Correlation between mRNA expression and clinical features
PANCANCER cohort with 12 disease types (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1TT4NX8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PANCANCER cohort with 12 disease types (Primary solid tumor cohort) - 21 April 2013: Correlation between mRNA expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TT4NX8
Overview
Introduction

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

Summary

Testing the association between 17814 genes and 19 clinical features across 1593 samples, statistically thresholded by Q value < 0.05, 16 clinical features related to at least one genes.

  • 3018 genes correlated to 'Time to Death'.

    • KLHL14 ,  ASS1 ,  IGSF11 ,  UPK1B ,  C4ORF32 ,  ...

  • 3682 genes correlated to 'AGE'.

    • GREB1 ,  COL18A1 ,  DUOX2 ,  LDOC1 ,  GALNTL1 ,  ...

  • 17315 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.

    • KLHL14 ,  ZG16 ,  SLC22A2 ,  PDZD3 ,  EMX2 ,  ...

  • 8993 genes correlated to 'GENDER'.

    • ESR1 ,  RSPO1 ,  DDX3Y ,  RPS4Y1 ,  EIF1AY ,  ...

  • 206 genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

    • PPP1R9A ,  VASN ,  MARCH7 ,  CCDC135 ,  POGZ ,  ...

  • 16971 genes correlated to 'HISTOLOGICAL.TYPE'.

    • KLHL14 ,  PDZD3 ,  EMX2 ,  NPR1 ,  FUT4 ,  ...

  • 5911 genes correlated to 'PATHOLOGY.T'.

    • C13ORF3 ,  NR3C1 ,  CDCA7 ,  LIFR ,  C20ORF151 ,  ...

  • 16 genes correlated to 'PATHOLOGY.N'.

    • TNFRSF10C ,  FAM73A ,  MGC50559 ,  ZNF273 ,  GABARAP ,  ...

  • 30 genes correlated to 'PATHOLOGICSPREAD(M)'.

    • KCNC2 ,  TCF7 ,  HCN1 ,  C8ORF30A ,  SPACA3 ,  ...

  • 7395 genes correlated to 'TUMOR.STAGE'.

    • FGF18 ,  WT1 ,  KITLG ,  RBM38 ,  ELL2 ,  ...

  • 5814 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • CYP3A5 ,  CYP3A7 ,  CYP3A4 ,  TCF21 ,  MAP2K7 ,  ...

  • 9 genes correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

    • PSME4 ,  C1ORF64 ,  LMNB2 ,  LONP1 ,  SLC25A1 ,  ...

  • 1 gene correlated to 'YEAROFTOBACCOSMOKINGONSET'.

    • MMP10

  • 2 genes correlated to 'LYMPH.NODE.METASTASIS'.

    • GUCA2A ,  ASZ1

  • 2319 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • NPR1 ,  WIT1 ,  DOK5 ,  THRSP ,  KLHL14 ,  ...

  • 5 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • PGC ,  BMPER ,  LRP4 ,  GPER ,  PRSS2

  • No genes correlated to 'NUMBERPACKYEARSSMOKED', 'DISTANT.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.

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=3018 shorter survival N=1360 longer survival N=1658
AGE Spearman correlation test N=3682 older N=1748 younger N=1934
PRIMARY SITE OF DISEASE ANOVA test N=17315        
GENDER t test N=8993 male N=4112 female N=4881
KARNOFSKY PERFORMANCE SCORE Spearman correlation test N=206 higher score N=129 lower score N=77
HISTOLOGICAL TYPE ANOVA test N=16971        
PATHOLOGY T Spearman correlation test N=5911 higher pT N=3176 lower pT N=2735
PATHOLOGY N Spearman correlation test N=16 higher pN N=3 lower pN N=13
PATHOLOGICSPREAD(M) ANOVA test N=30        
TUMOR STAGE Spearman correlation test N=7395 higher stage N=3996 lower stage N=3399
RADIATIONS RADIATION REGIMENINDICATION t test N=5814 yes N=2865 no N=2949
NUMBERPACKYEARSSMOKED Spearman correlation test   N=0        
TOBACCOSMOKINGHISTORYINDICATOR ANOVA test N=9        
YEAROFTOBACCOSMOKINGONSET Spearman correlation test N=1 higher yearoftobaccosmokingonset N=0 lower yearoftobaccosmokingonset N=1
DISTANT METASTASIS ANOVA test   N=0        
LYMPH NODE METASTASIS ANOVA test N=2        
COMPLETENESS OF RESECTION ANOVA test N=2319        
NUMBER OF LYMPH NODES Spearman correlation test   N=0        
NEOPLASM DISEASESTAGE ANOVA test N=5        
Clinical variable #1: 'Time to Death'

3018 genes related to 'Time to Death'.

