This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18025 genes and 13 clinical features across 271 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.
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64 genes correlated to 'AGE'.
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C12ORF52|84934 , DDX28|55794 , ZNF518B|85460 , DDIT4L|115265 , GPI|2821 , ...
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34 genes correlated to 'GENDER'.
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DDX3Y|8653 , ZFY|7544 , RPS4Y1|6192 , UTY|7404 , USP9Y|8287 , ...
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5329 genes correlated to 'HISTOLOGICAL.TYPE'.
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FN1|2335 , FAM176A|84141 , KCNN4|3783 , GABRB2|2561 , SYT12|91683 , ...
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36 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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FLJ37543|285668 , C14ORF180|400258 , A2ML1|144568 , HPR|3250 , TAS2R43|259289 , ...
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14 genes correlated to 'RADIATIONEXPOSURE'.
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FAM138F|641702 , GSG1|83445 , P2RX2|22953 , OR9A4|130075 , CSNK1A1P|161635 , ...
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19 genes correlated to 'DISTANT.METASTASIS'.
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ARRB1|408 , GJA5|2702 , RTN4RL1|146760 , GPATCH4|54865 , APOL3|80833 , ...
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93 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.
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THNSL2|55258 , VEGFA|7422 , FOXJ1|2302 , PLRG1|5356 , TUBB1|81027 , ...
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458 genes correlated to 'LYMPH.NODE.METASTASIS'.
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KCNN4|3783 , CREB5|9586 , CLCNKA|1187 , RASGRF1|5923 , TACSTD2|4070 , ...
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4 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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CATSPER2P1|440278 , CXORF56|63932 , MUC13|56667 , TRIM72|493829
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468 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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FAM60A|58516 , PCDP1|200373 , CBFB|865 , SPATS2L|26010 , SNX11|29916 , ...
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74 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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CYP26A1|1592 , KIAA1383|54627 , SEMA3G|56920 , AIFM1|9131 , ALDOA|226 , ...
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2 genes correlated to 'MULTIFOCALITY'.
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INMT|11185 , ETS1|2113
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1 gene correlated to 'TUMOR.SIZE'.
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LRRC55|219527
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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AGE | Spearman correlation test | N=64 | older | N=36 | younger | N=28 |
GENDER | t test | N=34 | male | N=13 | female | N=21 |
HISTOLOGICAL TYPE | ANOVA test | N=5329 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=36 | yes | N=19 | no | N=17 |
RADIATIONEXPOSURE | t test | N=14 | yes | N=2 | no | N=12 |
DISTANT METASTASIS | ANOVA test | N=19 | ||||
EXTRATHYROIDAL EXTENSION | ANOVA test | N=93 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=458 | ||||
COMPLETENESS OF RESECTION | ANOVA test | N=4 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=468 | higher number.of.lymph.nodes | N=230 | lower number.of.lymph.nodes | N=238 |
NEOPLASM DISEASESTAGE | ANOVA test | N=74 | ||||
