A pathology atlas of the human cancer transcriptome.
paper
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- Authors
- Uhlen, Mathias; Zhang, Cheng; Lee, Sunjae; SjΓΆstedt, Evelina; Fagerberg, Linn; Bidkhori, Gholamreza; Benfeitas, Rui; Arif, Muhammad; Liu, Zhengtao; Edfors, Fredrik; Sanli, Kemal; von Feilitzen, Kalle; Oksvold, Per; Lundberg, Emma; Hober, Sophia; Nilsson, Peter; Mattsson, Johanna; Schwenk, Jochen M; BrunnstrΓΆm, Hans; Glimelius, Bengt; SjΓΆblom, Tobias; Edqvist, Per-Henrik; Djureinovic, Dijana; Micke, Patrick; Lindskog, Cecilia; Mardinoglu, Adil; Ponten, Fredrik
- Year
- 2017
- Journal
- Science (New York, N.Y.)
- PMID
- 28818916
- DOI
- 10.1126/science.aan2507
Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.
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| HYENA detects oncogenes activated by distal enhancers in cancer. | Yu A et al. | β | 2024 | β |
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| Identification of modules and key genes associated with breast cancer subtypes through network analysis. | Mares-QuiΓ±ones MD et al. | β | 2024 | β |
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| An immune-related multi-omics analysis of dolichyl-diphosphooligosaccharide protein glycosyltransferase in glioma: Prognostic value exploration and competitive endogenous RNA network identification. | Liu J et al. | β | 2023 | β |
| A novel model based on disulfidptosis-related genes to predict prognosis and therapy of bladder urothelial carcinoma. | Xin S et al. | β | 2023 | β |
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| Anti-cancer pro-inflammatory effects of an IgE antibody targeting the melanoma-associated antigen chondroitin sulfate proteoglycan 4. | Chauhan J et al. | β | 2023 | β |
| Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments. | Nyffeler J et al. | β | 2023 | β |
| A prediction model for prognosis of gastric adenocarcinoma based on six metabolism-related genes. | Zhao J et al. | β | 2023 | β |
| A pyroptosis-related signature in colorectal cancer: exploring its prognostic value and immunological characteristics. | Jiang P et al. | β | 2023 | β |
| Aquaporins and Ion Channels as Dual Targets in the Design of Novel Glioblastoma Therapeutics to Limit Invasiveness. | Varricchio A et al. | β | 2023 | β |
| A real-world data analysis of topotecan in the FDA Adverse Event Reporting System (FAERS) database. | Yang H et al. | β | 2023 | β |
| ARHGAP21 Is Involved in the Carcinogenic Mechanism of Cholangiocarcinoma: A Study Based on Bioinformatic Analyses and Experimental Validation. | Wang Z et al. | β | 2023 | β |
| ARID1A in cancer: Friend or foe? | Fontana B et al. | β | 2023 | β |
| A TRIM21-based bioPROTAC highlights the therapeutic benefit of HuR degradation. | Fletcher A et al. | β | 2023 | β |
| AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation. | Guthrie J et al. | β | 2023 | β |
| Autophagy/Mitophagy Regulated by Ubiquitination: A Promising Pathway in Cancer Therapeutics. | Jee SC et al. | β | 2023 | β |
| BEX2 is poor prognostic factor and required for cancer stemness in gastric cancer. | Yasumoto A et al. | β | 2023 | β |
| Bioinformatic Analysis and Computer-Aided Study to Investigate the Potential Application of a Bioflavonoid Compound Bilobetin in Liver Cancer Treatment. | Zhang C et al. | β | 2023 | β |
| Breast Cancer Prognostic Hub Genes Identified by Integrated Transcriptomic and Weighted Network Analysis: A Road Toward Personalized Medicine. | Singh P et al. | β | 2023 | β |
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| C11-hydroxy and C11-oxo C<sub>19</sub> and C<sub>21</sub> Steroids: Pre-Receptor Regulation and Interaction with Androgen and Progesterone Steroid Receptors. | Gent R et al. | β | 2023 | β |
| CaaX-motif-adjacent residues influence G protein gamma (GΞ³) prenylation under suboptimal conditions. | Tennakoon M et al. | β | 2023 | β |
| CACNA1D overexpression and voltage-gated calcium channels in prostate cancer during androgen deprivation. | McKerr N et al. | β | 2023 | β |
| Cancer: Phosphodiesterase type 4C (PDE4C), the forgotten subfamily as a therapeutic target. | Wright TA et al. | β | 2023 | β |
| CDC25C Protein Expression Correlates with Tumor Differentiation and Clinical Outcomes in Lung Adenocarcinoma. | Stern E et al. | β | 2023 | β |
