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Depicting combinatorial complexity with the molecular interaction map notation.
Kohn KW, Aladjem MI, Kim S, Weinstein JN, and Pommier Y.
Mol Syst Biol. 2006;2:51. Epub 2006 Oct 3.
Abstract:
To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to
electronic circuit diagrams. Such diagrams must surmount the difficulties posed by complex patterns of protein modifications
and multiprotein complexes. To meet that challenge, we have designed the molecular interaction map (MIM) notation
(http://discover.nci.nih.gov/mim/). Here we show the advantages of the MIM notation for three important types of diagrams:
(1) explicit diagrams that define specific pathway models for computer simulation; (2) heuristic maps that organize the
available information about molecular interactions and encompass the possible processes or pathways; and (3) diagrams of
combinatorially complex models. We focus on signaling from the epidermal growth factor receptor family (EGFR, ErbB), a
network that reflects the major challenges of representing in a compact manner the combinatorial complexity of multimolecular
complexes. By comparing MIMs with other diagrams of this network that have recently been published, we show the utility of
the MIM notation. These comparisons may help cell and systems biologists adopt a graphical language that is unambiguous and
generally understood.
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