Fig. 2

Identification of FOX family, STAT family, TEAD family, and AP1 complex members as transcription factors changing during AEC differentiation in FAIRE-occupied regions. A) Enrichment of tag density from center of the epigenetic mark for both AT2 (top) and AT1-like (bottom) cells. B) HOMER-computer enrichment of TFBS in AT1-like (X-axis, D6) or AT2 (y-axis, D0) cells. Dotted line indicates -log10BH cutoff for significance. C) Distribution of all TFBS predicted motifs available in HOMER and their enrichment in AT1-like (red) vs. AT2 (blue) cells. The BH-corrected p value for each TFBS motif was computed in each cell type and AT2 cell enrichment was subtracted from AT1-like cell enrichment. TFBS motifs were then arranged from most AT2-cell specific (top) to most AT1-like cell-specific (bottom). D) Unsupervised hierarchical clustering of TFBS enrichment in FAIRE-occupied regions. Red = highly significantly enriched for the indicated TFBS, blue = not significantly enriched. Rows are scaled based on p values of motif enrichment significance. E) Supervised clustering analysis of gene expression changes for the indicated transcription factors during AEC differentiation. Purple = high expression, green = low expression, each column color scaled by standard deviation within the row. Transcription factors bolded have loss of predicted TFBS and loss of gene expression (AT2 cells, top cluster), or gain of predicted TFBS and corresponding increase in gene expression (AT1-like cells, bottom cluster). F) Tag density of TEAD1 motif enrichment within AT2 (blue) or AT1-like (red) FAIRE peaks. Tag densities are centered on the middle of the FAIRE peak (position 0) and normalized by millions-mapped. G) The peak height (Y axis) and area under the peak (size of circle) were calculated for all AT2 (blue) and AT1-like (red) enriched TF motifs in FAIRE peaks. TFs were ranked based on AT1-like peak height (smallest to largest)