Lung Adenocarcinoma: Correlation between mRNAseq expression and clinical features
Maintained by Juok Cho (Broad Institute)
Overview
Introduction

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

Summary

Testing the association between 18275 genes and 11 clinical features across 250 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

- 16 genes correlated to 'Time to Death'.

- ESYT3|83850 , MFSD2B|388931 , DKK1|22943 , UCN2|90226 , B3GNT8|374907 , ...

- 33 genes correlated to 'GENDER'.

- PRKY|5616 , ZFY|7544 , RPS4Y1|6192 , XIST|7503 , DDX3Y|8653 , ...

- 9 genes correlated to 'HISTOLOGICAL.TYPE'.

- TIGD2|166815 , MIA|8190 , GDPD2|54857 , DPCR1|135656 , A4GNT|51146 , ...

- 23 genes correlated to 'PATHOLOGY.T'.

- RAB30|27314 , FCRLA|84824 , STAP1|26228 , CD79A|973 , TTLL12|23170 , ...

- 3 genes correlated to 'PATHOLOGY.N'.

- RARS|5917 , FAM117A|81558 , YWHAG|7532

- 15 genes correlated to 'TUMOR.STAGE'.

- ST6GAL1|6480 , AMPD1|270 , FAM117A|81558 , KIAA0125|9834 , STAP1|26228 , ...

- 1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- SUN3|256979

- No genes correlated to 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'PATHOLOGICSPREAD(M)', and 'NEOADJUVANT.THERAPY'.

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=16 | shorter survival | N=10 | longer survival | N=6
AGE | Spearman correlation test | N=0 |  |  |  |
GENDER | t test | N=33 | male | N=13 | female | N=20
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 |  |  |  |
HISTOLOGICAL TYPE | ANOVA test | N=9 |  |  |  |
PATHOLOGY T | Spearman correlation test | N=23 | higher pT | N=2 | lower pT | N=21
PATHOLOGY N | Spearman correlation test | N=3 | higher pN | N=2 | lower pN | N=1
PATHOLOGICSPREAD(M) | ANOVA test | N=0 |  |  |  |
TUMOR STAGE | Spearman correlation test | N=15 | higher stage | N=1 | lower stage | N=14
RADIATIONS RADIATION REGIMENINDICATION | t test | N=1 | yes | N=1 | no | N=0
NEOADJUVANT THERAPY | t test | N=0 |  |  |  |

Clinical variable #1: 'Time to Death'

16 genes related to 'Time to Death'.

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

Time to Death | Duration (Months) | 0-224 (median=15)
| censored | N = 144
| death | N = 77
| Significant markers | N = 16
| associated with shorter survival | 10
| associated with longer survival | 6

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
--- | --- | --- | --- | ---
ESYT3|83850 | 0.71 | 2.016e-08 | 0.00037 | 0.331
MFSD2B|388931 | 1.81 | 3.245e-07 | 0.0059 | 0.683
DKK1|22943 | 1.21 | 3.746e-07 | 0.0068 | 0.718
UCN2|90226 | 1.36 | 3.812e-07 | 0.007 | 0.653
B3GNT8|374907 | 0.69 | 4.437e-07 | 0.0081 | 0.317
LYAR|55646 | 2.5 | 5.723e-07 | 0.01 | 0.664
HMGA1|3159 | 1.83 | 1.007e-06 | 0.018 | 0.676
RGS20|8601 | 1.25 | 1.391e-06 | 0.025 | 0.673
FAM189A2|9413 | 0.77 | 1.447e-06 | 0.026 | 0.341
ZFP3|124961 | 0.58 | 1.555e-06 | 0.028 | 0.359

Figure S1. Get High-res Image As an example, this figure shows the association of ESYT3|83850 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 2.02e-08 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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

AGE | Mean (SD) | 65.46 (9.7)
| Significant markers | N = 0

Clinical variable #3: 'GENDER'

33 genes related to 'GENDER'.

