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Fig. 1 | BMC Cancer

Fig. 1

From: An integrative pan-cancer investigation reveals common genetic and transcriptional alterations of AMPK pathway genes as important predictors of clinical outcomes across major cancer types

Fig. 1

The landscape of somatic copy number alterations of AMPK pathway genes. Heatmaps depict (a) fraction of samples within each cancer type that harbor somatic deletions and (b) somatic amplifications. Forty-nine genes are recurrently deleted in at least 20% of tumors within each cancer and in at least seven cancer types. Forty-six genes are recurrently amplified in at least 20% of tumors within each cancer and in at least seven cancer types. Stacked bar charts on the y-axes illustrate the fraction of samples that possess copy number variation of a gene under consideration grouped by shallow and deep deletions or amplifications. Stacked bar charts on the x-axes illustrate the fraction of samples within each cancer type that contain shallow and deep deletions or amplifications. The bar charts on the right of each heatmap depict the number of cancer types with at least 20% of samples affected by gene deletions and amplifications. The Venn diagrams demonstrate the identification of 24 putative loss- and seven gain-of-function genes from gene sets that are somatically altered and differentially expressed. Cancer cohorts analyzed with corresponding TCGA abbreviations are listed in parentheses: bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), esophageal carcinoma (ESCA), glioblastoma multiforme (GBM), glioma (GBMLGG), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), pan-kidney cohort (KIPAN), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), stomach adenocarcinoma (STAD), stomach and esophageal carcinoma (STES) and uterine corpus endometrial carcinoma (UCEC). Number of samples for each cancer type are indicated in parentheses: BLCA (408), BRCA (10939), CESC (304), CHOL (36), COAD (285), ESCA (184), GBM (153), GBMLGG (669), HNSC (520), KICH (66), KIPAN (889), KIRC (533), KIRP (290), LIHC (371), LUAD (515), LUSC (501), PAAD (178), SARC (259), STAD (415), STES (599) and UCEC (370)

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