Aire expression positively regulates a large set of tissue-restricted genes. (A) Genes differentially expressed between mature Aire-positive mTEC and mature Aire-KO mTEC (<5% FDR, more than twofold). A set of 474 housekeeping genes (de Jonge et al. 2007) showed little change in expression, indicating the absence of a systematic bias (yellow points). (B) At the population level, Aire expression elevates target gene transcription to a median FPKM of 1. (C) Aire expression differentially up-regulates individual target genes. Each gray vertical line represents the change in FPKM of a single gene between mature Aire-KO mTEC and mature Aire-positive mTEC. Genes are ordered by increasing expression in mature Aire-KO mTEC on the x-axis, being either dependent on or enhanced by Aire expression. The red line represents the moving average of FPKM in mature Aire-positive mTEC. (D) Genes induced by Aire expression are tissue-restricted in transcription. Tissue-restricted genes were identified from the GNF GeneAtlas using the dynamic step method (Methods; Supplemental Fig. 6). (E) Degree of tissue restriction is positively correlated with the requirement for Aire expression. The fraction of genes requiring Aire expression for detection was assessed for sets of genes restricted in expression to all possible branches, nodes, and leafs of the GNF GeneAtlas sample clustering (Supplemental Fig. 6A). Only gene sets with at least 10 members are shown. The red dot indicates 1586 genes restricted in expression to testis, a tissue with a transcriptome of abnormally high complexity (Ramsköld et al. 2009) that is known to express Aire and to undertake PGE (Schaller et al. 2008).
