This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 15 clinical features across 1593 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.
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3324 genes correlated to 'Time to Death'.
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KLHL14 , ASS1 , GNA11 , IGSF11 , UPK1B , ...
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3682 genes correlated to 'AGE'.
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GREB1 , COL18A1 , DUOX2 , LDOC1 , GALNTL1 , ...
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17229 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
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KLHL14 , ZG16 , SLC22A2 , FOXE1 , PDZD3 , ...
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10644 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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SCGB3A2 , MUPCDH , SCGB1A1 , PDZD3 , HNF1A , ...
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6862 genes correlated to 'PATHOLOGY.T.STAGE'.
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ADHFE1 , C13ORF3 , NR3C1 , LIFR , RAB6IP1 , ...
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233 genes correlated to 'PATHOLOGY.N.STAGE'.
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ARRDC1 , ZCCHC11 , LRFN2 , PBX1 , CACNB3 , ...
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576 genes correlated to 'PATHOLOGY.M.STAGE'.
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VIL1 , MUC13 , FABP1 , SPACA3 , ACF , ...
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8979 genes correlated to 'GENDER'.
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ESR1 , DDX3Y , RSPO1 , RPS4Y1 , EIF1AY , ...
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196 genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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PPP1R9A , VASN , METTL8 , MARCH7 , ZNF503 , ...
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17147 genes correlated to 'HISTOLOGICAL.TYPE'.
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KLHL14 , ZG16 , SLC22A2 , FOXE1 , PDZD3 , ...
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5948 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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CYP3A5 , CYP3A7 , CYP3A4 , MAP2K7 , TCF21 , ...
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2 genes correlated to 'YEAROFTOBACCOSMOKINGONSET'.
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MMP10 , ALS2CR4
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2152 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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NPR1 , WIT1 , THRSP , KLHL14 , S100A1 , ...
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No genes correlated to 'NUMBERPACKYEARSSMOKED', and 'NUMBER.OF.LYMPH.NODES'.
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=3324 | shorter survival | N=1554 | longer survival | N=1770 |
AGE | Spearman correlation test | N=3682 | older | N=1744 | younger | N=1938 |
PRIMARY SITE OF DISEASE | ANOVA test | N=17229 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=10644 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=6862 | higher stage | N=3197 | lower stage | N=3665 |
PATHOLOGY N STAGE | Spearman correlation test | N=233 | higher stage | N=169 | lower stage | N=64 |
PATHOLOGY M STAGE | ANOVA test | N=576 | ||||
GENDER | t test | N=8979 | male | N=4341 | female | N=4638 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=196 | higher score | N=92 | lower score | N=104 |
HISTOLOGICAL TYPE | ANOVA test | N=17147 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=5948 | yes | N=2850 | no | N=3098 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
YEAROFTOBACCOSMOKINGONSET | Spearman correlation test | N=2 | higher yearoftobaccosmokingonset | N=0 | lower yearoftobaccosmokingonset | N=2 |
COMPLETENESS OF RESECTION | ANOVA test | N=2152 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.1-234.2 (median=25.1) |
censored | N = 990 | |
death | N = 455 | |
Significant markers | N = 3324 | |
associated with shorter survival | 1554 | |
associated with longer survival | 1770 |
Table S2. Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
KLHL14 | 1.27 | 0 | 0 | 0.605 |
ASS1 | 1.32 | 0 | 0 | 0.621 |
GNA11 | 0.54 | 0 | 0 | 0.388 |
IGSF11 | 1.35 | 0 | 0 | 0.639 |
UPK1B | 1.21 | 0 | 0 | 0.636 |
KLK7 | 1.16 | 0 | 0 | 0.602 |
C4ORF32 | 0.78 | 0 | 0 | 0.382 |
ZRSR1 | 0.55 | 0 | 0 | 0.351 |
MDS1 | 1.39 | 0 | 0 | 0.625 |
LYPD2 | 1.28 | 0 | 0 | 0.596 |
Figure S1. Get High-res Image As an example, this figure shows the association of KLHL14 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 0 with univariate Cox regression analysis using continuous log-2 expression values.
