Correlation between mRNAseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1GH9GFM
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1GH9GFM
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.

Summary

Testing the association between 17994 genes and 15 clinical features across 476 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.

- 100 genes correlated to 'AGE'.

- ZNF518B|85460 , RANBP17|64901 , MSL3L2|151507 , HCG11|493812 , C12ORF52|84934 , ...

- 669 genes correlated to 'NEOPLASM.DISEASESTAGE'.

- GSPT2|23708 , SEMA3G|56920 , PIK3R3|8503 , FAM50B|26240 , SLC10A4|201780 , ...

- 594 genes correlated to 'PATHOLOGY.T.STAGE'.

- FBXO9|26268 , VIPR1|7433 , SLCO2A1|6578 , LTF|4057 , SYT15|83849 , ...

- 2518 genes correlated to 'PATHOLOGY.N.STAGE'.

- CREB5|9586 , CLCNKA|1187 , FN1|2335 , SFTPB|6439 , MLEC|9761 , ...

- 16 genes correlated to 'PATHOLOGY.M.STAGE'.

- CYP21A2|1589 , ST6GALNAC1|55808 , SELP|6403 , C4ORF6|10141 , C19ORF76|199800 , ...

- 43 genes correlated to 'GENDER'.

- RPS4Y1|6192 , ZFY|7544 , DDX3Y|8653 , NLGN4Y|22829 , UTY|7404 , ...

- 5511 genes correlated to 'HISTOLOGICAL.TYPE'.

- ITGA3|3675 , TM7SF4|81501 , FN1|2335 , ERBB3|2065 , SFTPB|6439 , ...

- 28 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- C14ORF180|400258 , FLJ37543|285668 , ADIPOQ|9370 , TAS2R43|259289 , HPR|3250 , ...

- 6 genes correlated to 'RADIATIONEXPOSURE'.

- CRNN|49860 , RNF17|56163 , CSNK1A1P|161635 , CYORF15A|246126 , EIF1AY|9086 , ...

- 1040 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

- ASAH2|56624 , SLC25A42|284439 , SRPX2|27286 , SLC10A4|201780 , COL1A1|1277 , ...

- 2 genes correlated to 'COMPLETENESS.OF.RESECTION'.

- SHOX2|6474 , CATSPER2P1|440278

- 1339 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

- CBFB|865 , PELI1|57162 , FAM60A|58516 , CREB5|9586 , TAGLN2|8407 , ...

- 11 genes correlated to 'TUMOR.SIZE'.

- C3ORF32|51066 , ISLR2|57611 , ZC3H10|84872 , CLDN2|9075 , LRRC55|219527 , ...

- No genes correlated to 'Time to Death', and 'MULTIFOCALITY'.

Results
Overview of the results

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 |
--- | --- | --- | --- | --- | --- | ---
Time to Death | Cox regression test | N=0 |  |  |  |
AGE | Spearman correlation test | N=100 | older | N=42 | younger | N=58
NEOPLASM DISEASESTAGE | ANOVA test | N=669 |  |  |  |
PATHOLOGY T STAGE | Spearman correlation test | N=594 | higher stage | N=111 | lower stage | N=483
PATHOLOGY N STAGE | t test | N=2518 | class1 | N=1226 | class0 | N=1292
PATHOLOGY M STAGE | ANOVA test | N=16 |  |  |  |
GENDER | t test | N=43 | male | N=19 | female | N=24
HISTOLOGICAL TYPE | ANOVA test | N=5511 |  |  |  |
RADIATIONS RADIATION REGIMENINDICATION | t test | N=28 | yes | N=18 | no | N=10
RADIATIONEXPOSURE | t test | N=6 | yes | N=3 | no | N=3
EXTRATHYROIDAL EXTENSION | ANOVA test | N=1040 |  |  |  |
COMPLETENESS OF RESECTION | ANOVA test | N=2 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=1339 | higher number.of.lymph.nodes | N=744 | lower number.of.lymph.nodes | N=595
MULTIFOCALITY | t test | N=0 |  |  |  |
TUMOR SIZE | Spearman correlation test | N=11 | higher tumor.size | N=0 | lower tumor.size | N=11

Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1. Basic characteristics of clinical feature: 'Time to Death'

Time to Death | Duration (Months) | 0-158.8 (median=14.8)
| censored | N = 457
| death | N = 14
| Significant markers | N = 0

Clinical variable #2: 'AGE'

100 genes related to 'AGE'.