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

Time to Death Duration (Months) 0.1-223.4 (median=23)
  censored N = 1000
  death N = 437
     
  Significant markers N = 3018
  associated with shorter survival 1360
  associated with longer survival 1658
List of top 10 genes significantly associated with 'Time to Death' by Cox regression test

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 1.26 0 0 0.6
ASS1 1.32 0 0 0.621
IGSF11 1.36 0 0 0.641
UPK1B 1.21 0 0 0.636
C4ORF32 0.77 0 0 0.38
ZRSR1 0.55 0 0 0.349
MDS1 1.37 0 0 0.621
GALNT12 1.31 0 0 0.616
MUC4 1.22 0 0 0.635
NUBP1 0.46 0 0 0.354

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.

Clinical variable #2: 'AGE'

3682 genes related to 'AGE'.

Table S3.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 61.39 (13)
  Significant markers N = 3682
  pos. correlated 1748
  neg. correlated 1934
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
GREB1 -0.288 1.648e-31 2.94e-27
COL18A1 -0.2771 3.469e-29 6.18e-25
DUOX2 0.2769 3.755e-29 6.69e-25
LDOC1 -0.2689 1.588e-27 2.83e-23
GALNTL1 -0.2672 3.515e-27 6.26e-23
OBSL1 -0.2646 1.107e-26 1.97e-22
FOXF1 0.262 3.685e-26 6.56e-22
CYP2C18 0.2605 6.935e-26 1.23e-21
BBOX1 -0.2573 2.842e-25 5.06e-21
SH3BP5 -0.2572 3.097e-25 5.51e-21

Figure S2.  Get High-res Image As an example, this figure shows the association of GREB1 to 'AGE'. P value = 1.65e-31 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'PRIMARY.SITE.OF.DISEASE'

17315 genes related to 'PRIMARY.SITE.OF.DISEASE'.

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 = 17315
List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

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
PDZD3 0 0
EMX2 0 0
NPR1 0 0
FUT4 0 0
ACF 0 0
FXYD2 0 0
UPK1B 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.

Clinical variable #4: 'GENDER'

8993 genes related to 'GENDER'.

Table S7.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 1304
  MALE 289
     
  Significant markers N = 8993
  Higher in MALE 4112
  Higher in FEMALE 4881
List of top 10 genes differentially expressed by 'GENDER'

Table S8.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
ESR1 -36.23 6.789e-167 1.21e-162 0.8781
RSPO1 -31.56 9.619e-167 1.71e-162 0.8493
DDX3Y 53.31 9.336e-164 1.66e-159 0.9839
RPS4Y1 51.76 1.437e-155 2.56e-151 0.9717
EIF1AY 48.93 2.175e-151 3.87e-147 0.9839
RPS4Y2 48.54 8.57e-148 1.53e-143 0.9816
ERBB4 -32.63 1.134e-147 2.02e-143 0.8588
JARID1D 44.53 5.72e-147 1.02e-142 0.9762
SCGB2A2 -29.47 7.483e-146 1.33e-141 0.8574
CYORF15A 43.55 3.378e-139 6.01e-135 0.9813

Figure S4.  Get High-res Image As an example, this figure shows the association of ESR1 to 'GENDER'. P value = 6.79e-167 with T-test analysis.

