Additional file 1 of Systematical analysis reveals a strong cancer relevance of CREB1-regulated genes
Creators: name: Zheng, Tianyu
name: Huang, Jinrong
name: Xiang, Xi
name: Li, Siyuan
name: Yu, Jiaying
name: Qu, Kunli
name: Xu, Zhe
name: Han, Peng
name: Dong, Zhanying
name: Liu, Yang
name: Xu, Fengping
name: Yang, Huanming
name: Jäättelä, Marja
name: Luo, Yonglun
name: Liu, Bin
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Figure S1. RNA-seq analysis of CREB1 KO cells, CREB1 rescue cells, and WT cells. A Hierarchical clustering heatmap showing overall similarity between samples based on Euclidean distance calculation between CREB1 KO vs WT and Rescue vs KO. B Principal component analysis (PCA) showing sample variance based on gene expression. Points that represent samples were projected onto the 2D plane. Sample variance was indicated by Variance Percent. C, D Summary of DEGs in paired comparison of CREB1 KO vs WT and Rescue vs KO respectively (R upset package). Side horizontal bars indicate the total number of DEGs of each paired comparison. Vertical bars indicate the total number of DEGs exclusively existed in indicated combinations of paired comparisons. Figure S2. Rank-rank analysis of CREB1 rescue vs CREB1 KO gene ranks and tumor vs para-carcinoma tissue gene ranks. Rank–rank hypergeometric overlap (RRHO) plots of lists of 24 types of cancer vs 1, 2, 3 separately. Figure S3. Integrative analysis of CREB1-downregulated gene network. A Gene distribution analysis of four different gene lists (R circlize package). They are (i) CREB1 commonly downregulated gene list; (ii) RRHO concordant downregulated gene list; (iii) commonly opposite regulated genes between Rescue vs KO and KO vs WT; (iv) CREB1 Chipseq gene list (genes with p value ≤ 0.001, CREB1 binding ratio ≥ 2 are selected). The stripes of different colors connect the portions uniquely shared by different combinations of the lists (i–iv) (Additional file 5: Table S4). 1 gene (red stripe) are present in all 4 lists. 19 genes (blue stripe) are uniquely shared by i, ii, and iv. B. 20 top-ranked CREB1-downregulated targets illustrated by their average log2 FC (CREB1 rescue vs CREB1 KO) and the tumor occurrence number in RRHO concordant gene list. The scale of log2 FC is displayed by the tomato gradient bar. C, D. CREB1 binding sites in Chipseq data, gene function annotation based on GO analysis and detailed tumor occurrence of the 20 overlapped genes. Figure S4. Cancer patient survival analysis of representative top-ranked CREB1 target genes. A, B Kaplan-Meier overall survival curves of top-ranked CREB1-upregulated targets (STC2, EGLN3) in different cancer types. C Kaplan-Meier overall survival curve of a top-ranked CREB1-downregulated target, SLC22A4, in different cancer types. log rank p value ≤ 0.05 was considered significant. Hazard ratio (HR) ≥ 1 and p (HR) &lt; 0.05 were considered significantly poor prognosis. n (high) and n (low) are the patient number. Figure S5. Validation of BDKRB2 as a novel CREB1-upregulated target by western blot. Western blot of indicated proteins in wild type (WT), CREB1 KO, and CREB1 rescue (R) cells. Due to a bipartite nuclear localization signal and a Flag tag at CREB1’s C-terminal, the molecular weight of CREB1 in CREB1 rescue cells is 8KD bigger than in WT cells.