Table S2. Basic characteristics of clinical feature: 'AGE'

AGE | Mean (SD) | 47.22 (16)
| Significant markers | N = 100
| pos. correlated | 42
| neg. correlated | 58

List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

Table S3. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
ZNF518B|85460 | -0.3429 | 1.413e-14 | 2.54e-10
RANBP17|64901 | -0.3308 | 1.527e-13 | 2.75e-09
MSL3L2|151507 | -0.3246 | 3.855e-13 | 6.94e-09
HCG11|493812 | -0.296 | 4.453e-11 | 8.01e-07
C12ORF52|84934 | 0.2877 | 1.583e-10 | 2.85e-06
ASB13|79754 | 0.286 | 2.077e-10 | 3.74e-06
IL20RA|53832 | 0.2817 | 4.264e-10 | 7.67e-06
ENTPD1|953 | -0.2809 | 4.418e-10 | 7.95e-06
DDIT4L|115265 | 0.2792 | 5.921e-10 | 1.06e-05
STL|7955 | -0.2779 | 6.902e-10 | 1.24e-05

Figure S1. Get High-res Image As an example, this figure shows the association of ZNF518B|85460 to 'AGE'. P value = 1.41e-14 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

669 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE | Labels | N
| STAGE I | 268
| STAGE II | 51
| STAGE III | 105
| STAGE IV | 2
| STAGE IVA | 42
| STAGE IVC | 6
| Significant markers | N = 669

List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S5. Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

| ANOVA_P | Q
--- | --- | ---
GSPT2|23708 | 1.583e-14 | 2.85e-10
SEMA3G|56920 | 7.832e-14 | 1.41e-09
PIK3R3|8503 | 8.513e-14 | 1.53e-09
FAM50B|26240 | 1.173e-13 | 2.11e-09
SLC10A4|201780 | 9.595e-13 | 1.73e-08
CYP26A1|1592 | 2.806e-12 | 5.05e-08
ITM2A|9452 | 7.833e-12 | 1.41e-07
DNASE1L3|1776 | 7.973e-12 | 1.43e-07
GJA5|2702 | 1.868e-11 | 3.36e-07
ANXA3|306 | 2.557e-11 | 4.6e-07

Figure S2. Get High-res Image As an example, this figure shows the association of GSPT2|23708 to 'NEOPLASM.DISEASESTAGE'. P value = 1.58e-14 with ANOVA analysis.

Clinical variable #4: 'PATHOLOGY.T.STAGE'

594 genes related to 'PATHOLOGY.T.STAGE'.

Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE | Mean (SD) | 2.14 (0.88)
|  | N
| 1 | 136
| 2 | 159
| 3 | 158
| 4 | 21
| Significant markers | N = 594
| pos. correlated | 111
| neg. correlated | 483

List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

Table S7. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
FBXO9|26268 | -0.3223 | 6.388e-13 | 1.15e-08
VIPR1|7433 | -0.3136 | 2.818e-12 | 5.07e-08
SLCO2A1|6578 | -0.2994 | 2.836e-11 | 5.1e-07
LTF|4057 | -0.2958 | 5.038e-11 | 9.06e-07
SYT15|83849 | -0.2908 | 1.09e-10 | 1.96e-06
FAM65C|140876 | -0.2857 | 2.342e-10 | 4.21e-06
KCNJ13|3769 | -0.2869 | 3.484e-10 | 6.27e-06
KDR|3791 | -0.2822 | 3.939e-10 | 7.08e-06
ZFP3|124961 | -0.2816 | 4.31e-10 | 7.75e-06
CLCNKB|1188 | -0.281 | 4.728e-10 | 8.5e-06

Figure S3. Get High-res Image As an example, this figure shows the association of FBXO9|26268 to 'PATHOLOGY.T.STAGE'. P value = 6.39e-13 with Spearman correlation analysis.

Clinical variable #5: 'PATHOLOGY.N.STAGE'

2518 genes related to 'PATHOLOGY.N.STAGE'.

Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE | Labels | N
| class0 | 216
| class1 | 214
| Significant markers | N = 2518
| Higher in class1 | 1226
| Higher in class0 | 1292

List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S9. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

| T(pos if higher in 'class1') | ttestP | Q | AUC
--- | --- | --- | --- | ---
CREB5|9586 | 9.5 | 2.387e-19 | 4.3e-15 | 0.7322
CLCNKA|1187 | -9.31 | 8.003e-19 | 1.44e-14 | 0.7341
FN1|2335 | 9.2 | 2.434e-18 | 4.38e-14 | 0.7201
SFTPB|6439 | 9.25 | 2.684e-18 | 4.83e-14 | 0.7127
MLEC|9761 | -9.17 | 3.405e-18 | 6.13e-14 | 0.7266
KCNN4|3783 | 9.17 | 3.408e-18 | 6.13e-14 | 0.7205
CBFB|865 | 9.15 | 4.017e-18 | 7.23e-14 | 0.7562
TMEM117|84216 | 8.81 | 3.358e-17 | 6.04e-13 | 0.723
PELI1|57162 | 8.77 | 4.445e-17 | 8e-13 | 0.7276
CYB561|1534 | -8.78 | 5.294e-17 | 9.52e-13 | 0.7224

Figure S4. Get High-res Image As an example, this figure shows the association of CREB5|9586 to 'PATHOLOGY.N.STAGE'. P value = 2.39e-19 with T-test analysis.

Clinical variable #6: 'PATHOLOGY.M.STAGE'

16 genes related to 'PATHOLOGY.M.STAGE'.

Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE | Labels | N
| M0 | 261
| M1 | 9
| MX | 205
| Significant markers | N = 16

List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S11. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

| ANOVA_P | Q
--- | --- | ---
CYP21A2|1589 | 1.071e-07 | 0.00193
ST6GALNAC1|55808 | 1.378e-07 | 0.00248
SELP|6403 | 1.541e-07 | 0.00277
C4ORF6|10141 | 2.744e-07 | 0.00494
C19ORF76|199800 | 1.076e-06 | 0.0194
IDH3A|3419 | 1.134e-06 | 0.0204
KYNU|8942 | 1.138e-06 | 0.0205
GPATCH4|54865 | 1.204e-06 | 0.0217
APOL3|80833 | 1.212e-06 | 0.0218
SLC27A6|28965 | 1.459e-06 | 0.0262

Figure S5. Get High-res Image As an example, this figure shows the association of CYP21A2|1589 to 'PATHOLOGY.M.STAGE'. P value = 1.07e-07 with ANOVA analysis.

Clinical variable #7: 'GENDER'

43 genes related to 'GENDER'.

Table S12. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 349
| MALE | 127
| Significant markers | N = 43
| Higher in MALE | 19
| Higher in FEMALE | 24

List of top 10 genes differentially expressed by 'GENDER'

Table S13. Get Full Table List of top 10 genes differentially expressed by 'GENDER'

| T(pos if higher in 'MALE') | ttestP | Q | AUC
--- | --- | --- | --- | ---
RPS4Y1|6192 | 89.47 | 3.157e-200 | 5.68e-196 | 1
ZFY|7544 | 92.06 | 1.072e-197 | 1.93e-193 | 1
DDX3Y|8653 | 98.11 | 2.723e-185 | 4.9e-181 | 1
NLGN4Y|22829 | 65.55 | 2.685e-154 | 4.83e-150 | 1
UTY|7404 | 91.17 | 1.207e-147 | 2.17e-143 | 1
PRKY|5616 | 41.53 | 5.754e-138 | 1.04e-133 | 0.9938
KDM5D|8284 | 82.98 | 2.444e-129 | 4.4e-125 | 1
USP9Y|8287 | 72.09 | 3.866e-122 | 6.95e-118 | 0.9999
XIST|7503 | -48.05 | 9.925e-89 | 1.79e-84 | 0.9939
CYORF15A|246126 | 55.9 | 1.539e-60 | 2.77e-56 | 1

Figure S6. Get High-res Image As an example, this figure shows the association of RPS4Y1|6192 to 'GENDER'. P value = 3.16e-200 with T-test analysis.

Clinical variable #8: 'HISTOLOGICAL.TYPE'

5511 genes related to 'HISTOLOGICAL.TYPE'.

