DRG co-culture microarray

Gene regulatory interactions that shape developmental processes can often can be inferred from microarray analysis of gene expression, but most computational methods used require extensive datasets that can be difficult to generate. Here, we show that maximumentropy network analysis allows extraction of genetic interactions from limited microarray datasets. Maximum-entropy networks indicated that the inflammatory cytokine TNF-_ plays a pivotal role in Schwann cell–axon interactions, and these data suggested that TNF mediates its effects by orchestrating cytoplasmic movement and axon guidance. In vivo and in vitro experiments confirmed these predictions, showing that Schwann cells in TNF_/_ peripheral sensory bundles fail to envelop axons efficiently, and that recombinant TNF can partially correct these defects. These data demonstrate the power of maximum-entropy network-based methods for analysis of microarray data, and they indicate that TNF-_ plays a direct role in Schwann cell–axon communication. Samples for microarray analysis were obtained in triplicate from separate coculture slips at 0, 0.5, 1, 6, 12, 24, 36, and 48 h after ascorbic acid addition and were prepared for use on Illumina Mouse-8 chips (Illumina) by the Rockefeller Microarray Core Facility (New York, NY).