This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 17733 genes and 7 clinical features across 79 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one genes.
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388 genes correlated to 'Time to Death'.
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DNA2|1763 , LMNB2|84823 , DAZAP1|26528 , ENPP4|22875 , NCAPH|23397 , ...
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1 gene correlated to 'AGE'.
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FAM40B|57464
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10 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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DIAPH3|81624 , ZWILCH|55055 , DCAF15|90379 , YJEFN3|374887 , C8ORFK29|340393 , ...
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101 genes correlated to 'PATHOLOGY.T.STAGE'.
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SETD8|387893 , FANCI|55215 , LMNB2|84823 , MCM10|55388 , DIAPH3|81624 , ...
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2 genes correlated to 'GENDER'.
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CLN8|2055 , MAFG|4097
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No genes correlated to 'PATHOLOGY.N.STAGE', and 'ETHNICITY'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=388 | shorter survival | N=272 | longer survival | N=116 |
AGE | Spearman correlation test | N=1 | older | N=1 | younger | N=0 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=10 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=101 | higher stage | N=99 | lower stage | N=2 |
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
GENDER | Wilcoxon test | N=2 | male | N=2 | female | N=0 |
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 4.1-153.6 (median=36.3) |
censored | N = 52 | |
death | N = 27 | |
Significant markers | N = 388 | |
associated with shorter survival | 272 | |
associated with longer survival | 116 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
DNA2|1763 | 3 | 1.428e-09 | 2.5e-05 | 0.831 |
LMNB2|84823 | 5.6 | 1.492e-09 | 2.6e-05 | 0.856 |
DAZAP1|26528 | 20 | 4.852e-09 | 8.6e-05 | 0.782 |
ENPP4|22875 | 0.64 | 9.109e-09 | 0.00016 | 0.211 |
NCAPH|23397 | 2.3 | 9.809e-09 | 0.00017 | 0.841 |
PIF1|80119 | 2.4 | 1.281e-08 | 0.00023 | 0.832 |
NCAPD2|9918 | 6.2 | 1.477e-08 | 0.00026 | 0.839 |
UBE2S|27338 | 3.3 | 1.517e-08 | 0.00027 | 0.837 |
TMEM194A|23306 | 4 | 2.086e-08 | 0.00037 | 0.782 |
NDRG4|65009 | 0.7 | 2.212e-08 | 0.00039 | 0.165 |
AGE | Mean (SD) | 46.7 (16) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
FAM40B|57464 | 0.4662 | 1.494e-05 | 0.265 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 9 | |
STAGE II | 36 | |
STAGE III | 16 | |
STAGE IV | 15 | |
Significant markers | N = 10 |
ANOVA_P | Q | |
---|---|---|
DIAPH3|81624 | 5.016e-06 | 0.089 |
ZWILCH|55055 | 6.91e-06 | 0.123 |
DCAF15|90379 | 7.364e-06 | 0.131 |
YJEFN3|374887 | 8.492e-06 | 0.151 |
C8ORFK29|340393 | 8.759e-06 | 0.155 |
CENPJ|55835 | 8.994e-06 | 0.159 |
C14ORF80|283643 | 9.751e-06 | 0.173 |
TRIP13|9319 | 1.1e-05 | 0.195 |
CCT6P1|643253 | 1.292e-05 | 0.229 |
MCM10|55388 | 1.314e-05 | 0.233 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.46 (0.99) |
N | ||
1 | 9 | |
2 | 41 | |
3 | 8 | |
4 | 18 | |
Significant markers | N = 101 | |
pos. correlated | 99 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SETD8|387893 | 0.6314 | 9.615e-10 | 1.71e-05 |
FANCI|55215 | 0.5639 | 1.132e-07 | 0.00201 |
LMNB2|84823 | 0.5565 | 1.793e-07 | 0.00318 |
MCM10|55388 | 0.5532 | 2.187e-07 | 0.00388 |
DIAPH3|81624 | 0.5512 | 2.976e-07 | 0.00528 |
C8ORFK29|340393 | 0.5558 | 4.02e-07 | 0.00713 |
TRIP13|9319 | 0.5408 | 4.589e-07 | 0.00813 |
UHRF1|29128 | 0.5377 | 5.486e-07 | 0.00972 |
CBFB|865 | 0.5349 | 6.419e-07 | 0.0114 |
CCT6P1|643253 | 0.5343 | 6.655e-07 | 0.0118 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 67 | |
class1 | 9 | |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 48 | |
MALE | 31 | |
Significant markers | N = 2 | |
Higher in MALE | 2 | |
Higher in FEMALE | 0 |
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Expresson data file = ACC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = ACC-TP.merged_data.txt
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Number of patients = 79
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Number of genes = 17733
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Number of clinical features = 7
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.