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We identified 50 highly expressed (active) genes (Table S1) and 50 lowly expressed or silent (inactive) genes (Table S2) on the basis of the microarray data of the RNAs of the TSA-treated cells of A. fumigatus.
At the same time, the germ cells migrated to the cortex and expressed PAR6 lowly within the cytoplasm of cysts, whereas the expression in somatic cells around the cysts turned weak (Fig. 1C).
We categorized genes into five groups according to expression levels (Additional file 15): 0 (silent genes), 0 1 (lowly expressed genes), 1 20 (moderately expressed genes), 20 1000 (highly expressed genes), and > 1000 (genes with the highest expression, housekeeping genes).
Based on the expression profile – a vector of expression levels under different biological conditions, the expression levels of a TF were clustered into either two or three categories (1: highly expressed, 0: normally expressed, -1: lowly expressed) using the K-means clustering algorithm, where the number of categories equals the number of types (>3, <−3, or between) of the expression situation.
A heterogeneity chi square test (χ2 highly biased + χ2 lowly biased – χ2 pooled) was used to identify divergent codon usage patterns between the two gene sets.
After discarding 9 lowly expressed miRNAs, a panel of 13 miRNAs were measured in 29 samples (benign n = 11, malignant n = 18).
When MCL1 is highly expressed (above the median) and BCL2 lowly expressed, the prognosis is not significantly improved (HR = 0.533[0.202, 1.4103]).
When FGFR2 is highly expressed (above the median) and FGF4 lowly expressed, the survival is not significantly improved (HR = 0.532 [0.202, 1.399]).
We found 68 aberrantly expressed miRNAs in our microarray, including 51 highly expressed miRNAs and 17 lowly expressed miRNAs (Table 2).
Generally, the tumor cells from well-differentiated carcinomas tended to highly expressed ALDH1 and those from poor-differentiated carcinomas tended to express ALDH1 lowly.