![](V1ex.png)
Table S3. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 61.39 (13) |
Significant markers | N = 3682 | |
pos. correlated | 1744 | |
neg. correlated | 1938 |
Table S4. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
GREB1 | -0.2892 | 9.188e-32 | 1.64e-27 |
COL18A1 | -0.2758 | 6.342e-29 | 1.13e-24 |
DUOX2 | 0.2752 | 8.485e-29 | 1.51e-24 |
LDOC1 | -0.2683 | 2.09e-27 | 3.72e-23 |
GALNTL1 | -0.267 | 3.747e-27 | 6.67e-23 |
OBSL1 | -0.2642 | 1.335e-26 | 2.38e-22 |
FOXF1 | 0.2611 | 5.404e-26 | 9.62e-22 |
CYP2C18 | 0.2585 | 1.69e-25 | 3.01e-21 |
NOTCH2 | -0.2559 | 5.25e-25 | 9.35e-21 |
BBOX1 | -0.2557 | 5.714e-25 | 1.02e-20 |
Figure S2. Get High-res Image As an example, this figure shows the association of GREB1 to 'AGE'. P value = 9.19e-32 with Spearman correlation analysis. The straight line presents the best linear regression.
![](V2ex.png)
Table S5. Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'
PRIMARY.SITE.OF.DISEASE | Labels | N |
BREAST | 526 | |
COLON | 152 | |
ENDOMETRIAL | 54 | |
KIDNEY | 72 | |
LUNG | 186 | |
OMENTUM | 2 | |
OVARY | 529 | |
PERITONEUM OVARY | 2 | |
RECTUM | 68 | |
Significant markers | N = 17229 |
Table S6. Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'
ANOVA_P | Q | |
---|---|---|
KLHL14 | 0 | 0 |
ZG16 | 0 | 0 |
SLC22A2 | 0 | 0 |
FOXE1 | 0 | 0 |
PDZD3 | 0 | 0 |
EMX2 | 0 | 0 |
NPR1 | 0 | 0 |
FUT4 | 0 | 0 |
ACF | 0 | 0 |
FXYD2 | 0 | 0 |
Figure S3. Get High-res Image As an example, this figure shows the association of KLHL14 to 'PRIMARY.SITE.OF.DISEASE'. P value = 0 with ANOVA analysis.
![](V3ex.png)
Table S7. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 133 | |
STAGE IA | 69 | |
STAGE IB | 78 | |
STAGE II | 28 | |
STAGE IIA | 258 | |
STAGE IIB | 145 | |
STAGE III | 24 | |
STAGE IIIA | 102 | |
STAGE IIIB | 52 | |
STAGE IIIC | 39 | |
STAGE IV | 57 | |
STAGE IVA | 1 | |
STAGE TIS | 1 | |
STAGE X | 16 | |
Significant markers | N = 10644 |
Table S8. Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'
ANOVA_P | Q | |
---|---|---|
SCGB3A2 | 2.669e-87 | 4.76e-83 |
MUPCDH | 1.832e-82 | 3.26e-78 |
SCGB1A1 | 6.483e-82 | 1.15e-77 |
PDZD3 | 1.151e-81 | 2.05e-77 |
HNF1A | 5.755e-81 | 1.03e-76 |
CLRN3 | 6.716e-81 | 1.2e-76 |
SFTPB | 1.454e-80 | 2.59e-76 |
SFTPA1 | 2.215e-80 | 3.94e-76 |
SFTPC | 7.77e-80 | 1.38e-75 |
LRRC19 | 8.924e-80 | 1.59e-75 |
Figure S4. Get High-res Image As an example, this figure shows the association of SCGB3A2 to 'NEOPLASM.DISEASESTAGE'. P value = 2.67e-87 with ANOVA analysis.
