This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17948 genes and 5 clinical features across 117 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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24 genes correlated to 'AGE'.
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KBTBD2|25948 , DUSP6|1848 , DDIT4L|115265 , CD97|976 , NDEL1|81565 , ...
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26 genes correlated to 'GENDER'.
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DDX3Y|8653 , RPS4Y1|6192 , ZFY|7544 , USP9Y|8287 , UTY|7404 , ...
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2373 genes correlated to 'HISTOLOGICAL.TYPE'.
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PDHA1|5160 , GOT2|2806 , ITGA3|3675 , KCNIP3|30818 , COQ9|57017 , ...
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20 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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FLJ37543|285668 , DNAH14|127602 , ORC1L|4998 , CUL7|9820 , C14ORF180|400258 , ...
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160 genes correlated to 'NEOADJUVANT.THERAPY'.
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SH2D1B|117157 , L3MBTL|26013 , KDM5C|8242 , SSR2|6746 , ZNF512|84450 , ...
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at Q value < 0.05.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
AGE | Spearman correlation test | N=24 | older | N=6 | younger | N=18 |
GENDER | t test | N=26 | male | N=14 | female | N=12 |
HISTOLOGICAL TYPE | ANOVA test | N=2373 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=20 | yes | N=5 | no | N=15 |
NEOADJUVANT THERAPY | t test | N=160 | yes | N=52 | no | N=108 |
Table S1. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 47.87 (16) |
Significant markers | N = 24 | |
pos. correlated | 6 | |
neg. correlated | 18 |
Table S2. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
KBTBD2|25948 | -0.4718 | 7.914e-08 | 0.00142 |
DUSP6|1848 | -0.4689 | 9.692e-08 | 0.00174 |
DDIT4L|115265 | 0.4576 | 2.136e-07 | 0.00383 |
CD97|976 | -0.4537 | 2.785e-07 | 0.005 |
NDEL1|81565 | -0.4515 | 3.223e-07 | 0.00578 |
MST1P9|11223 | -0.45 | 3.572e-07 | 0.00641 |
ZCCHC12|170261 | -0.4474 | 4.249e-07 | 0.00762 |
TMEM49|81671 | -0.4444 | 5.188e-07 | 0.00931 |
LOC401431|401431 | 0.4387 | 7.538e-07 | 0.0135 |
TUBGCP5|114791 | 0.4305 | 1.269e-06 | 0.0228 |
Figure S1. Get High-res Image As an example, this figure shows the association of KBTBD2|25948 to 'AGE'. P value = 7.91e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Table S3. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 82 | |
MALE | 35 | |
Significant markers | N = 26 | |
Higher in MALE | 14 | |
Higher in FEMALE | 12 |
Table S4. Get Full Table List of top 10 genes differentially expressed by 'GENDER'
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
DDX3Y|8653 | 59.71 | 6.161e-64 | 1.11e-59 | 1 |
RPS4Y1|6192 | 46.8 | 2.566e-62 | 4.6e-58 | 1 |
ZFY|7544 | 52.4 | 3.091e-60 | 5.55e-56 | 1 |
USP9Y|8287 | 53.54 | 2.669e-56 | 4.79e-52 | 1 |
UTY|7404 | 54.49 | 2.087e-49 | 3.74e-45 | 1 |
NLGN4Y|22829 | 39 | 1.549e-46 | 2.78e-42 | 1 |
KDM5D|8284 | 51.88 | 4.417e-41 | 7.92e-37 | 1 |
PRKY|5616 | 21.44 | 1.354e-40 | 2.43e-36 | 0.9981 |
CYORF15A|246126 | 42.66 | 4.364e-31 | 7.83e-27 | 1 |
TSIX|9383 | -17.49 | 8.176e-25 | 1.47e-20 | 0.9994 |
Figure S2. Get High-res Image As an example, this figure shows the association of DDX3Y|8653 to 'GENDER'. P value = 6.16e-64 with T-test analysis.

