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. 2014 Dec 20;10(12):768. doi: 10.15252/msb.20145654

Figure 6.

Figure 6

Application of bdHMM to chromatin modifications in human T cells identifies direction of chromatin states.

  1. Example of chromatin state annotation of ChromHMM and bdHMM (bottom tracks) with RefSeq gene annotation and input signal. State direction matches gene orientation of annotated convergent genes and divergent genes. The log-transformed signal (Ernst and Kellis, 2010) of all 41 data tracks is shown in black on top. Binarized input signal is shown for 18 acetylation marks in blue, 20 methylation marks in red and CTCF/PolII/H2A.Z in brown.
  2. bdHMM transitions between promoter-associated states 1–11 are shown for forward and reverse states. The asymmetric, transposed structure of these two submatrices (i.e., transition probabilities favor one direction for pairs aij and aji) uncouple the two reading directions.
  3. The symmetric ChromHMM transition matrix hides the underlying directed flow of chromatin states.