This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.
Testing the association between 528 miRs and 2 clinical features across 10 samples, statistically thresholded by Q value < 0.05, no clinical feature related to at least one miRs.
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No miRs correlated to 'AGE', and 'GENDER'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant miRs | Associated with | Associated with | ||
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AGE | Spearman correlation test | N=0 | ||||
GENDER | t test | N=0 |
AGE | Mean (SD) | 48.3 (11) |
Significant markers | N = 0 |
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Expresson data file = PCPG-TP.miRseq_RPKM_log2.txt
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Clinical data file = PCPG-TP.merged_data.txt
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Number of patients = 10
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Number of miRs = 528
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Number of clinical features = 2
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 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.