DOI: 10.6084/m9.figshare.13788252
title: Additional file 2 of Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer

description: Additional file 2 Supplementary Table 1. Summary of RNA Modification Writers. The annotation of 26 RNA modification “writers” based on the published data. Supplementary Table 2. Clinical information of CRC cohorts from GEO/TCGA. The accession number, platform of microarray, the number of tumor and normal samples, clinical characteristics (stage, gender), citation of CRC cohort. Supplementary Table 3. Samples clustering in eight GEO-CRC cohorts. The detailed information of eight GEO-CRC Cohorts with different group methods, including clustering, CMS subtypes, and WM_Score. Supplementary Table 4. Group information of samples in TCGA-COAD/READ cohorts. The WM_Score and the classification of WM_Score types and CMS subtypes in TCGA-COAD/READ cohorts. Supplementary Table 5. Enrichment score of KEGG pathways in eight GEO-CRC cohorts. The table shows enrichment score of KEGG pathways performed by Gene Set Variation Analysis (GSVA) in eight GEO-CRC cohorts. Supplementary Table 6. TME infiltration characteristics of samples in eight GEO-CRC cohorts. Table detailly lists the infiltration of 22 immune types of each sample which performed by CIBERSORT method in eight GEO-CRC cohorts. Supplementary Table 7. Difference of TME infiltration characteristics between Cluster_1 and Cluster_2 in Eight GEO-CRC Cohorts. The difference of TME infiltration characteristics between Cluster_1 and Cluster_2 in eight GEO-CRC cohorts. Supplementary Table 8. Difference of TME infiltration characteristics between WM_Score-high and WM_Score-low in eight GEO-CRC cohorts. The difference of TME infiltration characteristics between WM_Score-high and WM_Score-low in eight GEO-CRC cohorts. Supplementary Table 9. The correlation of writers and TME infiltration Characteristics. The Spearman correlation of gene expression of 26 writers and the infiltration of 22 immune cells in eight GEO-CRC cohorts. Supplementary Table 10. Differentially expressed genes between Cluster_1 and Cluters_2 associated with survival. The association of hypoxia status differentially expressed genes between Cluster_1 and Cluters_2, with patient overall survival times based on both univariate multivariate Cox proportional hazards models. Supplementary Table 11. Difference of miRNAs and miRNAs-DEGs target pathways between WM_Score-high and WM_Score-low in TCGA COAD/READ cohorts. The differentially expressed miRNA between WM_Score-high and WM_Score-low groups, and miRNA targeted mRNAs and mRNA enriched pathways. Supplementary Table 12. Difference of PDUI between WM_Score-high and WM_Score-low in TCGA COAD/READ cohorts. To compare PDUI between WM_Score-high and -low groups in TCGA COAD/READ cohorts, we used the t test and used Benjamini and Hochberg adjustment for FDR and considered an FDR &lt; 0.05 and PDUI difference &gt; 0.1 as statistical significance. Supplementary Table 13. The Univariate Cox regression analysis of PDUI and overall survival in TCGA COAD/READ cohorts. The association of PDUI for APA events with patient overall survival times Univariate Cox regression analysis in TCGA COAD/READ cohorts. Supplementary Table 14. Difference of A-to-I editing rate between WM_Score-high and WM_Score-low in TCGA COAD/READ cohorts. We used the t test to detect RNA editing sites with differential editing between WM_Score-high and -low groups in TCGA COAD/READ cohorts, and defined significantly differential editing sites as p &lt; 0.05 and difference &gt; 5%. Supplementary Table 15. The Univariate Cox regression analysis of A-to-I editing rate and overall survival in TCGA COAD/READ cohorts. The association of A-to-I editing rate with patient overall survival times Univariate Cox regression analysis in TCGA COAD/READ cohorts. Supplementary Table 16. The association of WM_Score and drug sensitivity in GDSC database. The Spearman correlation of WM_Score and drug sensitivity which quantified by AUC in GDSC database.