![](V4ex.png)
Table S9. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 2.11 (0.81) |
N | ||
1 | 225 | |
2 | 490 | |
3 | 237 | |
4 | 51 | |
Significant markers | N = 6862 | |
pos. correlated | 3197 | |
neg. correlated | 3665 |
Table S10. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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ADHFE1 | -0.4255 | 2.223e-45 | 3.96e-41 |
C13ORF3 | 0.4162 | 2.734e-43 | 4.87e-39 |
NR3C1 | -0.411 | 3.769e-42 | 6.71e-38 |
LIFR | -0.4037 | 1.361e-40 | 2.42e-36 |
RAB6IP1 | -0.4005 | 6.273e-40 | 1.12e-35 |
C1ORF165 | -0.4004 | 6.532e-40 | 1.16e-35 |
SLC26A6 | 0.3905 | 7.07e-38 | 1.26e-33 |
TBRG4 | 0.3861 | 5.202e-37 | 9.26e-33 |
C19ORF21 | 0.3856 | 6.539e-37 | 1.16e-32 |
EBP | 0.3846 | 1.026e-36 | 1.83e-32 |
Figure S5. Get High-res Image As an example, this figure shows the association of ADHFE1 to 'PATHOLOGY.T.STAGE'. P value = 2.22e-45 with Spearman correlation analysis.
![](V5ex.png)
Table S11. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Mean (SD) | 0.63 (0.84) |
N | ||
0 | 545 | |
1 | 260 | |
2 | 121 | |
3 | 34 | |
Significant markers | N = 233 | |
pos. correlated | 169 | |
neg. correlated | 64 |
Table S12. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
ARRDC1 | 0.2091 | 6.051e-11 | 1.08e-06 |
ZCCHC11 | -0.2058 | 1.214e-10 | 2.16e-06 |
LRFN2 | 0.2033 | 2.041e-10 | 3.64e-06 |
PBX1 | 0.2028 | 2.26e-10 | 4.03e-06 |
CACNB3 | 0.202 | 2.701e-10 | 4.81e-06 |
HIST1H2AG | 0.1969 | 7.595e-10 | 1.35e-05 |
RPL5 | -0.196 | 9.078e-10 | 1.62e-05 |
MMP11 | 0.1947 | 1.191e-09 | 2.12e-05 |
SPDEF | 0.1937 | 1.451e-09 | 2.58e-05 |
ERRFI1 | -0.1903 | 2.799e-09 | 4.98e-05 |
Figure S6. Get High-res Image As an example, this figure shows the association of ARRDC1 to 'PATHOLOGY.N.STAGE'. P value = 6.05e-11 with Spearman correlation analysis.
![](V6ex.png)
Table S13. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
CM0 (I+) | 2 | |
M0 | 925 | |
M1 | 58 | |
M1A | 1 | |
MX | 14 | |
Significant markers | N = 576 |
Table S14. Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'
ANOVA_P | Q | |
---|---|---|
VIL1 | 8.478e-13 | 1.51e-08 |
MUC13 | 2.841e-12 | 5.06e-08 |
FABP1 | 4.306e-12 | 7.67e-08 |
SPACA3 | 4.683e-12 | 8.34e-08 |
ACF | 7.447e-12 | 1.33e-07 |
CALML4 | 7.796e-12 | 1.39e-07 |
TMEM25 | 8.062e-12 | 1.44e-07 |
IL22RA1 | 8.786e-12 | 1.56e-07 |
PCLKC | 1.225e-11 | 2.18e-07 |
PDZD3 | 1.317e-11 | 2.35e-07 |
Figure S7. Get High-res Image As an example, this figure shows the association of VIL1 to 'PATHOLOGY.M.STAGE'. P value = 8.48e-13 with ANOVA analysis.
