Colon/Rectal 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 17880 genes and 10 clinical features across 264 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

- 120 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.

- DRD5|1816 , H1FX|8971 , LOC152217|152217 , C2CD4D|100191040 , CTU1|90353 , ...

- 32 genes correlated to 'GENDER'.

- RPS4Y1|6192 , ZFY|7544 , XIST|7503 , DDX3Y|8653 , KDM5D|8284 , ...

- 427 genes correlated to 'HISTOLOGICAL.TYPE'.

- SNHG11|128439 , SLC19A3|80704 , GTF2IRD1|9569 , PLAGL2|5326 , POFUT1|23509 , ...

- 1 gene correlated to 'PATHOLOGY.T'.

- NRG1|3084

- 1 gene correlated to 'PATHOLOGY.N'.

- DIRAS2|54769

- 1 gene correlated to 'PATHOLOGICSPREAD(M)'.

- GFI1|2672

- 2 genes correlated to 'TUMOR.STAGE'.

- GFI1|2672 , ENOSF1|55556

- 1 gene correlated to 'NEOADJUVANT.THERAPY'.

- IL22|50616

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

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=0 |  |  |  |
PRIMARY SITE OF DISEASE | t test | N=120 | rectum | N=104 | colon | N=16
GENDER | t test | N=32 | male | N=14 | female | N=18
HISTOLOGICAL TYPE | ANOVA test | N=427 |  |  |  |
PATHOLOGY T | Spearman correlation test | N=1 | higher pT | N=0 | lower pT | N=1
PATHOLOGY N | Spearman correlation test | N=1 | higher pN | N=1 | lower pN | N=0
PATHOLOGICSPREAD(M) | ANOVA test | N=1 |  |  |  |
TUMOR STAGE | Spearman correlation test | N=2 | higher stage | N=0 | lower stage | N=2
NEOADJUVANT THERAPY | t test | N=1 | yes | N=1 | no | N=0

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) | 0.9-72.1 (median=12)
| censored | N = 131
| death | N = 20
| Significant markers | N = 0

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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

AGE | Mean (SD) | 68.86 (12)
| Significant markers | N = 0

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

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

Table S3. Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'

PRIMARY.SITE.OF.DISEASE | Labels | N
| COLON | 191
| RECTUM | 71
| Significant markers | N = 120
| Higher in RECTUM | 104
| Higher in COLON | 16

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

Table S4. Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

| T(pos if higher in 'RECTUM') | ttestP | Q | AUC
--- | --- | --- | --- | ---
DRD5|1816 | -7.58 | 2.08e-11 | 3.72e-07 | 0.7857
H1FX|8971 | 6.83 | 1.277e-10 | 2.28e-06 | 0.7506
LOC152217|152217 | 6.81 | 1.606e-10 | 2.87e-06 | 0.7414
C2CD4D|100191040 | 6.82 | 1.792e-10 | 3.2e-06 | 0.7441
CTU1|90353 | 6.79 | 2.404e-10 | 4.3e-06 | 0.7404
HOXB13|10481 | 6.93 | 3.887e-10 | 6.95e-06 | 0.78
ANKHD1-EIF4EBP3|404734 | 6.64 | 4.925e-10 | 8.8e-06 | 0.7398
TMEM160|54958 | 6.31 | 2.735e-09 | 4.89e-05 | 0.7574
ANKRD9|122416 | 6.3 | 4.725e-09 | 8.44e-05 | 0.7437
ALKBH6|84964 | 6.26 | 5.559e-09 | 9.93e-05 | 0.7481

Figure S1. Get High-res Image As an example, this figure shows the association of DRD5|1816 to 'PRIMARY.SITE.OF.DISEASE'. P value = 2.08e-11 with T-test analysis.

Clinical variable #4: 'GENDER'

32 genes related to 'GENDER'.

Table S5. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 132
| MALE | 132
| Significant markers | N = 32
| Higher in MALE | 14
| Higher in FEMALE | 18

List of top 10 genes differentially expressed by 'GENDER'

Table S6. Get Full Table List of top 10 genes differentially expressed by 'GENDER'

| T(pos if higher in 'MALE') | ttestP | Q | AUC
--- | --- | --- | --- | ---
RPS4Y1|6192 | 29.28 | 6.211e-76 | 1.11e-71 | 0.9969
ZFY|7544 | 28.06 | 7.279e-61 | 1.3e-56 | 0.9887
XIST|7503 | -25.51 | 4.986e-59 | 8.91e-55 | 0.9867
DDX3Y|8653 | 28.71 | 2.332e-53 | 4.17e-49 | 0.9949
KDM5D|8284 | 27.27 | 1.744e-47 | 3.12e-43 | 0.9951
TMSB4Y|9087 | 21.2 | 3.22e-46 | 5.76e-42 | 0.9675
NLGN4Y|22829 | 18.43 | 6.952e-41 | 1.24e-36 | 0.9554
PRKY|5616 | 16.15 | 8.03e-41 | 1.44e-36 | 0.9126
TSIX|9383 | -16.55 | 1.141e-39 | 2.04e-35 | 0.9354
CYORF15A|246126 | 21.5 | 1.241e-39 | 2.22e-35 | 0.9831

Figure S2. Get High-res Image As an example, this figure shows the association of RPS4Y1|6192 to 'GENDER'. P value = 6.21e-76 with T-test analysis.

