One postgenomic strategy used to identify molecular networks functioning in tissue development is microarray analysis of individual cell types or tissues followed by in situ hybridization to identify temporal and spatial gene expression patterns. Compared with microarray analysis, the systematic in situ hybridization database presented here provides more detailed information on the spatial regulation of gene expression and allows identification of discrete clusters of transcribed genes. We created a whole-mount in situ hybridization (WISH) database, containing expression data of transcription factors, cofactors and microRNA expressed in mouse embryos a highly dynamic stage of skeletogenesis. Our approach, WISH provided us new regulators as a critical effector in a myogenic feedback mechanism, tendon development and cartilage homeostasis.