| CDKAL1 Drives the Maintenance of Cancer Stem-Like Cells by Assembling the eIF4F Translation Initiation Complex. | Huang R et al. | β | 2023 | β |
| CDKN1A/p21 in Breast Cancer: Part of the Problem, or Part of the Solution? | Manousakis E et al. | β | 2023 | β |
| Celecoxib Suppresses NF-ΞΊB p65 (RelA) and TNFΞ± Expression Signaling in Glioblastoma. | Ahsan H et al. | β | 2023 | β |
| Cellular functions of heat shock protein 20 (HSPB6) in cancer: A review. | Wu Y et al. | β | 2023 | β |
| Changes in Nucleolin Expression during Malignant Transformation Leading to Ovarian High-Grade Serous Carcinoma. | Paris EA et al. | β | 2023 | β |
| Changes of immune microenvironment in head and neck squamous cell carcinoma in 3D-4-culture compared to 2D-4-culture. | Xiao J et al. | β | 2023 | β |
| Characteristics of ABCC4 and ABCG2 High Expression Subpopulations in CRC-A New Opportunity to Predict Therapy Response. | Kryczka J et al. | β | 2023 | β |
| CHEK2 is a potential prognostic biomarker associated with immune infiltration in clear cell renal cell carcinoma. | Wu Q et al. | β | 2023 | β |
| Chitinase-like proteins promoting tumorigenesis through disruption of cell polarity <i>via</i> enlarged endosomal vesicles. | Khalili D et al. | β | 2023 | β |
| Chloroquine induces transitory attenuation of proliferation of human lung cancer cells through regulation of mutant P53 and YAP. | Saini H et al. | β | 2023 | β |
| Clear cell renal cell carcinoma molecular variations in non-Hispanic White and Hispanic patients. | Batai K et al. | β | 2023 | β |
| c-Myc-IMPDH1/2 axis promotes tumourigenesis by regulating GTP metabolic reprogramming. | Zhang Q et al. | β | 2023 | β |
| Co-chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta. | KΓΆrschgen H et al. | β | 2023 | β |
| Combination therapy with bevacizumab and a CCR2 inhibitor for human ovarian cancer: An in vivo validation study. | Zhai T et al. | β | 2023 | β |
| COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. | Bessell B et al. | β | 2023 | β |
| Comprehensive analysis, immune, and cordycepin regulation for SOX9 expression in pan-cancers and the matched healthy tissues. | Liu S et al. | β | 2023 | β |
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| Comprehensive landscape of the miRNA-regulated prognostic marker LAYN with immune infiltration and stemness in pan-cancer. | Jiawen W et al. | β | 2023 | β |
| Comprehensive multiomics and in silico approach uncovers prognostic, immunological, and therapeutic roles of ANLN in lung adenocarcinoma. | Singh P et al. | β | 2023 | β |
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| Copper homeostasis-associated gene PRNP regulates ferroptosis and immune infiltration in breast cancer. | Lin C et al. | β | 2023 | β |
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| CSNK2B modulates IRF1 binding to functional DNA elements and promotes basal and agonist-induced antiviral signaling. | Matsumoto M et al. | β | 2023 | β |
| Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy. | Stanojevic A et al. | β | 2023 | β |
| Data mining identifies novel RNA-binding proteins involved in colon and rectal carcinomas. | GarcΓa-CΓ‘rdenas JM et al. | β | 2023 | β |
| DDX43 mRNA expression and protein levels in relation to clinicopathological profile of breast cancer. | Amer NN et al. | β | 2023 | β |
| Delineating highly transcribed noncoding elements landscape in breast cancer. | Zhu W et al. | β | 2023 | β |
| DEPDC1B-mediated USP5 deubiquitination of Ξ²-catenin promotes breast cancer metastasis by activating the wnt/Ξ²-catenin pathway. | Wang Q et al. | β | 2023 | β |
| Dependency of Tamoxifen Sensitive and Resistant ER<sup>+</sup> Breast Cancer Cells on Semaphorin 3C (SEMA3C) for Growth. | Bhasin S et al. | β | 2023 | β |
| Development of a sandwich ELISA to detect circulating, soluble IRAP as a potential disease biomarker. | Vear A et al. | β | 2023 | β |
| Diagnostic and Prognostic Profiling of Nucleocytoplasmic Shuttling Genes in Hepatocellular Carcinoma. | Herceg S et al. | β | 2023 | β |
| Diagnostic, prognostic, and immunological roles of CD177 in cervical cancer. | Liao W et al. | β | 2023 | β |
| Differential Activation of NRF2 Signaling Pathway in Renal-Cell Carcinoma Caki Cell Lines. | Hitefield NL et al. | β | 2023 | β |