Table S4. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 135
| MALE | 115
| Significant markers | N = 33
| Higher in MALE | 13
| Higher in FEMALE | 20

List of top 10 genes differentially expressed by 'GENDER'

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

| T(pos if higher in 'MALE') | ttestP | Q | AUC
--- | --- | --- | --- | ---
PRKY|5616 | 37.83 | 3.701e-98 | 6.76e-94 | 0.999
ZFY|7544 | 41.9 | 6.15e-72 | 1.12e-67 | 0.9971
RPS4Y1|6192 | 38.43 | 2.921e-61 | 5.34e-57 | 0.9951
XIST|7503 | -31.14 | 6.5e-61 | 1.19e-56 | 0.9834
DDX3Y|8653 | 34.34 | 2.566e-40 | 4.69e-36 | 0.996
NLGN4Y|22829 | 20.94 | 5.849e-32 | 1.07e-27 | 0.9883
TSIX|9383 | -17.56 | 6.26e-32 | 1.14e-27 | 0.988
USP9Y|8287 | 26.12 | 6.671e-24 | 1.22e-19 | 0.9997
KDM5D|8284 | 24.56 | 4.34e-22 | 7.93e-18 | 0.9963
ZRSR2|8233 | -9.36 | 6.452e-18 | 1.18e-13 | 0.812

Figure S2. Get High-res Image As an example, this figure shows the association of PRKY|5616 to 'GENDER'. P value = 3.7e-98 with T-test analysis.

Clinical variable #4: 'KARNOFSKY.PERFORMANCE.SCORE'

No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S6. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 69.44 (39)
| Score | N
| 0 | 4
| 70 | 1
| 80 | 3
| 90 | 6
| 100 | 4
| Significant markers | N = 0

Clinical variable #5: 'HISTOLOGICAL.TYPE'

9 genes related to 'HISTOLOGICAL.TYPE'.

Table S7. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE | Labels | N
| LUNG ACINAR ADENOCARCINOMA | 3
| LUNG ADENOCARCINOMA MIXED SUBTYPE | 58
| LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | 160
| LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | 3
| LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | 8
| LUNG CLEAR CELL ADENOCARCINOMA | 2
| LUNG MICROPAPILLARY ADENOCARCINOMA | 2
| LUNG MUCINOUS ADENOCARCINOMA | 2
| LUNG PAPILLARY ADENOCARCINOMA | 9
| LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | 1
| MUCINOUS (COLLOID) ADENOCARCINOMA | 2
| Significant markers | N = 9

List of 9 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S8. Get Full Table List of 9 genes differentially expressed by 'HISTOLOGICAL.TYPE'

| ANOVA_P | Q
--- | --- | ---
TIGD2|166815 | 4.52e-08 | 0.000826
MIA|8190 | 1.816e-07 | 0.00332
GDPD2|54857 | 2.809e-07 | 0.00513
DPCR1|135656 | 3.149e-07 | 0.00575
A4GNT|51146 | 3.422e-07 | 0.00625
CA2|760 | 4.632e-07 | 0.00846
ELOVL5|60481 | 1.552e-06 | 0.0283
SOX10|6663 | 2.498e-06 | 0.0456
LOC342346|342346 | 2.641e-06 | 0.0482

Figure S3. Get High-res Image As an example, this figure shows the association of TIGD2|166815 to 'HISTOLOGICAL.TYPE'. P value = 4.52e-08 with ANOVA analysis.

Clinical variable #6: 'PATHOLOGY.T'

23 genes related to 'PATHOLOGY.T'.

Table S9. Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T | Mean (SD) | 1.94 (0.75)
|  | N
| T1 | 63
| T2 | 151
| T3 | 21
| T4 | 14
| Significant markers | N = 23
| pos. correlated | 2
| neg. correlated | 21

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

Table S10. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
RAB30|27314 | -0.3379 | 4.564e-08 | 0.000834
FCRLA|84824 | -0.325 | 1.563e-07 | 0.00286
STAP1|26228 | -0.3162 | 3.478e-07 | 0.00636
CD79A|973 | -0.3136 | 4.375e-07 | 0.00799
TTLL12|23170 | 0.313 | 4.611e-07 | 0.00842
CD19|930 | -0.3088 | 7.426e-07 | 0.0136
CR2|1380 | -0.3067 | 8.455e-07 | 0.0154
KCNA3|3738 | -0.3059 | 8.616e-07 | 0.0157
MS4A1|931 | -0.3059 | 9.077e-07 | 0.0166
POU2AF1|5450 | -0.3044 | 9.784e-07 | 0.0179

Figure S4. Get High-res Image As an example, this figure shows the association of RAB30|27314 to 'PATHOLOGY.T'. P value = 4.56e-08 with Spearman correlation analysis.