![](V7ex.png)
Table S15. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 1304 | |
MALE | 289 | |
Significant markers | N = 8979 | |
Higher in MALE | 4341 | |
Higher in FEMALE | 4638 |
Table S16. Get Full Table List of top 10 genes differentially expressed by 'GENDER'
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
ESR1 | -35.87 | 9.367e-164 | 1.67e-159 | 0.8775 |
DDX3Y | 53.23 | 5.05e-163 | 9e-159 | 0.9837 |
RSPO1 | -31.07 | 4.803e-162 | 8.56e-158 | 0.8428 |
RPS4Y1 | 51.71 | 2.642e-155 | 4.71e-151 | 0.9711 |
EIF1AY | 49.21 | 1.083e-151 | 1.93e-147 | 0.9842 |
RPS4Y2 | 48.53 | 1.689e-147 | 3.01e-143 | 0.9814 |
ERBB4 | -32.57 | 2.549e-147 | 4.54e-143 | 0.8586 |
JARID1D | 44.6 | 2.007e-146 | 3.57e-142 | 0.9767 |
SCGB2A2 | -29.39 | 1.805e-145 | 3.21e-141 | 0.8531 |
CYORF15A | 43.7 | 2.34e-139 | 4.17e-135 | 0.981 |
Figure S8. Get High-res Image As an example, this figure shows the association of ESR1 to 'GENDER'. P value = 9.37e-164 with T-test analysis.
![](V8ex.png)
196 genes related to 'KARNOFSKY.PERFORMANCE.SCORE'.
Table S17. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 60.22 (34) |
Significant markers | N = 196 | |
pos. correlated | 92 | |
neg. correlated | 104 |
Table S18. Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY.PERFORMANCE.SCORE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
PPP1R9A | 0.591 | 4.461e-10 | 7.95e-06 |
VASN | 0.5685 | 2.77e-09 | 4.93e-05 |
METTL8 | -0.5495 | 1.168e-08 | 0.000208 |
MARCH7 | -0.5488 | 1.234e-08 | 0.00022 |
ZNF503 | 0.5415 | 2.087e-08 | 0.000372 |
ADK | -0.5406 | 2.225e-08 | 0.000396 |
PCYT1A | -0.5405 | 2.235e-08 | 0.000398 |
INSIG2 | -0.5394 | 2.423e-08 | 0.000432 |
ARHGEF17 | 0.5392 | 2.453e-08 | 0.000437 |
POGZ | 0.5364 | 2.984e-08 | 0.000531 |
Figure S9. Get High-res Image As an example, this figure shows the association of PPP1R9A to 'KARNOFSKY.PERFORMANCE.SCORE'. P value = 4.46e-10 with Spearman correlation analysis. The straight line presents the best linear regression.
![](V9ex.png)
Table S19. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
COLON ADENOCARCINOMA | 129 | |
COLON MUCINOUS ADENOCARCINOMA | 22 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 41 | |
INFILTRATING DUCTAL CARCINOMA | 448 | |
INFILTRATING LOBULAR CARCINOMA | 41 | |
KIDNEY CLEAR CELL RENAL CARCINOMA | 72 | |
LUNG ADENOCARCINOMA MIXED SUBTYPE | 1 | |
LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | 30 | |
LUNG BASALOID SQUAMOUS CELL CARCINOMA | 5 | |
LUNG CLEAR CELL ADENOCARCINOMA | 1 | |
LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | 1 | |
LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | 148 | |
MEDULLARY CARCINOMA | 1 | |
MIXED HISTOLOGY (PLEASE SPECIFY) | 12 | |
MIXED SEROUS AND ENDOMETRIOID | 1 | |
MUCINOUS CARCINOMA | 2 | |
OTHER SPECIFY | 21 | |
RECTAL ADENOCARCINOMA | 58 | |
RECTAL MUCINOUS ADENOCARCINOMA | 7 | |
SEROUS CYSTADENOCARCINOMA | 533 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 12 | |
Significant markers | N = 17147 |
Table S20. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'
ANOVA_P | Q | |
---|---|---|
KLHL14 | 0 | 0 |
ZG16 | 0 | 0 |
SLC22A2 | 0 | 0 |
FOXE1 | 0 | 0 |
PDZD3 | 0 | 0 |
EMX2 | 0 | 0 |
NPR1 | 0 | 0 |
FUT4 | 0 | 0 |
ACF | 0 | 0 |
FXYD2 | 0 | 0 |
Figure S10. Get High-res Image As an example, this figure shows the association of KLHL14 to 'HISTOLOGICAL.TYPE'. P value = 0 with ANOVA analysis.