Table S5. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
OTHER | 3 | |
THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | 65 | |
THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | 33 | |
THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) | 16 | |
Significant markers | N = 2373 |
Table S6. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'
ANOVA_P | Q | |
---|---|---|
PDHA1|5160 | 2.634e-20 | 4.73e-16 |
GOT2|2806 | 1.895e-19 | 3.4e-15 |
ITGA3|3675 | 5.861e-19 | 1.05e-14 |
KCNIP3|30818 | 2.222e-18 | 3.99e-14 |
COQ9|57017 | 3.381e-18 | 6.07e-14 |
ERBB3|2065 | 5.06e-18 | 9.08e-14 |
MPZL2|10205 | 9.197e-18 | 1.65e-13 |
ALDH1B1|219 | 1.006e-17 | 1.81e-13 |
LDLR|3949 | 4.891e-17 | 8.77e-13 |
SFTPB|6439 | 4.901e-17 | 8.79e-13 |
Figure S3. Get High-res Image As an example, this figure shows the association of PDHA1|5160 to 'HISTOLOGICAL.TYPE'. P value = 2.63e-20 with ANOVA analysis.

20 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S7. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 11 | |
YES | 106 | |
Significant markers | N = 20 | |
Higher in YES | 5 | |
Higher in NO | 15 |
Table S8. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
FLJ37543|285668 | 8.88 | 2.01e-12 | 3.6e-08 | 0.8627 |
DNAH14|127602 | -8.49 | 9.44e-09 | 0.000169 | 0.9177 |
ORC1L|4998 | -6.59 | 7.223e-08 | 0.00129 | 0.8182 |
CUL7|9820 | -7.41 | 1.356e-07 | 0.00243 | 0.8868 |
C14ORF180|400258 | 6.14 | 1.798e-07 | 0.00322 | 0.8889 |
MCM10|55388 | -6.48 | 2.354e-07 | 0.00421 | 0.8062 |
ZNF695|57116 | -6.96 | 3.019e-07 | 0.0054 | 0.8533 |
HCFC1|3054 | -7.08 | 4.14e-07 | 0.00741 | 0.8619 |
GINS1|9837 | -5.66 | 4.536e-07 | 0.00811 | 0.7933 |
CDC45|8318 | -6.56 | 7.549e-07 | 0.0135 | 0.8459 |
Figure S4. Get High-res Image As an example, this figure shows the association of FLJ37543|285668 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.01e-12 with T-test analysis.

Table S9. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'
NEOADJUVANT.THERAPY | Labels | N |
NO | 3 | |
YES | 114 | |
Significant markers | N = 160 | |
Higher in YES | 52 | |
Higher in NO | 108 |
Table S10. Get Full Table List of top 10 genes differentially expressed by 'NEOADJUVANT.THERAPY'
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
SH2D1B|117157 | 17.79 | 3.175e-32 | 5.25e-28 | 0.9497 |
L3MBTL|26013 | -16.4 | 2.469e-28 | 4.08e-24 | 0.9444 |
KDM5C|8242 | -14.35 | 1.554e-26 | 2.57e-22 | 0.9591 |
SSR2|6746 | 13.74 | 8.9e-26 | 1.47e-21 | 0.9269 |
ZNF512|84450 | -12.96 | 3.994e-24 | 6.6e-20 | 0.9357 |
FCRL5|83416 | 15.22 | 1.584e-23 | 2.62e-19 | 0.9485 |
ZNF418|147686 | -13.15 | 1.649e-20 | 2.72e-16 | 0.9561 |
WBSCR22|114049 | 11.29 | 2.385e-20 | 3.94e-16 | 0.8655 |
SGSM1|129049 | -11.16 | 5.105e-20 | 8.43e-16 | 0.8947 |
C1ORF104|284618 | -13.15 | 5.32e-20 | 8.79e-16 | 0.886 |
Figure S5. Get High-res Image As an example, this figure shows the association of SH2D1B|117157 to 'NEOADJUVANT.THERAPY'. P value = 3.17e-32 with T-test analysis.

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Expresson data file = THCA.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = THCA.clin.merged.picked.txt
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Number of patients = 117
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Number of genes = 17948
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Number of clinical features = 5
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.