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. Author manuscript; available in PMC: 2018 Jan 22.
Published in final edited form as: Methods Cell Biol. 2015 Feb 14;127:349–386. doi: 10.1016/bs.mcb.2014.12.001

FIGURE 3. Profile clustering identifies 16 principal upregulation expression profiles organized into five pattern groups.

FIGURE 3

(A) The Arch pattern shows increased expression at 3 min, a peak expression at 10 min, and then decreasing expression. This profile accounts for 37% of the profiles. The Arch1 pattern shows expression that peaks at 10 or 30 min, but is still up at 60 min. The Arch2 pattern is similar to Arch1 except that the genes are not upregulated at the 60 min time point. (B) The staggered (Stag) pattern shows genes with a burst of expression at the 3, 10, 30, or 60 min time points. (C) The pulse pattern shows the upregulation at a single time point and accounts for 11% (N = 196) of the upregulated genes. (D) The Up-Tick (UT) pattern describes genes that show increased expression at one time point followed by downregulation at another time point followed by upregulation at a third time point. UT patterns make up 3% (N = 51) of upregulated genes. (E) Hump patterns make up 16% (N = 290) and are profiles that are pulse-like, but significant upregulation is sustained over two consecutive time points. 0.5% (N = 9) show profiles that are outliers in that their profiles are not adequately similar to any principal expression profile found in this analysis (Albee et al., 2013).