Clinical variable #5: 'HISTOLOGICAL.TYPE'

427 genes related to 'HISTOLOGICAL.TYPE'.

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

HISTOLOGICAL.TYPE | Labels | N
| COLON ADENOCARCINOMA | 162
| COLON MUCINOUS ADENOCARCINOMA | 27
| RECTAL ADENOCARCINOMA | 60
| RECTAL MUCINOUS ADENOCARCINOMA | 8
| Significant markers | N = 427

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

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

| ANOVA_P | Q
--- | --- | ---
SNHG11|128439 | 5.651e-15 | 1.01e-10
SLC19A3|80704 | 2.044e-13 | 3.65e-09
GTF2IRD1|9569 | 6.397e-13 | 1.14e-08
PLAGL2|5326 | 1.097e-12 | 1.96e-08
POFUT1|23509 | 1.632e-12 | 2.92e-08
NECAB3|63941 | 2.978e-12 | 5.32e-08
AGR2|10551 | 4.07e-12 | 7.27e-08
FAM46A|55603 | 4.67e-12 | 8.35e-08
HOXB13|10481 | 1.47e-11 | 2.63e-07
ZSWIM1|90204 | 1.835e-11 | 3.28e-07

Figure S3. Get High-res Image As an example, this figure shows the association of SNHG11|128439 to 'HISTOLOGICAL.TYPE'. P value = 5.65e-15 with ANOVA analysis.

Clinical variable #6: 'PATHOLOGY.T'

One gene related to 'PATHOLOGY.T'.

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

PATHOLOGY.T | Mean (SD) | 2.8 (0.64)
|  | N
| T1 | 11
| T2 | 53
| T3 | 176
| T4 | 22
| Significant markers | N = 1
| pos. correlated | 0
| neg. correlated | 1

List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table S10. Get Full Table List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
NRG1|3084 | -0.2969 | 1.199e-06 | 0.0214

Figure S4. Get High-res Image As an example, this figure shows the association of NRG1|3084 to 'PATHOLOGY.T'. P value = 1.2e-06 with Spearman correlation analysis.

Clinical variable #7: 'PATHOLOGY.N'

One gene related to 'PATHOLOGY.N'.

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

PATHOLOGY.N | Mean (SD) | 0.58 (0.78)
|  | N
| N0 | 158
| N1 | 57
| N2 | 48
| Significant markers | N = 1
| pos. correlated | 1
| neg. correlated | 0

List of one gene significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

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

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
DIRAS2|54769 | 0.4097 | 4.54e-07 | 0.00812

Figure S5. Get High-res Image As an example, this figure shows the association of DIRAS2|54769 to 'PATHOLOGY.N'. P value = 4.54e-07 with Spearman correlation analysis.

Clinical variable #8: 'PATHOLOGICSPREAD(M)'

One gene related to 'PATHOLOGICSPREAD(M)'.

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

PATHOLOGICSPREAD(M) | Labels | N
| M0 | 220
| M1 | 39
| M1A | 2
| Significant markers | N = 1

List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

Table S14. Get Full Table List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

| ANOVA_P | Q
--- | --- | ---
GFI1|2672 | 1.877e-06 | 0.0336

Figure S6. Get High-res Image As an example, this figure shows the association of GFI1|2672 to 'PATHOLOGICSPREAD(M)'. P value = 1.88e-06 with ANOVA analysis.

Clinical variable #9: 'TUMOR.STAGE'

2 genes related to 'TUMOR.STAGE'.

Table S15. Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE | Mean (SD) | 2.35 (0.97)
|  | N
| Stage 1 | 53
| Stage 2 | 98
| Stage 3 | 68
| Stage 4 | 37
| Significant markers | N = 2
| pos. correlated | 0
| neg. correlated | 2

List of 2 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

Table S16. Get Full Table List of 2 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
GFI1|2672 | -0.3179 | 2.025e-07 | 0.00362
ENOSF1|55556 | -0.296 | 1.428e-06 | 0.0255

Figure S7. Get High-res Image As an example, this figure shows the association of GFI1|2672 to 'TUMOR.STAGE'. P value = 2.03e-07 with Spearman correlation analysis.

Clinical variable #10: 'NEOADJUVANT.THERAPY'

One gene related to 'NEOADJUVANT.THERAPY'.

Table S17. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'

NEOADJUVANT.THERAPY | Labels | N
| NO | 16
| YES | 248
| Significant markers | N = 1
| Higher in YES | 1
| Higher in NO | 0

List of one gene differentially expressed by 'NEOADJUVANT.THERAPY'

Table S18. Get Full Table List of one gene differentially expressed by 'NEOADJUVANT.THERAPY'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
IL22|50616 | 9.44 | 1.158e-08 | 0.000207 | 0.9042

Figure S8. Get High-res Image As an example, this figure shows the association of IL22|50616 to 'NEOADJUVANT.THERAPY'. P value = 1.16e-08 with T-test analysis.

Methods & Data
Input

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

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

- Number of patients = 264

- Number of genes = 17880

- Number of clinical features = 10

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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