Figure 2.

Genome-wide RNA-seq screening of FOXO1 regulated genes in the endothelium

(A) MA plot of average gene expression (log₂, X axis (A)) and the mean of log₂-fold change (Y axis (M)) of si-FOXO1-mediated up or downregulated genes; these were compared with si-Control HUVECs treated with VEGF for 18 h. Red and blue dots indicate genes with substantial change in expression with M > 0.5 and A > −2.5.

(B) MA plot of average gene expression (log₂, X axis (A)) and the mean of log₂-fold change (Y axis (M)) of Ad-FOXO1-mediated up or downregulated genes compared with that in Ad-Control treated HUVECs. Green and orange dots indicate genes with significantly altered expression with M > 0.5 and A > −3.0.

(C) Venn diagram of overlapping si-FOXO1-, or Ad-FOXO1-mediated up or downregulated genes and genes responsive to 18-h VEGF treatment. Each number indicates gene volume. Yellow indicates the common responsive gene number.

(D) Clustering and heatmap representation of the 44 common FOXO1-regulated genes from D. The color intensity indicates the log₂-fold expression levels: yellow-higher and blue-lower, relative to the median in black. The gene name based on the reference sequence is shown on the right.

(E) FOXO1-mediated Tip cell enrichment from Gene set enrichment analysis (GSEA). The normalized enrichment score (NES), P and q-values for the datasets from VEGF 18h vs. 0h (left), si-FOXO1 vs. si-control with 18h VEGF treatment (right), and Ad-FOXO1 vs. Ad-Control (bottom).

See also Figure S4 and Tables S1, S2, S3, and S4.