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Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

Figure 4

Learned Boolean networks.

(A–B) Networks with learned Boolean logic transition functions consisting of 30 genes/proteins. Learning was achieved using the serum/LIF (A) or 2i/LIF (B) single cell data. Light cyan nodes represent genes; gray squares represent learned regulatory logic transition functions. The shadowed inset box exemplifies one such learned transition function upstream of Gata6. The sign represents ‘NOT’, ∧ represents ‘AND’ and ^∨ represents ‘OR’ logic operators. Boolean functions for all genes are available in Supplementary Information. Links from upstream parent nodes appearing in more than 90% of equally well-fitted Boolean functions are colored in green (activation) and red (repression). Other links are not shown. Novel links that resulted from the learning process are highlighted in dark red. (C) Overlap between the networks learned using data from mESCs cultured in serum/LIF or 2i/LIF. Links that are shared in the two conditions are in gray. Non-shared links are solid or dashed based on their source (solid for serum/LIF and dashed for 2i/LIF).

doi: https://doi.org/10.1371/journal.pcbi.1003777.g004