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Background  Microdeletion of chromosome 22q11 is associated with significant developmental anomalies, including disruption of the cardiac outflow tract, thymic/parathyroid aplasia and cleft palate. Amongst the genes within this region,  TBX1  is a major candidate for many of these developmental defects. Targeted deletion of  Tbx1  in the mouse has provided significant insight into the function of this transcription factor during early development of the cardiac and pharyngeal systems. However, less is known about its role during palatogenesis. To assess the influence of  Tbx1  function on gene expression profile within the developing palate we performed a microarray screen using total RNA isolated from the secondary palate of E13.5 mouse embryos wild type, heterozygous and mutant for  Tbx1 .    Results  Expression-level filtering and statistical analysis revealed a total of 577 genes differentially expressed across genotypes. Data were clustered into 3 groups based on comparison between genotypes. Group A was composed of differentially expressed genes in mutant compared to wild type ( n  = 89); Group B included differentially expressed genes in heterozygous compared to wild type ( n  = 400) and Group C included differentially expressed genes in mutant compared to heterozygous ( n  = 88). High-throughput quantitative real-time PCR (RT-PCR) confirmed a total of 27 genes significantly changed between wild type and mutant; and 27 genes between heterozygote and mutant. Amongst these, the majority were present in both groups A and C (26 genes). Associations existed with hypertrophic cardiomyopathy, cardiac muscle contraction, dilated cardiomyopathy, focal adhesion, tight junction and calcium signalling pathways. No significant differences in gene expression were found between wild type and heterozygous palatal shelves.    Conclusions  Significant differences in gene expression profile within the secondary palate of wild type and mutant embryos is consistent with a primary role for  Tbx1  during palatogenesis.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4782-y) contains supplementary material, which is available to authorized users.

Gene expression profiling in the developing secondary palate in the absence of Tbx1 function