This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 18239 genes and 5 clinical features across 161 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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1 gene correlated to 'AGE'.
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ADAP2|55803
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9 genes correlated to 'PATHOLOGY.T.STAGE'.
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KIAA0319L|79932 , GMDS|2762 , ABAT|18 , CHRNA2|1135 , EPHX2|2053 , ...
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4 genes correlated to 'PATHOLOGY.N.STAGE'.
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CRHR2|1395 , NKX6-2|84504 , SEC24A|10802 , PRTN3|5657
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3 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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GLP2R|9340 , MRPS6|64968 , CNGB3|54714
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No genes correlated to '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 | ||
|---|---|---|---|---|---|---|
| AGE | Spearman correlation test | N=1 | older | N=1 | younger | N=0 |
| PATHOLOGY T STAGE | Spearman correlation test | N=9 | higher stage | N=2 | lower stage | N=7 |
| PATHOLOGY N STAGE | t test | N=4 | class1 | N=1 | class0 | N=3 |
| COMPLETENESS OF RESECTION | ANOVA test | N=3 | ||||
| NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |
Table S1. Basic characteristics of clinical feature: 'AGE'
| AGE | Mean (SD) | 60.34 (6.9) |
| Significant markers | N = 1 | |
| pos. correlated | 1 | |
| neg. correlated | 0 |
Table S2. Get Full Table List of one gene significantly correlated to 'AGE' by Spearman correlation test
| SpearmanCorr | corrP | Q | |
|---|---|---|---|
| ADAP2|55803 | 0.3633 | 2.343e-06 | 0.0427 |
Figure S1. Get High-res Image As an example, this figure shows the association of ADAP2|55803 to 'AGE'. P value = 2.34e-06 with Spearman correlation analysis. The straight line presents the best linear regression.
Table S3. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
| PATHOLOGY.T.STAGE | Mean (SD) | 2.6 (0.55) |
| N | ||
| 2 | 69 | |
| 3 | 86 | |
| 4 | 5 | |
| Significant markers | N = 9 | |
| pos. correlated | 2 | |
| neg. correlated | 7 |
Table S4. Get Full Table List of 9 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test
| SpearmanCorr | corrP | Q | |
|---|---|---|---|
| KIAA0319L|79932 | -0.3928 | 2.787e-07 | 0.00508 |
| GMDS|2762 | -0.3908 | 3.224e-07 | 0.00588 |
| ABAT|18 | -0.3878 | 4.042e-07 | 0.00737 |
| CHRNA2|1135 | -0.3861 | 4.612e-07 | 0.00841 |
| EPHX2|2053 | -0.3835 | 5.55e-07 | 0.0101 |
| TSPAN1|10103 | -0.3718 | 1.291e-06 | 0.0235 |
| ELAVL4|1996 | 0.3912 | 1.619e-06 | 0.0295 |
| KCNK6|9424 | -0.3648 | 2.104e-06 | 0.0384 |
| FAM171B|165215 | 0.3629 | 2.403e-06 | 0.0438 |
Figure S2. Get High-res Image As an example, this figure shows the association of KIAA0319L|79932 to 'PATHOLOGY.T.STAGE'. P value = 2.79e-07 with Spearman correlation analysis.
Table S5. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
| PATHOLOGY.N.STAGE | Labels | N |
| class0 | 127 | |
| class1 | 15 | |
| Significant markers | N = 4 | |
| Higher in class1 | 1 | |
| Higher in class0 | 3 |
Table S6. Get Full Table List of 4 genes differentially expressed by 'PATHOLOGY.N.STAGE'
| T(pos if higher in 'class1') | ttestP | Q | AUC | |
|---|---|---|---|---|
| CRHR2|1395 | -8.74 | 8.893e-08 | 0.00162 | 0.9421 |
| NKX6-2|84504 | -6.07 | 3.342e-07 | 0.00609 | 0.8651 |
| SEC24A|10802 | 5.72 | 1.949e-06 | 0.0355 | 0.7717 |
| PRTN3|5657 | -6.32 | 1.989e-06 | 0.0362 | 0.783 |
Figure S3. Get High-res Image As an example, this figure shows the association of CRHR2|1395 to 'PATHOLOGY.N.STAGE'. P value = 8.89e-08 with T-test analysis.
Table S7. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'
| COMPLETENESS.OF.RESECTION | Labels | N |
| R0 | 120 | |
| R1 | 31 | |
| RX | 3 | |
| Significant markers | N = 3 |
Table S8. Get Full Table List of 3 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'
| ANOVA_P | Q | |
|---|---|---|
| GLP2R|9340 | 6.285e-10 | 1.15e-05 |
| MRPS6|64968 | 9.64e-07 | 0.0176 |
| CNGB3|54714 | 1.7e-06 | 0.031 |
Figure S4. Get High-res Image As an example, this figure shows the association of GLP2R|9340 to 'COMPLETENESS.OF.RESECTION'. P value = 6.28e-10 with ANOVA analysis.
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Expresson data file = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = PRAD-TP.clin.merged.picked.txt
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Number of patients = 161
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Number of genes = 18239
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Number of clinical features = 5
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 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 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 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.