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were only in the combined dataset profile.
The combined dataset profile included two known molecular markers of breast cancer: BCL2 and ESR1.
The DAVID functional annotation tool [ 24] was applied to the combined dataset profile while all 5,569 Unigene clusters were used as the genomic background.
While both profiles performed better when they were applied to ER-positive patients only, the combined dataset profile further outperformed the Rosetta profile.
Respectively 17 and 37 of 51 genes in combined dataset profile had one-sided p values less than 0.01 and 0.1.
Fisher's exact test rejected the independence of 3-year prognosis on both of combined dataset profile (p = 0.0002, odds ratio = 3.08) and Rosetta profile (p = 0.0006, odds ratio = 2.82).
Similar(53)
The 'Golub' cancer dataset profiled the expression of 7129 genes in 47 subjects with acute lymphoblastic leukemia (ALL) and 25 subjects with acute myeloid leukemia (AML) to develop a class predictor [5].
This dataset profiled mRNA expression on days 0, 2, 4, and 10 after birth.
The Miller dataset [ 35] is a well-annotated gene expression dataset profiling 251 primary human breast tumors.
The extensive dataset profiled some 2000 genes, which limits detailed comparisons with the present study within this manuscript [ 33].
We generated two types of source tree dataset profiles: those containing only scaffolds, and those containing one scaffold and several clade-based datasets (as described earlier).
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