Table S14. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE | Labels | N
| OTHER SPECIFY | 9
| THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | 334
| THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | 99
| THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) | 34
| Significant markers | N = 5511

List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S15. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

| ANOVA_P | Q
--- | --- | ---
ITGA3|3675 | 3.166e-46 | 5.7e-42
TM7SF4|81501 | 1.173e-45 | 2.11e-41
FN1|2335 | 6.308e-45 | 1.13e-40
ERBB3|2065 | 2.942e-44 | 5.29e-40
SFTPB|6439 | 1.154e-42 | 2.08e-38
TMPRSS4|56649 | 1.154e-42 | 2.08e-38
KCNN4|3783 | 1.81e-41 | 3.26e-37
SERPINA1|5265 | 2.998e-41 | 5.39e-37
FAM176A|84141 | 3.66e-41 | 6.58e-37
UNC5CL|222643 | 4.556e-41 | 8.19e-37

Figure S7. Get High-res Image As an example, this figure shows the association of ITGA3|3675 to 'HISTOLOGICAL.TYPE'. P value = 3.17e-46 with ANOVA analysis.

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

28 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N
| NO | 13
| YES | 463
| Significant markers | N = 28
| Higher in YES | 18
| Higher in NO | 10

List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
C14ORF180|400258 | 13.86 | 2.106e-13 | 3.78e-09 | 0.8935
FLJ37543|285668 | 14.61 | 4.382e-13 | 7.86e-09 | 0.8848
ADIPOQ|9370 | 11.35 | 3.167e-11 | 5.68e-07 | 0.9207
TAS2R43|259289 | 9.8 | 8.419e-11 | 1.51e-06 | 0.7869
HPR|3250 | 11.58 | 4.031e-09 | 7.23e-05 | 0.9308
ENPP3|5169 | 9.55 | 1.71e-08 | 0.000307 | 0.8692
LOC440173|440173 | 9.29 | 3.254e-08 | 0.000584 | 0.8813
CXORF48|54967 | 9.27 | 1.273e-07 | 0.00228 | 0.8409
C6ORF203|51250 | 8.82 | 2.385e-07 | 0.00428 | 0.8727
HCFC1|3054 | -8.86 | 3.227e-07 | 0.00579 | 0.8988

Figure S8. Get High-res Image As an example, this figure shows the association of C14ORF180|400258 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.11e-13 with T-test analysis.

Clinical variable #10: 'RADIATIONEXPOSURE'

6 genes related to 'RADIATIONEXPOSURE'.

Table S18. Basic characteristics of clinical feature: 'RADIATIONEXPOSURE'

RADIATIONEXPOSURE | Labels | N
| NO | 402
| YES | 17
| Significant markers | N = 6
| Higher in YES | 3
| Higher in NO | 3

List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

Table S19. Get Full Table List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
CRNN|49860 | -11.42 | 2.184e-13 | 3.93e-09 | 0.9138
RNF17|56163 | -8.39 | 5.339e-13 | 9.6e-09 | 0.8716
CSNK1A1P|161635 | -8.14 | 8.345e-13 | 1.5e-08 | 0.8183
CYORF15A|246126 | 6.92 | 1.409e-10 | 2.53e-06 | 0.6296
EIF1AY|9086 | 5.78 | 5.256e-08 | 0.000945 | 0.7612
TTTY15|64595 | 5.43 | 5.411e-07 | 0.00973 | 0.722

Figure S9. Get High-res Image As an example, this figure shows the association of CRNN|49860 to 'RADIATIONEXPOSURE'. P value = 2.18e-13 with T-test analysis.

Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

1040 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S20. Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION | Labels | N
| MINIMAL (T3) | 124
| MODERATE/ADVANCED (T4A) | 16
| NONE | 320
| VERY ADVANCED (T4B) | 1
| Significant markers | N = 1040

List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S21. Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

| ANOVA_P | Q
--- | --- | ---
ASAH2|56624 | 1.737e-15 | 3.13e-11
SLC25A42|284439 | 3.895e-15 | 7.01e-11
SRPX2|27286 | 9.145e-15 | 1.65e-10
SLC10A4|201780 | 1.546e-14 | 2.78e-10
COL1A1|1277 | 2.697e-14 | 4.85e-10
FAM69C|125704 | 4.76e-14 | 8.56e-10
COL3A1|1281 | 7.191e-14 | 1.29e-09
POSTN|10631 | 7.309e-14 | 1.31e-09
FLJ42875|440556 | 9.572e-14 | 1.72e-09
CYP26A1|1592 | 9.722e-14 | 1.75e-09

Figure S10. Get High-res Image As an example, this figure shows the association of ASAH2|56624 to 'EXTRATHYROIDAL.EXTENSION'. P value = 1.74e-15 with ANOVA analysis.

Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

2 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S22. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 368
| R1 | 46
| R2 | 4
| RX | 29
| Significant markers | N = 2

List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S23. Get Full Table List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

| ANOVA_P | Q
--- | --- | ---
SHOX2|6474 | 2.167e-07 | 0.0039
CATSPER2P1|440278 | 5.881e-07 | 0.0106

Figure S11. Get High-res Image As an example, this figure shows the association of SHOX2|6474 to 'COMPLETENESS.OF.RESECTION'. P value = 2.17e-07 with ANOVA analysis.

Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

1339 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S24. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES | Mean (SD) | 3.53 (6.1)
| Significant markers | N = 1339
| pos. correlated | 744
| neg. correlated | 595

List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S25. Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
CBFB|865 | 0.4005 | 6.376e-16 | 1.15e-11
PELI1|57162 | 0.3976 | 1.087e-15 | 1.96e-11
FAM60A|58516 | 0.389 | 4.944e-15 | 8.89e-11
CREB5|9586 | 0.3854 | 9.246e-15 | 1.66e-10
TAGLN2|8407 | 0.382 | 1.65e-14 | 2.97e-10
CLCNKA|1187 | -0.3786 | 2.937e-14 | 5.28e-10
S100A10|6281 | 0.3743 | 6.019e-14 | 1.08e-09
ZNF346|23567 | -0.3706 | 1.09e-13 | 1.96e-09
GPR153|387509 | 0.3695 | 1.317e-13 | 2.37e-09
ARF6|382 | 0.3692 | 1.374e-13 | 2.47e-09

Figure S12. Get High-res Image As an example, this figure shows the association of CBFB|865 to 'NUMBER.OF.LYMPH.NODES'. P value = 6.38e-16 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #14: 'MULTIFOCALITY'

No gene related to 'MULTIFOCALITY'.

Table S26. Basic characteristics of clinical feature: 'MULTIFOCALITY'

MULTIFOCALITY | Labels | N
| MULTIFOCAL | 215
| UNIFOCAL | 251
| Significant markers | N = 0

Clinical variable #15: 'TUMOR.SIZE'

11 genes related to 'TUMOR.SIZE'.

Table S27. Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE | Mean (SD) | 2.96 (1.6)
| Significant markers | N = 11
| pos. correlated | 0
| neg. correlated | 11

List of top 10 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

Table S28. Get Full Table List of top 10 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
C3ORF32|51066 | -0.2926 | 1.014e-08 | 0.000183
ISLR2|57611 | -0.2797 | 2.941e-08 | 0.000529
ZC3H10|84872 | -0.2708 | 8.268e-08 | 0.00149
CLDN2|9075 | -0.2638 | 2.104e-07 | 0.00378
LRRC55|219527 | -0.2578 | 3.999e-07 | 0.00719
SLC14A1|6563 | -0.2562 | 4.132e-07 | 0.00743
FOXI2|399823 | -0.2563 | 5.068e-07 | 0.00912
CXCL12|6387 | -0.2461 | 1.197e-06 | 0.0215
PI16|221476 | -0.2459 | 1.478e-06 | 0.0266
IFT57|55081 | -0.2412 | 1.97e-06 | 0.0354

Figure S13. Get High-res Image As an example, this figure shows the association of C3ORF32|51066 to 'TUMOR.SIZE'. P value = 1.01e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Methods & Data
Input

- Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Clinical data file = THCA-TP.merged_data.txt

- Number of patients = 476

- Number of genes = 17994

- Number of clinical features = 15

Survival analysis

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

Correlation analysis

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

ANOVA analysis

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

Student's t-test analysis

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

Q value calculation

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.

Download Results

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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