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. 2015 Mar 31;16(1):63. doi: 10.1186/s13059-015-0624-2

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© Cheng et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Properties of the inferred hierarchical structure for the yeast phosphorylome generated by HSM algorithm. (A) The distribution of feed-forward loop (FFL) motifs in the hierarchical network. In a FFL motif, a kinase X phosphorylates another kinase Y and both target a common substrate Z. Depending on the location of X and Y in the hierarchical structure, the X-- > Y interaction can be categorized into nine combinations. Downward interactions (TM, TB, and MB), upward interactions (MT, BT, and BM), and horizontal interactions (TT, MM, and BB) are shown with red, blue, and gray bars, respectively. (B) The Venn diagram of substrates of kinases at different levels.