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. Author manuscript; available in PMC: 2015 Jul 2.
Published in final edited form as: Neuron. 2014 Jul 2;83(1):69–86. doi: 10.1016/j.neuron.2014.05.035

Figure 3.

Figure 3

TMAP identifies in vivo developmental period and cortical laminae most similar to differentiating phNPCs. Rank-rank hypergeometric overlap (RRHO) maps (Plaisier et al., 2010) comparing the transitions between in vivo developmental periods (A–C) or laminae in the developing cortex (D–E) to differentiation of phNPCs from 1 to 12 wks. (A,D) Each pixel represents the overlap between in vivo and in vitro transcriptome, color-coded according to the -log10 p-value of a hypergeometric test (step size = 200). On each map, the extent of shared upregulated genes is displayed in the bottom left corner, whereas shared downregulated genes are displayed in the top right corners (see schematic on rightmost panel). (B,E) Venn diagrams display the extent of overlap between in vivo and in vitro transcriptomes at the best matched periods (1 vs 6; B) and between SZ and CPi (E). Gene ontology (GO Elite) analysis shows co-upregulated genes are related to synaptic transmission and nervous system development, whereas co-downregulated genes are involved in mitosis. (C) Selected genes co-upregulated and co-downregulated are graphed through time both in developing phNPCs and in vivo.