A|ARID1A-M-V | 0.3335 | 1.095e-06 | 0.000175 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | -0.2974 | 1.558e-05 | 0.00248 |
RPS6|S6_PS240_S244-R-V | -0.292 | 2.253e-05 | 0.00356 |
RPS6|S6_PS235_S236-R-V | -0.2897 | 2.644e-05 | 0.00415 |
AKT1 AKT2 AKT3|AKT_PS473-R-V | -0.2709 | 8.895e-05 | 0.0139 |
MAPK14|P38_PT180_Y182-R-V | -0.2475 | 0.0003584 | 0.0555 |
SRC|SRC_PY527-R-V | -0.2423 | 0.0004812 | 0.0741 |
CCNB1|CYCLIN_B1-R-V | 0.239 | 0.0005756 | 0.0881 |
CDC2|CDK1-R-V | 0.2294 | 0.0009677 | 0.147 |
PATHOLOGY.N.STAGE | Mean (SD) | 1.09 (0.97) |
N | ||
0 | 72 | |
1 | 21 | |
2 | 79 | |
3 | 4 | |
Significant markers | N = 8 | |
pos. correlated | 3 | |
neg. correlated | 5 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SRC|SRC_PY416-R-C | -0.3268 | 9.593e-06 | 0.00153 |
ANXA1|ANNEXIN_I-R-V | -0.2868 | 0.0001137 | 0.0181 |
YAP1|YAP_PS127-R-C | -0.2743 | 0.0002296 | 0.0363 |
MAPK9|JNK2-R-C | 0.2675 | 0.0003315 | 0.052 |
PRKCA |PKC-ALPHA_PS657-R-V | 0.2574 | 0.0005621 | 0.0877 |
SRC|SRC_PY527-R-V | -0.2556 | 0.0006167 | 0.0956 |
SYP|SYNAPTOPHYSIN-R-E | 0.2532 | 0.0006964 | 0.107 |
ERBB2|HER2_PY1248-R-V | -0.2498 | 0.0008275 | 0.127 |
GENDER | Labels | N |
FEMALE | 62 | |
MALE | 150 | |
Significant markers | N = 6 | |
Higher in MALE | 6 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
YAP1|YAP_PS127-R-C | 2903 | 1.719e-05 | 0.00275 | 0.6878 |
MAPK14|P38_PT180_Y182-R-V | 3126 | 0.000177 | 0.0281 | 0.6639 |
MAPK1 MAPK3|MAPK_PT202_Y204-R-V | 3207 | 0.0003847 | 0.0608 | 0.6552 |
RPS6|S6_PS235_S236-R-V | 3284 | 0.000777 | 0.122 | 0.6469 |
BAD|BAD_PS112-R-V | 3289 | 0.0008123 | 0.127 | 0.6463 |
SRC|SRC_PY527-R-V | 3354 | 0.00143 | 0.222 | 0.6394 |
2 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 61 | |
YES | 151 | |
Significant markers | N = 2 | |
Higher in YES | 2 | |
Higher in NO | 0 |
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
BCL2|BCL-2-M-V | 2759 | 4.985e-06 | 0.000798 | 0.7005 |
COL6A1|COLLAGEN_VI-R-V | 3254 | 0.0008342 | 0.133 | 0.6467 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 48.65 (38) |
Significant markers | N = 2 | |
pos. correlated | 2 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
TP63|P63-R-E | 0.3768 | 6.318e-05 | 0.0101 |
CHEK2|CHK2-M-C | 0.352 | 0.0002006 | 0.0319 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.86 (5.1) |
Significant markers | N = 8 | |
pos. correlated | 4 | |
neg. correlated | 4 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ANXA1|ANNEXIN_I-R-V | -0.3176 | 2.437e-05 | 0.0039 |
SRC|SRC_PY416-R-C | -0.2914 | 0.0001158 | 0.0184 |
YAP1|YAP_PS127-R-C | -0.2676 | 0.0004187 | 0.0662 |
PRKCA |PKC-ALPHA_PS657-R-V | 0.2594 | 0.0006366 | 0.0999 |
FN1|FIBRONECTIN-R-C | 0.2556 | 0.0007665 | 0.12 |
SYP|SYNAPTOPHYSIN-R-E | 0.2553 | 0.0007787 | 0.121 |
AXL|AXL-M-C | 0.2481 | 0.001105 | 0.17 |
SRC|SRC_PY527-R-V | -0.2371 | 0.001848 | 0.283 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 1 | |
ASIAN | 3 | |
BLACK OR AFRICAN AMERICAN | 19 | |
WHITE | 182 | |
Significant markers | N = 0 |
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Expresson data file = HNSC-TP.rppa.txt
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Clinical data file = HNSC-TP.merged_data.txt
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Number of patients = 212
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Number of genes = 160
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Number of clinical features = 11
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 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 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 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.