![](V10ex.png)
5948 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S21. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 186 | |
YES | 1407 | |
Significant markers | N = 5948 | |
Higher in YES | 2850 | |
Higher in NO | 3098 |
Table S22. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
CYP3A5 | 22.66 | 1.209e-80 | 2.15e-76 | 0.7899 |
CYP3A7 | 20.95 | 2.298e-72 | 4.09e-68 | 0.7691 |
CYP3A4 | 20.76 | 8.829e-72 | 1.57e-67 | 0.7742 |
MAP2K7 | 21.83 | 2.06e-68 | 3.67e-64 | 0.81 |
TCF21 | 21.34 | 2.229e-68 | 3.97e-64 | 0.7936 |
CCDC71 | 21.44 | 2.765e-64 | 4.92e-60 | 0.8204 |
REG1A | 19.55 | 4.379e-62 | 7.8e-58 | 0.7762 |
PDZD3 | 17.65 | 2.746e-61 | 4.89e-57 | 0.6934 |
AADAC | 19.37 | 3.443e-60 | 6.13e-56 | 0.7666 |
CHMP4B | 20.44 | 7.419e-60 | 1.32e-55 | 0.8129 |
Figure S11. Get High-res Image As an example, this figure shows the association of CYP3A5 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 1.21e-80 with T-test analysis.
![](V11ex.png)
Table S23. Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'
NUMBERPACKYEARSSMOKED | Mean (SD) | 53.05 (35) |
Significant markers | N = 0 |
Table S24. Basic characteristics of clinical feature: 'YEAROFTOBACCOSMOKINGONSET'
YEAROFTOBACCOSMOKINGONSET | Mean (SD) | 1959.74 (11) |
Significant markers | N = 2 | |
pos. correlated | 0 | |
neg. correlated | 2 |
Table S25. Get Full Table List of 2 genes significantly correlated to 'YEAROFTOBACCOSMOKINGONSET' by Spearman correlation test
SpearmanCorr | corrP | Q | |
---|---|---|---|
MMP10 | -0.4479 | 4.625e-07 | 0.00824 |
ALS2CR4 | -0.4273 | 1.724e-06 | 0.0307 |
Figure S12. Get High-res Image As an example, this figure shows the association of MMP10 to 'YEAROFTOBACCOSMOKINGONSET'. P value = 4.63e-07 with Spearman correlation analysis. The straight line presents the best linear regression.
![](V13ex.png)
2152 genes related to 'COMPLETENESS.OF.RESECTION'.
Table S26. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 403 | |
R1 | 38 | |
R2 | 36 | |
RX | 8 | |
Significant markers | N = 2152 |
Table S27. Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'
ANOVA_P | Q | |
---|---|---|
NPR1 | 1.498e-36 | 2.67e-32 |
WIT1 | 4.526e-35 | 8.06e-31 |
THRSP | 1.497e-34 | 2.67e-30 |
KLHL14 | 1.442e-32 | 2.57e-28 |
S100A1 | 7.985e-32 | 1.42e-27 |
WT1 | 1.091e-31 | 1.94e-27 |
DOK5 | 8.19e-31 | 1.46e-26 |
LYPD1 | 7.039e-28 | 1.25e-23 |
SCGB1D2 | 5.083e-27 | 9.05e-23 |
SCGB1C1 | 1.454e-26 | 2.59e-22 |
Figure S13. Get High-res Image As an example, this figure shows the association of NPR1 to 'COMPLETENESS.OF.RESECTION'. P value = 1.5e-36 with ANOVA analysis.
![](V14ex.png)
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Expresson data file = PANCAN12-TP.medianexp.txt
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Clinical data file = PANCAN12-TP.clin.merged.picked.txt
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Number of patients = 1593
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Number of genes = 17814
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Number of clinical features = 15
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 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 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 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.
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.