This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 9 clinical features across 72 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one genes.
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2 genes correlated to 'AGE'.
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COL18A1 , C5ORF35
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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NOP5/NOP58 , GNL3L
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4 genes correlated to 'PATHOLOGY.T.STAGE'.
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TRIM11 , LOC201725 , TARS2 , ZNF652
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4 genes correlated to 'GENDER'.
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CYORF15A , JARID1D , CYORF15B , UCHL5IP
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No genes correlated to 'Time to Death', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'RACE', and 'ETHNICITY'.
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 P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=2 | older | N=1 | younger | N=1 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=2 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=4 | higher stage | N=3 | lower stage | N=1 |
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
PATHOLOGY M STAGE | Wilcoxon test | N=0 | ||||
GENDER | Wilcoxon test | N=4 | male | N=4 | female | N=0 |
RACE | Kruskal-Wallis test | N=0 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Months) | 0.5-101.1 (median=36.6) |
censored | N = 58 | |
death | N = 14 | |
Significant markers | N = 0 |
Table S2. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 60.54 (12) |
Significant markers | N = 2 | |
pos. correlated | 1 | |
neg. correlated | 1 |
Table S3. Get Full Table List of 2 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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COL18A1 | -0.5036 | 7.595e-06 | 0.135 |
C5ORF35 | 0.4881 | 1.575e-05 | 0.281 |
Table S4. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 40 | |
STAGE II | 13 | |
STAGE III | 14 | |
STAGE IV | 5 | |
Significant markers | N = 2 |
Table S5. Get Full Table List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'
ANOVA_P | Q | |
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NOP5/NOP58 | 9.01e-06 | 0.161 |
GNL3L | 1.626e-05 | 0.29 |
Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 1.67 (0.84) |
N | ||
1 | 41 | |
2 | 14 | |
3 | 17 | |
Significant markers | N = 4 | |
pos. correlated | 3 | |
neg. correlated | 1 |
Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Labels | N |
class0 | 35 | |
class1 | 3 | |
Significant markers | N = 0 |
Table S9. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 67 | |
M1 | 5 | |
Significant markers | N = 0 |
Table S10. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 29 | |
MALE | 43 | |
Significant markers | N = 4 | |
Higher in MALE | 4 | |
Higher in FEMALE | 0 |
Table S11. Get Full Table List of 4 genes differentially expressed by 'GENDER'. 11 significant gene(s) located in sex chromosomes is(are) filtered out.
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
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CYORF15A | 1204 | 2.753e-11 | 4.9e-07 | 0.9655 |
JARID1D | 1195 | 5.531e-11 | 9.85e-07 | 0.9583 |
CYORF15B | 1174 | 2.705e-10 | 4.82e-06 | 0.9415 |
UCHL5IP | 1000 | 1.581e-05 | 0.281 | 0.8019 |
Table S12. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
ASIAN | 1 | |
BLACK OR AFRICAN AMERICAN | 5 | |
WHITE | 62 | |
Significant markers | N = 0 |
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Expresson data file = KIRC-TP.medianexp.txt
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Clinical data file = KIRC-TP.merged_data.txt
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Number of patients = 72
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Number of genes = 17814
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Number of clinical features = 9
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.