Fig. 9

Schematic diagram summarizing the systems approach undertaken here to reconstruct and analyze the plant cell wall degradation network (PCWDN) of N. crassa. We compiled information from diverse sources to build the network of biochemical reactions responsible for degrading plant cell wall polysaccharides into simple sugars. The combined annotation information was encapsulated in the form of a feature matrix and a simple method was devised to assign an annotation confidence score to each PCWDN gene. To demonstrate the utility of our PCWDN, we performed comparative transcriptomics analysis using RNA-seq data and integrated genome-wide binding data from ChIP-seq experiments for three key transcription factors regulating the plant cell wall degradation response. Integration of next-generation sequencing data within the PCWDN led to the hypothesis that CLR-2 is a key TF for deconstruction of mannan and XG, a hypothesis that was subsequently validated through experimentation