Clinical variable #5: 'KARNOFSKY.PERFORMANCE.SCORE'

206 genes related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S9.  Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE Mean (SD) 60.22 (34)
  Significant markers N = 206
  pos. correlated 129
  neg. correlated 77
List of top 10 genes significantly correlated to 'KARNOFSKY.PERFORMANCE.SCORE' by Spearman correlation test

Table S10.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY.PERFORMANCE.SCORE' by Spearman correlation test

SpearmanCorr corrP Q
PPP1R9A 0.5916 4.259e-10 7.59e-06
VASN 0.5749 1.671e-09 2.98e-05
MARCH7 -0.5551 7.711e-09 0.000137
CCDC135 0.5548 7.875e-09 0.00014
POGZ 0.5503 1.102e-08 0.000196
INSIG2 -0.5485 1.255e-08 0.000223
ZNF503 0.5479 1.318e-08 0.000235
TLE1 0.5448 1.642e-08 0.000292
ADK -0.5439 1.761e-08 0.000314
PCYT1A -0.5421 1.996e-08 0.000355

Figure S5.  Get High-res Image As an example, this figure shows the association of PPP1R9A to 'KARNOFSKY.PERFORMANCE.SCORE'. P value = 4.26e-10 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #6: 'HISTOLOGICAL.TYPE'

16971 genes related to 'HISTOLOGICAL.TYPE'.

Table S11.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  COLON ADENOCARCINOMA 126
  COLON MUCINOUS ADENOCARCINOMA 24
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA 41
  INFILTRATING DUCTAL CARCINOMA 110
  INFILTRATING LOBULAR CARCINOMA 12
  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
  MIXED HISTOLOGY (PLEASE SPECIFY) 5
  MIXED SEROUS AND ENDOMETRIOID 1
  OTHER SPECIFY 10
  RECTAL ADENOCARCINOMA 58
  RECTAL MUCINOUS ADENOCARCINOMA 7
  SEROUS CYSTADENOCARCINOMA 533
  SEROUS ENDOMETRIAL ADENOCARCINOMA 12
     
  Significant markers N = 16971
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
KLHL14 0 0
PDZD3 0 0
EMX2 0 0
NPR1 0 0
FUT4 0 0
ACF 0 0
FXYD2 0 0
SPINK4 0 0
SFTPC 0 0
SLC12A2 0 0

Figure S6.  Get High-res Image As an example, this figure shows the association of KLHL14 to 'HISTOLOGICAL.TYPE'. P value = 0 with ANOVA analysis.

Clinical variable #7: 'PATHOLOGY.T'

5911 genes related to 'PATHOLOGY.T'.

Table S13.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 2.3 (0.85)
  N
  T1 92
  T2 179
  T3 178
  T4 29
     
  Significant markers N = 5911
  pos. correlated 3176
  neg. correlated 2735
List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table S14.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

SpearmanCorr corrP Q
C13ORF3 0.5211 1.264e-34 2.25e-30
NR3C1 -0.5184 3.085e-34 5.49e-30
CDCA7 0.5156 7.924e-34 1.41e-29
LIFR -0.5143 1.235e-33 2.2e-29
C20ORF151 0.5111 3.619e-33 6.45e-29
NOXO1 0.5077 1.096e-32 1.95e-28
PDSS1 0.5062 1.784e-32 3.18e-28
B3GNT3 0.5004 1.188e-31 2.12e-27
MAL -0.4987 2.023e-31 3.6e-27
POF1B 0.4978 2.687e-31 4.78e-27

Figure S7.  Get High-res Image As an example, this figure shows the association of C13ORF3 to 'PATHOLOGY.T'. P value = 1.26e-34 with Spearman correlation analysis.

Clinical variable #8: 'PATHOLOGY.N'

16 genes related to 'PATHOLOGY.N'.

Table S15.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.51 (0.77)
  N
  N0 290
  N1 90
  N2 60
  N3 5
     
  Significant markers N = 16
  pos. correlated 3
  neg. correlated 13
List of top 10 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

Table S16.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

SpearmanCorr corrP Q
TNFRSF10C -0.2603 2.519e-08 0.000449
FAM73A -0.2572 3.746e-08 0.000667
MGC50559 -0.2477 1.198e-07 0.00213
ZNF273 0.2452 1.624e-07 0.00289
GABARAP -0.2423 2.285e-07 0.00407
LUZP2 0.2388 3.561e-07 0.00634
CNDP2 -0.2304 8.931e-07 0.0159
DHCR7 0.2301 9.331e-07 0.0166
ZFP2 -0.2294 1.007e-06 0.0179
DCTN6 -0.2263 1.417e-06 0.0252

Figure S8.  Get High-res Image As an example, this figure shows the association of TNFRSF10C to 'PATHOLOGY.N'. P value = 2.52e-08 with Spearman correlation analysis.

Clinical variable #9: 'PATHOLOGICSPREAD(M)'

30 genes related to 'PATHOLOGICSPREAD(M)'.

