(primary solid tumor cohort)
This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18257 genes and 8 clinical features across 835 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.
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4 genes correlated to 'Time to Death'.
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DIP2B|57609 , PGK1|5230 , CAND1|55832 , IRF2|3660
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673 genes correlated to 'AGE'.
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ESR1|2099 , LRFN5|145581 , TFPI2|7980 , TMEFF1|8577 , SOBP|55084 , ...
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18 genes correlated to 'GENDER'.
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NLGN4Y|22829 , ZFY|7544 , PRKY|5616 , C7ORF10|79783 , SYT9|143425 , ...
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73 genes correlated to 'LYMPH.NODE.METASTASIS'.
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PIK3CA|5290 , BTBD10|84280 , RPL35|11224 , HSPA8|3312 , C19ORF21|126353 , ...
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2 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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HMSD|284293 , FITM2|128486
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3 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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C20ORF43|51507 , CSTF1|1477 , PGGT1B|5229
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No genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'DISTANT.METASTASIS'.
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=4 | shorter survival | N=3 | longer survival | N=1 |
AGE | Spearman correlation test | N=673 | older | N=160 | younger | N=513 |
GENDER | t test | N=18 | male | N=8 | female | N=10 |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
DISTANT METASTASIS | ANOVA test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=73 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=2 | higher number.of.lymph.nodes | N=1 | lower number.of.lymph.nodes | N=1 |
NEOPLASM DISEASESTAGE | ANOVA test | N=3 |
Time to Death | Duration (Months) | 0-223.4 (median=18.9) |
censored | N = 684 | |
death | N = 94 | |
Significant markers | N = 4 | |
associated with shorter survival | 3 | |
associated with longer survival | 1 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
DIP2B|57609 | 2.9 | 1.607e-07 | 0.0029 | 0.635 |
PGK1|5230 | 2 | 1.667e-06 | 0.03 | 0.685 |
CAND1|55832 | 2.1 | 1.679e-06 | 0.031 | 0.629 |
IRF2|3660 | 0.28 | 1.979e-06 | 0.036 | 0.329 |
AGE | Mean (SD) | 58.2 (13) |
Significant markers | N = 673 | |
pos. correlated | 160 | |
neg. correlated | 513 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ESR1|2099 | 0.3525 | 8.392e-26 | 1.53e-21 |
LRFN5|145581 | -0.2691 | 5.304e-15 | 9.68e-11 |
TFPI2|7980 | -0.2668 | 5.899e-15 | 1.08e-10 |
TMEFF1|8577 | -0.2533 | 1.116e-13 | 2.04e-09 |
SOBP|55084 | -0.2511 | 1.844e-13 | 3.37e-09 |
DBX2|440097 | -0.2696 | 2.528e-13 | 4.61e-09 |
PCDH18|54510 | -0.2449 | 7.421e-13 | 1.35e-08 |
DZIP1|22873 | -0.2443 | 8.413e-13 | 1.54e-08 |
RELN|5649 | -0.2465 | 9.581e-13 | 1.75e-08 |
FXYD6|53826 | -0.2401 | 2.095e-12 | 3.82e-08 |
GENDER | Labels | N |
FEMALE | 826 | |
MALE | 9 | |
Significant markers | N = 18 | |
Higher in MALE | 8 | |
Higher in FEMALE | 10 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
NLGN4Y|22829 | 41.17 | 2.285e-12 | 4.11e-08 | 1 |
ZFY|7544 | 41.95 | 1.793e-11 | 3.22e-07 | 1 |
PRKY|5616 | 27.62 | 6.125e-10 | 1.1e-05 | 1 |
C7ORF10|79783 | 8.64 | 3.708e-09 | 6.66e-05 | 0.663 |
SYT9|143425 | 12.47 | 6.329e-09 | 0.000114 | 0.7947 |
GSTA1|2938 | -16.01 | 9.34e-09 | 0.000168 | 0.8831 |
MMP11|4320 | 11.05 | 1.629e-08 | 0.000293 | 0.7459 |
RND2|8153 | 12.33 | 2.586e-08 | 0.000465 | 0.8354 |
SNORA74B|677841 | -11.93 | 9.366e-08 | 0.00168 | 0.8343 |
HTR4|3360 | -12.07 | 1.118e-07 | 0.00201 | 0.7909 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 209 | |
YES | 626 | |
Significant markers | N = 0 |
DISTANT.METASTASIS | Labels | N |
CM0 (I+) | 2 | |
M0 | 747 | |
M1 | 15 | |
MX | 71 | |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 240 | |
N0 (I+) | 22 | |
N0 (I-) | 129 | |
N0 (MOL+) | 1 | |
N1 | 100 | |
N1A | 124 | |
N1B | 32 | |
N1C | 2 | |
N1MI | 22 | |
N2 | 50 | |
N2A | 50 | |
N3 | 17 | |
N3A | 29 | |
N3B | 1 | |
N3C | 1 | |
NX | 15 | |
Significant markers | N = 73 |
ANOVA_P | Q | |
---|---|---|
PIK3CA|5290 | 2.648e-15 | 4.83e-11 |
BTBD10|84280 | 1.757e-13 | 3.21e-09 |
RPL35|11224 | 1.138e-10 | 2.08e-06 |
HSPA8|3312 | 4.599e-10 | 8.39e-06 |
C19ORF21|126353 | 1.183e-09 | 2.16e-05 |
SERINC3|10955 | 1.136e-08 | 0.000207 |
POLR2B|5431 | 1.483e-08 | 0.000271 |
RPL12|6136 | 1.534e-08 | 0.00028 |
RPL34|6164 | 3.759e-08 | 0.000686 |
RPS19|6223 | 4.851e-08 | 0.000885 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.17 (4.3) |
Significant markers | N = 2 | |
pos. correlated | 1 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
HMSD|284293 | -0.2591 | 9.257e-08 | 0.00169 |
FITM2|128486 | 0.1772 | 2.645e-06 | 0.0483 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 69 | |
STAGE IA | 63 | |
STAGE IB | 7 | |
STAGE II | 8 | |
STAGE IIA | 289 | |
STAGE IIB | 186 | |
STAGE III | 2 | |
STAGE IIIA | 117 | |
STAGE IIIB | 23 | |
STAGE IIIC | 37 | |
STAGE IV | 15 | |
STAGE TIS | 1 | |
STAGE X | 17 | |
Significant markers | N = 3 |
ANOVA_P | Q | |
---|---|---|
C20ORF43|51507 | 1.291e-10 | 2.36e-06 |
CSTF1|1477 | 7.227e-09 | 0.000132 |
PGGT1B|5229 | 3.004e-08 | 0.000548 |
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Expresson data file = BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = BRCA-TP.clin.merged.picked.txt
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Number of patients = 835
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Number of genes = 18257
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Number of clinical features = 8
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.