Fig. 4. BioTapestry models of Hh-driven cis-regulatory networks in mouse. Transcriptional targets of the Hh pathway can be defined by a globally responsive signaling cassette (A), containing components that are either known (unbroken lines) or likely (broken lines) to be part of a negative feedback loop. (B) A model for a Shh-driven transcriptional network underlying ventral neuronal specification. In this diagram, depicted in standard BioTapestry nomenclature (Longabaugh et al., 2005), neuronal specification is depicted as a sequential series of cell states. All genes not expressed are in gray, whereas currently expressed genes are in black or other colors. Similarly, inactive links (active in previous stages of specification) are depicted in gray, whereas active activation or repression is depicted using lines of other colors. An animation of these events can be viewed in Movie 1 in the supplementary material. This diagram focuses explicitly on ventral cell specification; thus previous events in general neuronal specification are not shown. Validated Gli targets (all identified or confirmed in our study) are indicated by blue diamonds (ChIP peak), orange diamonds (transgenic validation) or green diamonds (mutation of binding site in transgenic embryos).