DOI: 10.6084/m9.figshare.14926912.v1
title: Additional file 2 of Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis

description: Additional file 2:Supplementary Table 1. . Primers used for isogenic cell model generation and validation. List of primers for generating isogenic cell models for different KRAS and BRAF mutations using rAAV mediated genome editing (2 A). Primers for validations by Sanger sequencing for presence of mutations of interest of KRAS and BRAF (2B) and the validation results (2 C). Supplementary Table 2. Differentially Expressed Genes (DEGs) in KRAS and BRAF isogenic cell models. Differentially expressed genes (DEGs) with ㅣlog2 FCㅣ &gt; 1 and FDR ≤ 0.05 from comparisons of RKO cells with KRAS G12C/D/V/G13D to wildtype (2 A, C, E, G) or BRAF V600E (2B, D, F, H) and HCT116 BRAF V600E to HCT116 (2I) or HCT116 KRAS WT (2 J). FDR, False Discovery Rate; log2FC, log2 transformed fold change of gene expression. Supplementary Table 3. Differentially Expressed Genes (DEGs) from overlapped Venn regions (Supplementary Fig. 5 A-D and F) and their trend of expression in the transcriptome datasets with logFC values. Differentially expressed genes (DEGs) with ㅣlog2 FCㅣ &gt; 1 and FDR ≤ 0.05 from comparisons of RKO cells with KRAS G12C/D/V and G13D to wildtype or BRAF V600E were identified in the overlapped regions of the Venn diagramme analysis (Supplementary Fig. 5 A-D and F, Additional File 1).The “Trend of expressions” were determined as all negative, negative log2FC value in both of the comparisons; all positive, positive log2FC value in both of the comparisons and mixed, negative and positive log2FC value in one or another. Here, FDR, False Discovery Rate; log2FC, log2 transformed fold change of gene expression. Supplementary Table 4. Expression status of Differentially Expressed Genes (DEGs) from KRAS and BRAF isogenic cell models in TCGA CRC samples harboring different KRAS mutations. The representations of DEGs from our transcriptome datasets into TCGA transcriptome datasets of colon and rectum samples harboring KRAS G12/C/D/V/13D mutation in comparisons to samples with no mutations in this study. Here, TCGA log2FC, the log2FC from TCGA data; DiffExpr log2FC, log2FC from our data and Directionality, directionality of the expression (positive, if log2FC values in both TCGA and our dataset are positive; negative, if log2FC values in both TCGA and our dataset are negative and opposing, if log2FC values in both TCGA and our dataset are positive and negative or vice versa). Supplementary Table 5. Differentially Expressed Proteins (DEPs) in KRAS and BRAF isogenic cell models. Differentially expressed proteins with ㅣlog2 FCㅣ ≥ 1 and adjusted P value ≤ 0,05 from comparisons of KRAS G12C/D/V and G13D to wildtype (3 A, C, E, G) or BRAF V600E (3B, D, F, H) and HCT116 BRAF V600E to KRAS G13D. log2FC, log2-transformed fold change of the expression between contrast groups; AveExpr, Average protein expression; t, moderated t-statistics; P.Value, p-value; Adj.P.val, Benjamini-Hochberg adjusted p-value; B, log-odds of the protein being differentially expressed. Supplementary Table 6. Pathway analysis of differentially expressed genes (DEGs) in KRAS mutant RKO cells. Ingenuity Pathway Analysis (IPA) of differentially expressed genes with ㅣlog2 FCㅣ &gt; 1 and FDR ≤ 0.05 from KRAS G13D, G12C/D/V knock-ins compared to wild-type and BRAF V600E (5 A-D). -log(p-value), -log10 of the Benjamini-Hochberg corrected p-value obtained from the Fisher’s Exact test; zScore, A score indicating predicted activation (z-score &gt; 2) or inactivation (z-score &lt; -2) of a pathway in question ; Ratio, no. of differentially expressed genes in a given pathway divided by the total number of genes that make up that pathway and that are in the reference gene set; P-Value, reverse log of the -log10 p-values; geneNames, HGNC symbols of the differentially expressed genes associated with the pathway in question; Adj. p-value, p-values adjusted for multiple testing using the Benjamini-Hochberg procedure and cut-off 1 and FDR ≤ 0.05 from comparisons of KRAS G12D and G13D to wild-type and BRAF V600E cells (6 A-B). -log(p-value), -log10 of the Benjamini-Hochberg corrected p-value obtained from the Fisher’s Exact test; zScore, A score indicating predicted activation (z-score &gt; 2) or inactivation (z-score &lt; -2) of a pathway in question ; Ratio, no. of differentially expressed genes in a given pathway divided by the total number of genes that make up that pathway and that are in the reference gene set; P-Value, reverse log of the -log10 p-values; geneNames, HGNC symbols of the differentially expressed genes associated with the pathway in question; Adj. p-value, p-values adjusted for multiple testing using the Benjamini-Hochberg procedure and cut-off