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Figure 1 | BMC Bioinformatics

Figure 1

From: In search of functional association from time-series microarray data based on the change trend and level of gene expression

Figure 1

Illustration of calculating the change trend score sc and the correlation coefficient cc of the match change trend. The two genes X and Y in this example have a positive relationship (here expression levels are not normalized). Only the change trend between time points 5 and 6 is different. The number of matched change after time shifts (by dynamic programming) is less than 7. Thus, the maximal match change trend score sc is 7 in this example with 9 time points. To calculate the correlation coefficient, we first extract the change levels of the matched change trends: X m c 1 2 = 1 , X m c 2 3 = 1 , X m c 3 4 = 1 , X m c 4 5 = 2 , X m c 5 6 = 4 , X m c 6 7 = 2 , X m c 7 8 = 3 Y m c 1 2 = 1 , Y m c 2 3 = 1 , Y m c 3 4 = 1 , Y m c 4 5 = 2 , Y m c 5 6 = 3 , Y m c 6 7 = 3 , Y m c 7 8 = 4 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=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@AB67@ The change level between time points 5 and 6 is excluded because the change (inverted) trend is different from the main (positive) change trend. Using the above matched change levels we can obtain a correlation coefficient cc = 0.9597 according to Eq.1.

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