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Fig. 4 | Genome Biology

Fig. 4

From: Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

Fig. 4

Expression analysis of RMPs in human tumor-normal paired samples. a Heatmap of z-scaled dysregulation scores of RMPs in tumor-normal paired samples, across 28 cancer types. Positive (red) values indicate upregulation in tumor samples, whereas negative (blue) values indicate downregulation. Genes labeled as red (upregulated) and blue (downregulated) represent top significantly dysregulated genes, which are also individually listed in panel c. b Scatter plot comparing RMP expression levels of matched tumor-normal samples, for the following cancer types: LAML (acute myeloid leukemia) and UCS (uterine carcinosarcoma) BRCA (breast invasive carcinoma) and KIRP (kidney renal papillary cell carcinoma). Values represent median log(TPM) across all patients. Black data points indicate the expression of RMPs, where dysregulated genes are highlighted in red (upregulated) or blue (downregulated). Non-RMP genes are depicted in gray. c Barplot illustrates the number of cancer types in which significantly dysregulated genes are highlighted in red (upregulated) or blue (downregulated). Only RMPs that are dysregulated in more than 2 cancer types are shown. For the full list of dysregulated RMPs, see TableĀ 1. d Boxplots of log(TPM) mRNA expression values of HENMT1 (upper panel) and LAGE3 (bottom panel) across all 28 cancer types analyzed in this work. Green box plots represent normal samples, whereas red box plots represent tumor samples. Tumor-normal pairs highlighted in cyan represent cancer types in which the RMP is significantly downregulated, whereas those highlighted in orange represent those cancer types in which the RMP is upregulated. Error bars represent standard deviation of mRNA expression levels across patients. Each data point represents a different patient sample. Abbreviations: ACC (adrenocortical carcinoma), BLCA (bladder urothelial carcinoma), BRCA (breast invasive carcinoma), CESC (cervical squamous cell carcinoma and endocervical adenocarcinoma), COAD (colon adenocarcinoma), ESCA (esophageal carcinoma), GBM (glioblastoma multiforme), HNSC (head and neck squamous cell carcinoma), KICH (kidney chromophobe), KIRC (kidney renal clear cell carcinoma), KIRP (kidney renal papillary cell carcinoma), LAML (acute myeloid leukemia), LGG (brain lower-grade glioma), LIHC (liver hepatocellular carcinoma), LUAD (lung adenocarcinoma), LUSC (lung squamous cell carcinoma), OV (ovarian serous cystadenocarcinoma), PAAD (pancreatic adenocarcinoma), PCPG (pheochromocytoma and paraganglioma), PRAD (prostate adenocarcinoma), READ (rectum adenocarcinoma), SARC (sarcoma), SKCM (skin cutaneous melanoma), STAD (stomach adenocarcinoma), TGCT (testicular germ cell tumors), THCA (thyroid carcinoma), UCEC (uterine corpus endometrial carcinoma), UCS (uterine carcinosarcoma)

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