Clinical variable #7: 'PATHOLOGY.N'

3 genes related to 'PATHOLOGY.N'.

Table S11. Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N | Mean (SD) | 0.62 (0.81)
|  | N
| N0 | 142
| N1 | 54
| N2 | 48
| N3 | 1
| Significant markers | N = 3
| pos. correlated | 2
| neg. correlated | 1

List of 3 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

Table S12. Get Full Table List of 3 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
RARS|5917 | 0.3539 | 1.224e-08 | 0.000224
FAM117A|81558 | -0.3135 | 5.5e-07 | 0.0101
YWHAG|7532 | 0.2986 | 1.949e-06 | 0.0356

Figure S5. Get High-res Image As an example, this figure shows the association of RARS|5917 to 'PATHOLOGY.N'. P value = 1.22e-08 with Spearman correlation analysis.

Clinical variable #8: 'PATHOLOGICSPREAD(M)'

No gene related to 'PATHOLOGICSPREAD(M)'.

Table S13. Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) | Labels | N
| M0 | 183
| M1 | 14
| MX | 46
| Significant markers | N = 0

Clinical variable #9: 'TUMOR.STAGE'

15 genes related to 'TUMOR.STAGE'.

Table S14. Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE | Mean (SD) | 1.82 (0.96)
|  | N
| Stage 1 | 125
| Stage 2 | 53
| Stage 3 | 54
| Stage 4 | 13
| Significant markers | N = 15
| pos. correlated | 1
| neg. correlated | 14

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

Table S15. Get Full Table List of top 10 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
ST6GAL1|6480 | -0.3316 | 1.069e-07 | 0.00195
AMPD1|270 | -0.3347 | 1.665e-07 | 0.00304
FAM117A|81558 | -0.3258 | 1.828e-07 | 0.00334
KIAA0125|9834 | -0.3156 | 4.826e-07 | 0.00882
STAP1|26228 | -0.3081 | 8.755e-07 | 0.016
POU2AF1|5450 | -0.3071 | 9.556e-07 | 0.0175
RARS|5917 | 0.3048 | 1.16e-06 | 0.0212
ZFP3|124961 | -0.3044 | 1.193e-06 | 0.0218
CD79A|973 | -0.3016 | 1.511e-06 | 0.0276
GPR55|9290 | -0.3024 | 1.653e-06 | 0.0302

Figure S6. Get High-res Image As an example, this figure shows the association of ST6GAL1|6480 to 'TUMOR.STAGE'. P value = 1.07e-07 with Spearman correlation analysis.

Clinical variable #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

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

RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N
| NO | 11
| YES | 239
| Significant markers | N = 1
| Higher in YES | 1
| Higher in NO | 0

List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17. Get Full Table List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
SUN3|256979 | 6.62 | 3.402e-07 | 0.00619 | 0.75

Figure S7. Get High-res Image As an example, this figure shows the association of SUN3|256979 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 3.4e-07 with T-test analysis.

Clinical variable #11: 'NEOADJUVANT.THERAPY'

No gene related to 'NEOADJUVANT.THERAPY'.

Table S18. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'

NEOADJUVANT.THERAPY | Labels | N
| NO | 38
| YES | 212
| Significant markers | N = 0

Methods & Data
Input

- Expresson data file = LUAD.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Clinical data file = LUAD.clin.merged.picked.txt

- Number of patients = 250

- Number of genes = 18275

- Number of clinical features = 11

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

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

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

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.

- 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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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