MULTIFOCALITY | t test | N=2 | unifocal | N=0 | multifocal | N=2 |
TUMOR SIZE | Spearman correlation test | N=1 | higher tumor.size | N=0 | lower tumor.size | N=1 |
AGE | Mean (SD) | 46.69 (16) |
Significant markers | N = 64 | |
pos. correlated | 36 | |
neg. correlated | 28 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
C12ORF52|84934 | 0.3809 | 8.707e-11 | 1.57e-06 |
DDX28|55794 | 0.362 | 8.185e-10 | 1.48e-05 |
ZNF518B|85460 | -0.3472 | 4.277e-09 | 7.71e-05 |
DDIT4L|115265 | 0.3431 | 6.637e-09 | 0.00012 |
GPI|2821 | 0.3351 | 1.551e-08 | 0.000279 |
EPN3|55040 | 0.3298 | 2.687e-08 | 0.000484 |
IL20RA|53832 | 0.3266 | 3.934e-08 | 0.000709 |
ASB13|79754 | 0.3201 | 7.157e-08 | 0.00129 |
RAB3A|5864 | 0.3166 | 1.007e-07 | 0.00181 |
HADH|3033 | 0.3154 | 1.135e-07 | 0.00204 |
GENDER | Labels | N |
FEMALE | 200 | |
MALE | 71 | |
Significant markers | N = 34 | |
Higher in MALE | 13 | |
Higher in FEMALE | 21 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
DDX3Y|8653 | 84.95 | 1.392e-127 | 2.51e-123 | 1 |
ZFY|7544 | 78.78 | 7.518e-126 | 1.36e-121 | 1 |
RPS4Y1|6192 | 70.36 | 9.547e-125 | 1.72e-120 | 1 |
UTY|7404 | 79.58 | 2.222e-101 | 4e-97 | 1 |
USP9Y|8287 | 73.24 | 2.491e-97 | 4.49e-93 | 1 |
NLGN4Y|22829 | 55.83 | 1.138e-94 | 2.05e-90 | 1 |
KDM5D|8284 | 75.72 | 1.451e-88 | 2.62e-84 | 1 |
PRKY|5616 | 32.98 | 8.546e-88 | 1.54e-83 | 0.9983 |
CYORF15A|246126 | 62.1 | 1.059e-60 | 1.91e-56 | 1 |
XIST|7503 | -37.44 | 1.503e-52 | 2.71e-48 | 0.9992 |
HISTOLOGICAL.TYPE | Labels | N |
OTHER | 17 | |
THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | 159 | |
THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | 67 | |
THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) | 28 | |
Significant markers | N = 5329 |
ANOVA_P | Q | |
---|---|---|
FN1|2335 | 7.798e-43 | 1.41e-38 |
FAM176A|84141 | 1.031e-40 | 1.86e-36 |
KCNN4|3783 | 5.044e-40 | 9.09e-36 |
GABRB2|2561 | 2.95e-37 | 5.32e-33 |
SYT12|91683 | 3.307e-37 | 5.96e-33 |
LDLR|3949 | 3.42e-37 | 6.16e-33 |
PTPRE|5791 | 6.751e-37 | 1.22e-32 |
SFTPB|6439 | 2.357e-36 | 4.25e-32 |
CREB5|9586 | 5.577e-36 | 1e-31 |
FLJ42709|441094 | 1.094e-35 | 1.97e-31 |
36 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 12 | |
YES | 259 | |
Significant markers | N = 36 | |
Higher in YES | 19 | |
Higher in NO | 17 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
FLJ37543|285668 | 12.27 | 6.36e-15 | 1.14e-10 | 0.8665 |
C14ORF180|400258 | 10.2 | 5.806e-14 | 1.04e-09 | 0.8571 |
A2ML1|144568 | 9.36 | 3.925e-10 | 7.05e-06 | 0.8098 |
HPR|3250 | 8.76 | 9.629e-10 | 1.73e-05 | 0.9123 |
TAS2R43|259289 | 7.85 | 1.019e-09 | 1.83e-05 | 0.7595 |
HCFC1|3054 | -10.57 | 4.406e-09 | 7.91e-05 | 0.9064 |
LOC440173|440173 | 7.61 | 1.554e-08 | 0.000279 | 0.8731 |
ARHGEF18|23370 | -7.74 | 7.291e-08 | 0.00131 | 0.8012 |
TMEM218|219854 | 8.54 | 1.026e-07 | 0.00184 | 0.852 |
GINS1|9837 | -6.69 | 1.351e-07 | 0.00242 | 0.7551 |
RADIATIONEXPOSURE | Labels | N |
NO | 225 | |
YES | 10 | |
Significant markers | N = 14 | |
Higher in YES | 2 | |
Higher in NO | 12 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
FAM138F|641702 | -9.01 | 2.971e-14 | 5.3e-10 | 0.837 |
GSG1|83445 | -8.44 | 6.433e-13 | 1.15e-08 | 0.8244 |
P2RX2|22953 | -7.89 | 2.595e-11 | 4.63e-07 | 0.8826 |
OR9A4|130075 | -8.06 | 2.634e-11 | 4.7e-07 | 0.8458 |
CSNK1A1P|161635 | -7.47 | 7.498e-11 | 1.34e-06 | 0.8552 |
RPRML|388394 | -7.4 | 3.959e-10 | 7.06e-06 | 0.8423 |
LOC100133050|100133050 | -7.05 | 7.91e-08 | 0.00141 | 0.8102 |
TNNT3|7140 | -9.77 | 8.83e-08 | 0.00157 | 0.8992 |
CYORF15A|246126 | 5.72 | 1.672e-07 | 0.00298 | 0.6188 |
DLX2|1746 | -7.08 | 4.668e-07 | 0.00833 | 0.7468 |
DISTANT.METASTASIS | Labels | N |
M0 | 123 | |
M1 | 4 | |
MX | 143 | |
Significant markers | N = 19 |
ANOVA_P | Q | |
---|---|---|
ARRB1|408 | 3.58e-09 | 6.45e-05 |
