Fig. 2

RNA-seq analysis of CREB1 KO cells, CREB1 rescue cells, and WT cells. A Volcano plots of CREB1 knockout (KO) clone 1–3 vs WT and CREB1 rescue clone 1–3 vs CREB1 KO clone 1–3. Differential gene expression profiles are displayed according to log2 Fold Change (log2 FC) and p adjusted (Additional file 3: Table S2). The threshold of differentially expressed genes (DEGs) was set to p-adjusted ≤ 0.05 and |log₂ FC| ≥ 1. B Heatmaps of DEGs in indicated pairwise comparisons. Res is short for rescue. C Heatmaps of DEGs with opposite expression profiles between CREB1 KO vs WT and Rescue vs KO. Twenty three genes were upregulated in all CREB1 KO cell lines (compared to WT) and downregulated in all CREB1 rescue cell lines (compared to KO), while 39 genes were downregulated in all CREB1 KO cell lines and upregulated in all CREB1 rescue cell lines. D Gene Ontology (GO) analysis of DEGs in CREB1 commonly regulated gene list (genes showing similar differential expression patterns in at least two pairs of rescue clones and corresponding KO clones) (Additional file 3: Table S2). It contains both upregulated and downregulated genes. The X-axis shows the NO. of genes in the enriched GO terms. The Y-axis shows the top 10 GO terms of biological process. All GO terms were selected by p value ≤ 0.01. E. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of DEGs in CREB1 commonly regulated gene list. The NO. in each rectangle shows NO. of genes enriched in the corresponding pathway. The scale of p value is displayed by the gradient bar. The pathways highlighted by red boxes are enriched in both down and upregulated DEGs lists. As a cancer-related pathway, PI3K-Akt pathway has 18 cancer-related differentially expressed genes. They are listed at the bottom. Information about cancer-related genes in PI3K-Akt pathway was obtained from Networks of Cancer Genes (NCG 6.0) (http://ncg.kcl.ac.uk/index.php)