| Differential co-expression network analysis elucidated genes associated with sensitivity to farnesyltransferase inhibitor and prognosis of acute myeloid leukemia. | Kelesoglu N et al. | β | 2023 | β |
| Digital spatial profiling of intraductal papillary mucinous neoplasms: Toward a molecular framework for risk stratification. | Iyer MK et al. | β | 2023 | β |
| Discovery of two new isoforms of the human DUT gene. | RΓ‘cz GA et al. | β | 2023 | β |
| Downregulation of Glycine N-Acyltransferase in Kidney Renal Clear Cell Carcinoma: A Bioinformatic-Based Screening. | MuΓ±oz JP et al. | β | 2023 | β |
| DSCC1 interacts with HSP90AB1 and promotes the progression of lung adenocarcinoma via regulating ER stress. | Lin X et al. | β | 2023 | β |
| Dual Blockade of EP2 and EP4 Signaling is Required for Optimal Immune Activation and Antitumor Activity Against Prostaglandin-Expressing Tumors. | Francica BJ et al. | β | 2023 | β |
| Dynein-Powered Cell Locomotion Guides Metastasis of Breast Cancer. | Tagay Y et al. | β | 2023 | β |
| Dysregulation of core neurodevelopmental pathways-a common feature of cancers with perineural invasion. | GonzΓ‘lez-CastrillΓ³n LM et al. | β | 2023 | β |
| Early-life origin of prostate cancer through deregulation of miR-206 networks in maternally malnourished offspring rats. | Portela LMF et al. | β | 2023 | β |
| Eculizumab treatment alters the proteometabolome beyond the inhibition of complement. | Nelke C et al. | β | 2023 | β |
| Effectively utilizing publicly available databases for cancer target evaluation. | Croft D et al. | β | 2023 | β |
| Effect of DPP4/CD26 expression on SARSβCoVβ2 susceptibility, immune response, adenosine (derivatives m<sup>6</sup><sub>2</sub>A and CD) regulations on patients with cancer and healthy individuals. | Du J et al. | β | 2023 | β |
| Effects of SMC1A on immune microenvironment and cancer stem cells in colon adenocarcinoma. | Li J et al. | β | 2023 | β |
| Elucidating Novel Targets for Ovarian Cancer Antibody-Drug Conjugate Development: Integrating In Silico Prediction and Surface Plasmon Resonance to Identify Targets with Enhanced Antibody Internalization Capacity. | Onyido EK et al. | β | 2023 | β |
| Emerging peptide therapeutics for the treatment of ovarian cancer. | Veneziani AC et al. | β | 2023 | β |
| EMP1 as a Potential Biomarker in Liver Fibrosis: A Bioinformatics Analysis. | Chen X et al. | β | 2023 | β |
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| Estimating copy number to determine BRCA2 deletion status and to expect prognosis in localized prostate cancer. | Nukaya T et al. | β | 2023 | β |
| Estradiol and Estrone Have Different Biological Functions to Induce NF-ΞΊB-Driven Inflammation, EMT and Stemness in ER+ Cancer Cells. | Diaz-Ruano AB et al. | β | 2023 | β |
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| Experimental Murine Models for Colorectal Cancer Research. | Neto Γ et al. | β | 2023 | β |
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| FAM83H Expression Is Associated with Tumor-Infiltrating PD1-Positive Lymphocytes and Predicts the Survival of Breast Carcinoma Patients. | Choi JE et al. | β | 2023 | β |
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| Finding miRNA-RNA Network Biomarkers for Predicting Metastasis and Prognosis in Cancer. | Lee S et al. | β | 2023 | β |
| Five Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma. | Liu Y et al. | β | 2023 | β |
| Folate receptor alpha in ovarian cancer tissue and patient serum is associated with disease burden and treatment outcomes. | Bax HJ et al. | β | 2023 | β |
| Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins. | Llobet MO et al. | β | 2023 | β |
| Functional Assessment of Cancer-Linked Mutations in Sensitive Regions of Regulators of G Protein Signaling Predicted by Three-Dimensional Missense Tolerance Ratio Analysis. | MontaΓ±ez-Miranda C et al. | β | 2023 | β |
| Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management. | Melone V et al. | β | 2023 | β |
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| GBA Regulates EMT/MET and Chemoresistance in Squamous Cell Carcinoma Cells by Modulating the Cellular Glycosphingolipid Profile. | Clark LE et al. | β | 2023 | β |
