SOX9 and Alzheimer disease: To this end, we combined ChIP-seq analyses from the ENCODE Consortium (the exception being SOX9, whose transcriptional program was mined from published literature) (35) with the ChIPmera CREB3L2-ATF4 readout and contrasted these datasets against the AD transcriptome (top 3000 DEGs; bulk tissue level) as well as our own RNA-seq results using the Metascape platform (Fig. 4, C and D, and fig.