Inferring the structures of signaling motifs from paired dynamic traces of single cells
Fig 3
Inferring the underlying signaling motif from simulated single-cell dynamics.
(A) An incoherent feedforward loop (IFFL) signaling motif was used to generate a synthetic data set for 50 single cells. Individual upstream signals X were generated as shown in Fig 2A. Each signal was then subjected to the IFFL signaling motif using ODEs to calculate a unique downstream response Z for each cell (see S1 Text). The resulting X and Z pairs for all cells were then analyzed to infer the underlying signaling motif. (B) Heat map representation of motif structures for all possible 3-factor signaling motifs. (left) A conventional representation of motif structure consisting of circles and arrows can be represented by (right) a single column of shaded rectangles in which each rectangle denotes a specific interaction within the motif: black, positive regulation; red, negative regulation; white, no regulation. The heat map representation for the IFFL is shown next to the conventional diagram. (Right) All 402 possible unique motif structures are shown for a 3-component network (X, Y, and Z). (C) To infer the mechanism underlying X and Z, a separate downstream response, Z’, is calculated for each possible parameterized signaling motif and compared to the original downstream response, Z. Each motif is assigned an error score that reflects the average difference in fold change between Z and Z’ per cell per unit time. (D) Distribution of error scores. The error scores are distributed such that they approach the asymptote of the worst possible score (i.e., the output of an unconnected graph). The top graphs are defined as those before the “elbow” of the graph and are determined by looking at the first derivative. (E) The top-scoring motifs. The links for the incoherent feed forward loop, as well as its simpler sub-motif structures, are overrepresented among the best-performing motifs. (F) Heat map representation of the consensus motif. Asterisks indicate a greater than 50% confidence in that link being correct. Darker colors mean more confidence and lighter colors mean less confidence. The distance from the consensus motif to the known motif was XX which has a p-value of 9.95x105.