Skip to main content

Table 5 Table 5

From: Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior

Symbol Range Annotation
d il 1,2,...,G Number of genes in a dataset with FDR lower than the threshold l
EL g (0,Inf) Expected value of the log likelihood with respect to the FDR threshold
f il 1,2,...,d il Number of false positives using the FDR threshold l
F gi (0,1) Gene-specific false discovery rate in dataset i: proportion of false positives among the significant calls
FDR g (0,1) Gene-specific false discovery rate for having consistently differentially expressed patterns among the datasets studied
g 1,2,...,G Index for a gene from the union of gene sets across all datasets
h 1,2,...,H i Index for fold change comparison between a case and a control from a dataset, where m i * n i = H i
i 1,2,...,D Index for a gene expression microarray dataset (consists of m i cases and n i controls)
l (0,1) FDR threshold used to enumerate number of genes with FDR lower than this threshold in a dataset and to estimate the number of false positives under this threshold
L(r gl |Data) (0,1) Gene- and FDR threshold- specific likelihood of observing the differential expressed pattern among the datasets
M u p ¯ i ( M d o w n ¯ i ) 1,2,...,G number of genes that are not up(not down)-regulated in dataset i
Q gl (0,Inf) Minus log likelihood
r ^ u p i l ( r ^ d o w n i l  ) (0,1) False positive rate: the probability of a non-up-regulated (non-down-regulated) gene being falsely called as over-expressed (under-expressed)
δ g i l u p (or δ g i l d o w n ) 0[1] Binary variable indicating gene g is identified as up(or down)-regulated in dataset i for threshold l
γ gih 1,2,...,G rank of fold change for gene g in the hth comparison of dataset i