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Figure 2 | BMC Genomics

Figure 2

From: Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Figure 2

Procedure to derive the discretized representation of a gene. a) Examination of the expression levels under the eight cultivation conditions led to the observation that for many genes the expression pattern across the four nutrient limitations when grown aerobically is a scaled and offset version of its anaerobic counterpart. (Permutation tests were performed to confirm this notion (Additional file 3)). b) This "global oxygen effect", i.e. the effect that presence of oxygen has on the expression levels across all or most of the nutrient limitations, is modeled as a linear relationship and estimated using a regression strategy. c) The estimated regression parameters (slope and offset) are employed to isolate the oxygen effect by transforming the aerobic expression values. Discretization of this pattern allows for identification of up- or downregulation as a consequence of specific nutrient limitations and possible nutrient-limitation-specific effects of oxygen presence. d) Pairwise T-tests are performed to compare the original aerobic and anaerobic expression values for each nutrient limitation. The results of these tests are combined to detect possible consistent and significant higher or lower expression as a consequence of oxygen presence. e) The derived discrete representation of the expression of a gene is visualized in a nine-bit ternary (-1,0,1) vector.

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