Table S17.  Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) Labels N
  M0 428
  M1 44
  M1A 1
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGICSPREAD(M)'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGICSPREAD(M)'

ANOVA_P Q
KCNC2 1.224e-09 2.18e-05
TCF7 2.424e-08 0.000432
HCN1 5.782e-08 0.00103
C8ORF30A 1.136e-07 0.00202
SPACA3 2.624e-07 0.00467
F10 4.444e-07 0.00791
RBM26 5.393e-07 0.0096
SERPINA4 6.055e-07 0.0108
NPAS2 7.627e-07 0.0136
PLOD3 9.144e-07 0.0163

Figure S9.  Get High-res Image As an example, this figure shows the association of KCNC2 to 'PATHOLOGICSPREAD(M)'. P value = 1.22e-09 with ANOVA analysis.

Clinical variable #10: 'TUMOR.STAGE'

7395 genes related to 'TUMOR.STAGE'.

Table S19.  Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE Mean (SD) 2.55 (0.95)
  N
  Stage 1 206
  Stage 2 163
  Stage 3 512
  Stage 4 120
     
  Significant markers N = 7395
  pos. correlated 3996
  neg. correlated 3399
List of top 10 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

Table S20.  Get Full Table List of top 10 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FGF18 0.5209 1.067e-70 1.9e-66
WT1 0.5115 7.953e-68 1.42e-63
KITLG -0.4949 5.798e-63 1.03e-58
RBM38 0.4891 2.517e-61 4.48e-57
ELL2 -0.4855 2.59e-60 4.61e-56
RIMS4 0.4826 1.629e-59 2.9e-55
DOK7 0.4818 2.551e-59 4.54e-55
ZNF503 0.4817 2.85e-59 5.07e-55
KLK8 0.4805 5.754e-59 1.02e-54
KLK6 0.4795 1.078e-58 1.92e-54

Figure S10.  Get High-res Image As an example, this figure shows the association of FGF18 to 'TUMOR.STAGE'. P value = 1.07e-70 with Spearman correlation analysis.

Clinical variable #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

5814 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S21.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 180
  YES 1413
     
  Significant markers N = 5814
  Higher in YES 2865
  Higher in NO 2949
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

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 22.2 4.3e-77 7.66e-73 0.7877
CYP3A7 20.4 1.717e-68 3.06e-64 0.7635
CYP3A4 20.24 6.476e-68 1.15e-63 0.7729
TCF21 21.02 1.431e-65 2.55e-61 0.7939
MAP2K7 21.32 8.132e-65 1.45e-60 0.8098
AADAC 20.04 4.24e-63 7.55e-59 0.7714
CCDC71 21.22 1.383e-62 2.46e-58 0.8195
REG1A 19.08 5.442e-59 9.69e-55 0.773
CHMP4B 20.11 6.206e-58 1.11e-53 0.8105
PDZD3 17.13 1.326e-57 2.36e-53 0.6836

Figure S11.  Get High-res Image As an example, this figure shows the association of CYP3A5 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 4.3e-77 with T-test analysis.

Clinical variable #12: 'NUMBERPACKYEARSSMOKED'

No gene related to 'NUMBERPACKYEARSSMOKED'.

Table S23.  Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'

NUMBERPACKYEARSSMOKED Mean (SD) 53.05 (35)
  Significant markers N = 0
Clinical variable #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

9 genes related to 'TOBACCOSMOKINGHISTORYINDICATOR'.

Table S24.  Basic characteristics of clinical feature: 'TOBACCOSMOKINGHISTORYINDICATOR'

TOBACCOSMOKINGHISTORYINDICATOR Labels N
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS 93
  CURRENT REFORMED SMOKER FOR > 15 YEARS 49
  CURRENT SMOKER 31
  LIFELONG NON-SMOKER 11
     
  Significant markers N = 9
List of 9 genes differentially expressed by 'TOBACCOSMOKINGHISTORYINDICATOR'

Table S25.  Get Full Table List of 9 genes differentially expressed by 'TOBACCOSMOKINGHISTORYINDICATOR'

ANOVA_P Q
PSME4 6.816e-08 0.00121
C1ORF64 1.645e-07 0.00293
LMNB2 1.211e-06 0.0216
LONP1 1.573e-06 0.028
SLC25A1 1.62e-06 0.0289
IGFBP7 1.965e-06 0.035
N6AMT2 2.361e-06 0.0421
CATSPER3 2.469e-06 0.044
LAS1L 2.63e-06 0.0468

Figure S12.  Get High-res Image As an example, this figure shows the association of PSME4 to 'TOBACCOSMOKINGHISTORYINDICATOR'. P value = 6.82e-08 with ANOVA analysis.

