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 77 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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283 genes correlated to 'Time to Death'.
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DNA2|1763 , DAZAP1|26528 , ENPP4|22875 , LMNB2|84823 , TMEM194A|23306 , ...
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6 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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YJEFN3|374887 , SFRS16|11129 , DIAPH3|81624 , CENPJ|55835 , C8ORFK29|340393 , ...
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83 genes correlated to 'PATHOLOGY.T.STAGE'.
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SETD8|387893 , LMNB2|84823 , SFRS16|11129 , MCM10|55388 , YJEFN3|374887 , ...
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4 genes correlated to 'GENDER'.
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RND2|8153 , CLN8|2055 , MAFG|4097 , FAM117A|81558
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No genes correlated to 'AGE', '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 | ||
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Time to Death | Cox regression test | N=283 | shorter survival | N=211 | longer survival | N=72 |
AGE | Spearman correlation test | N=0 | ||||
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=6 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=83 | higher stage | N=81 | lower stage | N=2 |
PATHOLOGY N STAGE | Wilcoxon test | N=0 | ||||
GENDER | Wilcoxon test | N=4 | male | N=4 | female | N=0 |
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 4.1-153.6 (median=32.7) |
censored | N = 52 | |
death | N = 25 | |
Significant markers | N = 283 | |
associated with shorter survival | 211 | |
associated with longer survival | 72 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
DNA2|1763 | 3.1 | 2.21e-09 | 3.9e-05 | 0.85 |
DAZAP1|26528 | 26 | 1.033e-08 | 0.00018 | 0.79 |
ENPP4|22875 | 0.62 | 1.127e-08 | 2e-04 | 0.205 |
LMNB2|84823 | 5.6 | 1.364e-08 | 0.00024 | 0.851 |
TMEM194A|23306 | 4.5 | 1.761e-08 | 0.00031 | 0.794 |
NCAPD2|9918 | 7.2 | 2.103e-08 | 0.00037 | 0.855 |
LIN9|286826 | 5.7 | 2.9e-08 | 0.00051 | 0.83 |
NCAPH|23397 | 2.3 | 3.644e-08 | 0.00065 | 0.844 |
KIF11|3832 | 2.9 | 3.908e-08 | 0.00069 | 0.846 |
NCAPD3|23310 | 7.7 | 4.271e-08 | 0.00076 | 0.819 |
AGE | Mean (SD) | 46.74 (16) |
Significant markers | N = 0 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 8 | |
STAGE II | 33 | |
STAGE III | 16 | |
STAGE IV | 15 | |
Significant markers | N = 6 |
ANOVA_P | Q | |
---|---|---|
YJEFN3|374887 | 1.087e-05 | 0.193 |
SFRS16|11129 | 1.114e-05 | 0.198 |
DIAPH3|81624 | 1.193e-05 | 0.211 |
CENPJ|55835 | 1.278e-05 | 0.227 |
C8ORFK29|340393 | 1.431e-05 | 0.254 |
ZWILCH|55055 | 1.52e-05 | 0.269 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.5 (0.99) |
N | ||
1 | 8 | |
2 | 38 | |
3 | 8 | |
4 | 18 | |
Significant markers | N = 83 | |
pos. correlated | 81 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SETD8|387893 | 0.6252 | 4.328e-09 | 7.68e-05 |
LMNB2|84823 | 0.5613 | 2.908e-07 | 0.00516 |
SFRS16|11129 | 0.5613 | 2.914e-07 | 0.00517 |
MCM10|55388 | 0.5598 | 3.172e-07 | 0.00562 |
YJEFN3|374887 | 0.5558 | 4.855e-07 | 0.00861 |
FANCI|55215 | 0.5508 | 5.365e-07 | 0.00951 |
DIAPH3|81624 | 0.5482 | 7.464e-07 | 0.0132 |
CDK1|983 | 0.5422 | 8.661e-07 | 0.0154 |
C8ORFK29|340393 | 0.5555 | 8.789e-07 | 0.0156 |
UHRF1|29128 | 0.5396 | 1.002e-06 | 0.0178 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 64 | |
class1 | 9 | |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 48 | |
MALE | 29 | |
Significant markers | N = 4 | |
Higher in MALE | 4 | |
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 = 77
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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.