CancerSCEM: a database of single-cell expression map across various human cancers

Zeng, Jingyao; Zhang, Yadong; Shang, Yunfei; Mai, Jialin; Shi, Shuo; Lu, Mingming; Bu, Congfan; Zhang, Zhewen; Zhang, Zaichao; Li, Yang; Du, Zhenglin; Xiao, Jingfa

doi:10.1093/nar/gkab905

Cited by 80 publications

(54 citation statements)

References 65 publications

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“…Cell types were identified by the markers compared with information in the CellMarker database ( http://biocc.hrbmu.edu.cn/CellMarker/index.jsp ) ( Satija et al, 2015 ; Zhang et al, 2019b ). Single-cell RNA-seq analysis of ovarian carcinoma was performed by the CancerSCEM database (Cancer Single-cell Expression Map database) ( Zeng et al, 2021 ). We applied the E-MTAB-8559 dataset for further analysis ( Nelson et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem Cells

Yao

et al. 2022

Front. Cell Dev. Biol.

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Abnormal activation of protein kinases and phosphatases is implicated in various tumorigenesis, including hepatocellular carcinoma (HCC). Advanced HCC patients are treated with systemic therapy, including tyrosine kinase inhibitors, which extend overall survival. Investigation of the underlying mechanism of protein kinase signaling will help to improve the efficacy of HCC therapy. Combining single-cell RNA sequencing data and TCGA RNA-seq data, we profiled the protein kinases, phosphatases, and other phosphorylation-related genes (PRGs) of HCC patients in this study. We found nine protein kinases and PRGs with high expression levels that were mainly detected in HCC cancer stem cells, including POLR2G, PPP2R1A, POLR2L, PRC1, ITBG1BP1, MARCKSL1, EZH2, DTYMK, and AURKA. Survival analysis with the TCGA dataset showed that these genes were associated with poor prognosis of HCC patients. Further correlation analysis showed that these genes were involved in cell cycle-related pathways that may contribute to the development of HCC. Among them, AURKA and EZH2 were identified as two hub genes by Ingenuity Pathway Analysis. Treatment with an AURKA inhibitor (alisertib) and an EZH2 inhibitor (gambogenic) inhibited HCC cell proliferation, migration, and invasion. We also found that both AURKA and EZH2 were highly expressed in TP53-mutant HCC samples. Our comprehensive analysis of PRGs contributes to illustrating the mechanisms underlying HCC progression and identifying potential therapeutic targets for future clinical trials.

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Section: Methodsmentioning

confidence: 99%

Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem Cells

Yao

et al. 2022

Front. Cell Dev. Biol.

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“…A myriad of analytical options maximise the data's value in, for example, biomarker discovery and understanding drug resistance mechanisms. Other new cancer-related databases include CancerMIRNome ( 93 ) that covers miRNAs in cancer cells and offers particularly rich analytical options; CancerSCEM ( 94 ) that offers similarly diverse options for studying single cancer cell gene expression data; GPEdit ( 95 ) which links A-to-I RNA editing in cancer cells to pharmacogenomic responses and patient survival; and OncoDB ( 96 ), which focuses on the contributions of gene expression dysregulation and viral infection to cancer development and progression. This year also sees Update papers from two major general resources in drug design.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

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“…The R package “GSVA” in the R software was used to determine the correlation between CDK1 expression and infiltration of 24 common immune cells in tumors of the TCGA dataset by single-sample GESA (ssGESA) [ 27 , 28 ]. Cellular heterogeneity of CDK1 expression in tumors was conducted using Cancer Single-cell Expression Map ( , last accessed on 30 April 2022) [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

An Integrative Human Pan-Cancer Analysis of Cyclin-Dependent Kinase 1 (CDK1)

Liu

2022

Cancers

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Cyclin-dependent kinase 1 (CDK1) is essential for cell division by regulating the G2/M phase and mitosis. CDK1 overexpression can also promote the development and progression of a variety of cancers. However, the significance of CDK1 in the formation, progression, and prognosis of human pan-cancer remains unclear. In the present study, we used The Cancer Genome Atlas database, Clinical Proteomic Tumor Analysis Consortium, Human Protein Atlas, Genotype-Tissue Expression, and other well-established databases to comprehensively examine CDK1 genetic alterations and gene/protein expression in various cancers and their relationships with the prognosis, immune reactivities, and clinical outcomes for 33 tumor types. Gene set enrichment analysis was also conducted to examine the potential mechanisms of CDK1 in tumorigenesis. The data showed that CDK1 mutation was frequently present in multiple tumors. CDK1 expression was significantly increased in various types of tumors as compared with normal tissues and was associated with poor overall and disease-free survival. In addition, CDK1 expression was significantly correlated with oncogenic genes, proteins, cellular components, myeloid-derived suppressor cell infiltration, ESTMATEScore, and signaling pathways associated with tumor development and progression and tumor microenvironments. These data indicate that CDK1 could serve as a promising biomarker for predicting tumor prognosis and a potential target for cancer treatment.

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CancerSCEM: a database of single-cell expression map across various human cancers

Cited by 80 publications

References 65 publications

Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem Cells

Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem Cells

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

An Integrative Human Pan-Cancer Analysis of Cyclin-Dependent Kinase 1 (CDK1)

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