Clinical variable #14: 'YEAROFTOBACCOSMOKINGONSET'

One gene related to 'YEAROFTOBACCOSMOKINGONSET'.

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

YEAROFTOBACCOSMOKINGONSET Mean (SD) 1959.74 (11)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene significantly correlated to 'YEAROFTOBACCOSMOKINGONSET' by Spearman correlation test

Table S27.  Get Full Table List of one gene significantly correlated to 'YEAROFTOBACCOSMOKINGONSET' by Spearman correlation test

SpearmanCorr corrP Q
MMP10 -0.4473 4.812e-07 0.00857

Figure S13.  Get High-res Image As an example, this figure shows the association of MMP10 to 'YEAROFTOBACCOSMOKINGONSET'. P value = 4.81e-07 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #15: 'DISTANT.METASTASIS'

No gene related to 'DISTANT.METASTASIS'.

Table S28.  Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS Labels N
  CM0 (I+) 2
  M0 369
  M1 8
  MX 10
     
  Significant markers N = 0
Clinical variable #16: 'LYMPH.NODE.METASTASIS'

2 genes related to 'LYMPH.NODE.METASTASIS'.

Table S29.  Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS Labels N
  N0 118
  N0 (I+) 7
  N0 (I-) 59
  N1 41
  N1A 62
  N1B 14
  N1C 2
  N1MI 11
  N2 24
  N2A 24
  N3 5
  N3A 16
  NX 6
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

Table S30.  Get Full Table List of 2 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

ANOVA_P Q
GUCA2A 6.031e-12 1.07e-07
ASZ1 3.589e-08 0.000639

Figure S14.  Get High-res Image As an example, this figure shows the association of GUCA2A to 'LYMPH.NODE.METASTASIS'. P value = 6.03e-12 with ANOVA analysis.

Clinical variable #17: 'COMPLETENESS.OF.RESECTION'

2319 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S31.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 403
  R1 39
  R2 34
  RX 7
     
  Significant markers N = 2319
List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S32.  Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
NPR1 2.596e-40 4.62e-36
WIT1 2.503e-37 4.46e-33
DOK5 4.72e-35 8.41e-31
THRSP 5.822e-35 1.04e-30
KLHL14 3.091e-34 5.51e-30
WT1 1.009e-33 1.8e-29
S100A1 2.162e-33 3.85e-29
LYPD1 3.811e-30 6.79e-26
MUC16 8.048e-29 1.43e-24
SCGB1D2 1.049e-28 1.87e-24

Figure S15.  Get High-res Image As an example, this figure shows the association of NPR1 to 'COMPLETENESS.OF.RESECTION'. P value = 2.6e-40 with ANOVA analysis.

Clinical variable #18: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S33.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 1.94 (4)
  Significant markers N = 0
Clinical variable #19: 'NEOPLASM.DISEASESTAGE'

5 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S34.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 41
  STAGE IA 22
  STAGE IB 2
  STAGE IIA 136
  STAGE IIB 83
  STAGE IIIA 60
  STAGE IIIB 12
  STAGE IIIC 14
  STAGE IV 8
  STAGE X 11
     
  Significant markers N = 5
List of 5 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S35.  Get Full Table List of 5 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
PGC 4.234e-14 7.54e-10
BMPER 2.903e-09 5.17e-05
LRP4 2.449e-08 0.000436
GPER 1.558e-07 0.00277
PRSS2 5.544e-07 0.00987

Figure S16.  Get High-res Image As an example, this figure shows the association of PGC to 'NEOPLASM.DISEASESTAGE'. P value = 4.23e-14 with ANOVA analysis.

Methods & Data
Input

  • Expresson data file = PANCAN12-TP.medianexp.txt

  • Clinical data file = PANCAN12-TP.clin.merged.picked.txt

  • Number of patients = 1593

  • Number of genes = 17814

  • Number of clinical features = 19

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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