GJA5|2702 | 1.504e-08 | 0.000271 |
RTN4RL1|146760 | 1.524e-08 | 0.000275 |
GPATCH4|54865 | 3.266e-08 | 0.000589 |
APOL3|80833 | 1.65e-07 | 0.00297 |
SEMA3G|56920 | 2.272e-07 | 0.00409 |
PTPRR|5801 | 2.571e-07 | 0.00463 |
KIAA1383|54627 | 2.589e-07 | 0.00467 |
SNRNP40|9410 | 3.79e-07 | 0.00683 |
KYNU|8942 | 4.618e-07 | 0.00832 |
EXTRATHYROIDAL.EXTENSION | Labels | N |
MINIMAL (T3) | 62 | |
MODERATE/ADVANCED (T4A) | 4 | |
NONE | 191 | |
Significant markers | N = 93 |
ANOVA_P | Q | |
---|---|---|
THNSL2|55258 | 1.123e-09 | 2.02e-05 |
VEGFA|7422 | 3.686e-09 | 6.64e-05 |
FOXJ1|2302 | 4.344e-09 | 7.83e-05 |
PLRG1|5356 | 4.626e-09 | 8.34e-05 |
TUBB1|81027 | 8.155e-09 | 0.000147 |
FZD9|8326 | 1.69e-08 | 0.000305 |
FLJ42875|440556 | 2.081e-08 | 0.000375 |
BEGAIN|57596 | 2.637e-08 | 0.000475 |
CETP|1071 | 2.899e-08 | 0.000522 |
CYP26A1|1592 | 3.389e-08 | 0.000611 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 134 | |
N1 | 14 | |
N1A | 56 | |
N1B | 40 | |
NX | 27 | |
Significant markers | N = 458 |
ANOVA_P | Q | |
---|---|---|
KCNN4|3783 | 4.444e-11 | 8.01e-07 |
CREB5|9586 | 1.529e-10 | 2.76e-06 |
CLCNKA|1187 | 2.766e-10 | 4.98e-06 |
RASGRF1|5923 | 3.818e-10 | 6.88e-06 |
TACSTD2|4070 | 8.084e-10 | 1.46e-05 |
MEX3C|51320 | 1.044e-09 | 1.88e-05 |
FN1|2335 | 1.329e-09 | 2.4e-05 |
IL1RAP|3556 | 1.579e-09 | 2.84e-05 |
SYT12|91683 | 1.777e-09 | 3.2e-05 |
PELI1|57162 | 1.795e-09 | 3.23e-05 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 212 | |
R1 | 17 | |
R2 | 1 | |
RX | 20 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
CATSPER2P1|440278 | 1.698e-14 | 3.06e-10 |
CXORF56|63932 | 1.034e-07 | 0.00186 |
MUC13|56667 | 5.443e-07 | 0.00981 |
TRIM72|493829 | 1.321e-06 | 0.0238 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.85 (5.3) |
Significant markers | N = 468 | |
pos. correlated | 230 | |
neg. correlated | 238 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
FAM60A|58516 | 0.4736 | 2.615e-13 | 4.71e-09 |
PCDP1|200373 | -0.4494 | 5.515e-12 | 9.94e-08 |
CBFB|865 | 0.4246 | 9.815e-11 | 1.77e-06 |
SPATS2L|26010 | 0.4189 | 1.852e-10 | 3.34e-06 |
SNX11|29916 | -0.4176 | 2.13e-10 | 3.84e-06 |
MEX3C|51320 | 0.4078 | 6.119e-10 | 1.1e-05 |
CREB5|9586 | 0.4072 | 6.473e-10 | 1.17e-05 |
PELI1|57162 | 0.4072 | 6.53e-10 | 1.18e-05 |
TMEM99|147184 | -0.4071 | 6.603e-10 | 1.19e-05 |
CLCNKA|1187 | -0.4068 | 6.753e-10 | 1.22e-05 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 152 | |
STAGE II | 33 | |
STAGE III | 58 | |
STAGE IVA | 24 | |
STAGE IVC | 3 | |
Significant markers | N = 74 |
ANOVA_P | Q | |
---|---|---|
CYP26A1|1592 | 1.942e-11 | 3.5e-07 |
KIAA1383|54627 | 1.259e-09 | 2.27e-05 |
SEMA3G|56920 | 1.578e-09 | 2.84e-05 |
AIFM1|9131 | 4.93e-09 | 8.88e-05 |
ALDOA|226 | 5.543e-09 | 9.99e-05 |
GOT2|2806 | 7.535e-09 | 0.000136 |
GJA5|2702 | 2.148e-08 | 0.000387 |
CS|1431 | 5.425e-08 | 0.000977 |
GPI|2821 | 7.655e-08 | 0.00138 |
ALPL|249 | 7.856e-08 | 0.00142 |
MULTIFOCALITY | Labels | N |
MULTIFOCAL | 133 | |
UNIFOCAL | 129 | |
Significant markers | N = 2 | |
Higher in UNIFOCAL | 0 | |
Higher in MULTIFOCAL | 2 |
T(pos if higher in 'UNIFOCAL') | ttestP | Q | AUC | |
---|---|---|---|---|
INMT|11185 | -5.04 | 8.698e-07 | 0.0157 | 0.6663 |
ETS1|2113 | -4.88 | 1.926e-06 | 0.0347 | 0.6609 |
TUMOR.SIZE | Mean (SD) | 2.74 (1.5) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
LRRC55|219527 | -0.3459 | 5.616e-07 | 0.0101 |
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Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = THCA-TP.clin.merged.picked.txt
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Number of patients = 271
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Number of genes = 18025
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Number of clinical features = 13
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.