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| High Expression of COA6 Is Related to Unfavorable Prognosis and Enhanced Oxidative Phosphorylation in Lung Adenocarcinoma. | Zhang M et al. | β | 2023 | β |
| High expression of IL4I1 is correlated with poor prognosis and immune infiltration in thyroid cancer. | Zhu L et al. | β | 2023 | β |
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| High Level of GMFG Correlated to Poor Clinical Outcome and Promoted Cell Migration and Invasion through EMT Pathway in Triple-Negative Breast Cancer. | Zhao Y et al. | β | 2023 | β |
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| Histone Demethylation Profiles in Nonalcoholic Fatty Liver Disease and Prognostic Values in Hepatocellular Carcinoma: A Bioinformatic Analysis. | Liu Y et al. | β | 2023 | β |
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| Identification and validation of a novel cuproptosis-related gene signature in multiple myeloma. | Zhang B et al. | β | 2023 | β |
| Identification and Validation of Cyclin A2 and Cyclin E2 as Potential Biomarkers in Small Cell Lung Cancer. | Zhang X et al. | β | 2023 | β |
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| Identification of a NACC1-Regulated Gene Signature Implicated in the Features of Triple-Negative Breast Cancer. | Ngule CM et al. | β | 2023 | β |
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| Identification of ferroptosis-associated biomarkers in Stanford type A aortic dissection based on machine learning. | Pan H et al. | β | 2023 | β |
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| <i>MKX-AS1</i> Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients. | Gonzalez RD et al. | β | 2023 | β |
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| Increased Neuromedin B is Associated with a Favorable Prognosis in Glioblastoma. | Li S et al. | β | 2023 | β |
| Indacaterol inhibits collective cell migration and IGDQ-mediated single cell migration in metastatic breast cancer MDA-MB-231 cells. | Ayama-Canden S et al. | β | 2023 | β |
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| Integrated analyzes identify CCT3 as a modulator to shape immunosuppressive tumor microenvironment in lung adenocarcinoma. | Huang J et al. | β | 2023 | β |
| Integrated multi-omics analysis reveals the molecular interplay between circadian clocks and cancer pathogenesis. | PΓ©rez-Villa A et al. | β | 2023 | β |
| Integrated single-cell and bulk RNA sequencing revealed the molecular characteristics and prognostic roles of neutrophils in pancreatic cancer. | Zhang B et al. | β | 2023 | β |
| Integrative analysis of histone acetyltransferase KAT2A in human cancer. | Li H et al. | β | 2023 | β |
| Interleukin-34 and immune checkpoint inhibitors: Unified weapons against cancer. | Alshaebi F et al. | β | 2023 | β |
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| Ion channel gene <i>GJB2</i> influences the intercellular communication by Up-regulating the SPP1 signaling pathway identified by the single-cell RNA sequencing in lung adenocarcinoma. | Liu Z et al. | β | 2023 | β |
| <i>PIWIL1</i> gene polymorphism and pediatric acute lymphoblastic leukemia relapse susceptibility among Chinese children: a five-center case-control study. | Ding W et al. | β | 2023 | β |
| <i>PTRH2</i> Gene Variants: Recent Review of the Phenotypic Features and Their Bioinformatics Analysis. | Sharkia R et al. | β | 2023 | β |
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| Metabolism as a New Avenue for Hepatocellular Carcinoma Therapy. | Gnocchi D et al. | β | 2023 | β |
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| MicroRNA-155-5p Targets JADE-1, Promoting Proliferation, Migration, and Invasion in Clear Cell Renal Cell Carcinoma Cells. | Kalantzakos T et al. | β | 2023 | β |
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| Mortalin: Protein partners, biological impacts, pathological roles, and therapeutic opportunities. | Esfahanian N et al. | β | 2023 | β |
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| Multi-omics and experimental analysis unveil theragnostic value and immunological roles of inner membrane mitochondrial protein (IMMT) in breast cancer. | Lin HY et al. | β | 2023 | β |
| Myocardial Fibrosis and Cardiomyopathy Risk: A Genetic Link in the MESA. | Shabani M et al. | β | 2023 | β |
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