(Regional_LN cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18122 genes and 6 clinical features across 112 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.
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8 genes correlated to 'Time to Death'.
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PRKAR2B|5577 , NUDT7|283927 , ATP8B4|79895 , RBM14|10432 , CASC4|113201 , ...
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10 genes correlated to 'AGE'.
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MICALL2|79778 , ACOX2|8309 , TCEAL5|340543 , ETFB|2109 , C4ORF46|201725 , ...
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16 genes correlated to 'GENDER'.
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ZFY|7544 , PRKY|5616 , CYORF15B|84663 , XIST|7503 , RPS4Y1|6192 , ...
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1 gene correlated to 'DISTANT.METASTASIS'.
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TMEM147|10430
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2 genes correlated to 'LYMPH.NODE.METASTASIS'.
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AMY1A|276 , PPAN-P2RY11|692312
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1 gene correlated to 'NEOPLASM.DISEASESTAGE'.
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SRRM4|84530
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=8 | shorter survival | N=1 | longer survival | N=7 |
AGE | Spearman correlation test | N=10 | older | N=4 | younger | N=6 |
GENDER | t test | N=16 | male | N=11 | female | N=5 |
DISTANT METASTASIS | ANOVA test | N=1 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=2 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=1 |
Time to Death | Duration (Months) | 2.6-346 (median=47.3) |
censored | N = 55 | |
death | N = 55 | |
Significant markers | N = 8 | |
associated with shorter survival | 1 | |
associated with longer survival | 7 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
PRKAR2B|5577 | 0.6 | 6.113e-08 | 0.0011 | 0.312 |
NUDT7|283927 | 0.66 | 1.981e-07 | 0.0036 | 0.349 |
ATP8B4|79895 | 0.62 | 5.392e-07 | 0.0098 | 0.328 |
RBM14|10432 | 5.3 | 8.553e-07 | 0.015 | 0.683 |
CASC4|113201 | 0.48 | 9.414e-07 | 0.017 | 0.35 |
PLEKHA3|65977 | 0.4 | 1.125e-06 | 0.02 | 0.353 |
TLR1|7096 | 0.59 | 1.447e-06 | 0.026 | 0.308 |
PION|54103 | 0.67 | 1.969e-06 | 0.036 | 0.344 |
AGE | Mean (SD) | 55.44 (16) |
Significant markers | N = 10 | |
pos. correlated | 4 | |
neg. correlated | 6 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MICALL2|79778 | -0.5099 | 9.302e-09 | 0.000169 |
ACOX2|8309 | -0.4847 | 6.137e-08 | 0.00111 |
TCEAL5|340543 | -0.4548 | 4.7e-07 | 0.00852 |
ETFB|2109 | -0.4529 | 5.331e-07 | 0.00966 |
C4ORF46|201725 | 0.4397 | 1.233e-06 | 0.0223 |
ZBED4|9889 | 0.4349 | 1.65e-06 | 0.0299 |
CDHR3|222256 | 0.4331 | 1.849e-06 | 0.0335 |
MGST2|4258 | -0.4323 | 1.936e-06 | 0.0351 |
CHUK|1147 | 0.4311 | 2.088e-06 | 0.0378 |
COX7A1|1346 | -0.4273 | 2.623e-06 | 0.0475 |
GENDER | Labels | N |
FEMALE | 35 | |
MALE | 77 | |
Significant markers | N = 16 | |
Higher in MALE | 11 | |
Higher in FEMALE | 5 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
ZFY|7544 | 25.17 | 1.487e-42 | 2.69e-38 | 0.9903 |
PRKY|5616 | 20.74 | 5.42e-30 | 9.82e-26 | 0.9935 |
CYORF15B|84663 | 31.14 | 9.066e-30 | 1.64e-25 | 1 |
XIST|7503 | -16.28 | 6.09e-29 | 1.1e-24 | 0.9691 |
RPS4Y1|6192 | 25.58 | 1.253e-26 | 2.27e-22 | 1 |
DDX3Y|8653 | 24 | 2.832e-18 | 5.13e-14 | 0.9981 |
TSIX|9383 | -11.42 | 1.317e-17 | 2.38e-13 | 0.9673 |
NLGN4Y|22829 | 11.27 | 2.281e-14 | 4.13e-10 | 0.9633 |
TTTY15|64595 | 18.09 | 1.57e-13 | 2.84e-09 | 0.9833 |
KDM5D|8284 | 18.95 | 1.348e-11 | 2.44e-07 | 0.9909 |
DISTANT.METASTASIS | Labels | N |
M0 | 98 | |
M1 | 1 | |
M1B | 2 | |
M1C | 1 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
TMEM147|10430 | 2.733e-06 | 0.0493 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 61 | |
N1 | 1 | |
N1A | 3 | |
N1B | 10 | |
N2 | 1 | |
N2A | 3 | |
N2B | 8 | |
N2C | 1 | |
N3 | 13 | |
NX | 2 | |
Significant markers | N = 2 |
ANOVA_P | Q | |
---|---|---|
AMY1A|276 | 3.587e-07 | 0.0065 |
PPAN-P2RY11|692312 | 4.781e-07 | 0.00866 |
NEOPLASM.DISEASESTAGE | Labels | N |
I OR II NOS | 1 | |
STAGE I | 15 | |
STAGE IA | 7 | |
STAGE IB | 11 | |
STAGE II | 13 | |
STAGE IIA | 5 | |
STAGE IIB | 5 | |
STAGE IIC | 2 | |
STAGE III | 4 | |
STAGE IIIA | 3 | |
STAGE IIIB | 10 | |
STAGE IIIC | 18 | |
STAGE IV | 3 | |
Significant markers | N = 1 |
ANOVA_P | Q | |
---|---|---|
SRRM4|84530 | 3.58e-07 | 0.00649 |
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Expresson data file = SKCM-Regional_LN.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = SKCM-Regional_LN.clin.merged.picked.txt
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Number of patients = 112
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Number of genes = 18122
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Number of clinical features = 6
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.