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. 2021 May 3;118(19):e2102050118. doi: 10.1073/pnas.2102050118

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Copyright © 2021 the Author(s). Published by PNAS.

This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

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Fig. 5. — Gene signatures of pseudotime clusters closer to the mesenchymal state are associated with worse survival. (A) Schematic of identification of differentially expressed (DE) genes from each cluster and signature enrichment in cancer types based on normalized RNA expression data from TCGA. Cancer cohorts (∼11,000 patients) analyzed were adrenocortical carcinoma (ACC), bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), cervical and endocervical cancers (CESC), cholangiocarcinoma (CHOL), colon cancer (COAD), lymphoid neoplasm diffuse large B cell lymphoma (DLBC), esophageal carcinoma (ESCA), glioblastoma multiforme (GBM), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), acute myeloid leukemia (LAML), brain lower grade glioma (LGG), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), mesothelioma (MESO), ovarian serous cystadenocarcinoma (OV), pancreatic adenocarcinoma (PAAD), pheochromocytoma and paraganglioma (PCPG), prostate adenocarcinoma (PRAD), rectal adenocarcinoma (READ), sarcoma (SARC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), testicular germ cell tumors (TGCT), thyroid carcinoma (THCA), thymoma (THYM), uterine corpus endometrial carcinoma (UCEC), uterine carcinosarcoma (UCS), and uveal melanoma (UVM). (B) Hazard ratios for PFI for TCGA breast cancer cohort (n = 1,092) for patients with each cluster-specific signature. The dashed line indicates hazard ratio 1. (C) Hazard ratios for patients with indicated cancers for each cluster-specific signature. (D) Univariate cox analysis-based hazard ratio observed using PFI data for each cluster in each cancer cohort. (E) Log fold-changes for the cluster C0, C10, and C13 signature genes.