Mining the Biomarkers and Associated-Drugs for Esophageal Squamous Cell Carcinoma by Bioinformatic Methods

Kuang, Xiuying; Liu, Zhihui

doi:10.1620/tjem.256.27

Cited by 2 publications

(2 citation statements)

References 41 publications

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“…6B ), supporting its role in the development of esophageal lesions. The function of A2ML1 in tissues with mucosal squamous epithelia is unknown, although gene expression has been shown to be downregulated in squamous cell carcinoma of the esophagus ( 58 ). In addition, the protein ALDH3A1 is one of the main proteins in cornea which plays a protective role against oxidative stress, including UV-induced oxidative stress ( 59 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide single cell annotation of the human protein-coding genes

Karlsson

Álvez

Shi

et al. 2022

Preprint

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An important quest for the life science community is to deliver a complete annotation of the human building-blocks of life, the genes and the proteins. Here, we report on a genome-wide effort to annotate all protein-coding genes based on single cell transcriptomics data representing all major tissues and organs in the human body, integrated with data from bulk transcriptomics and antibody-based tissue profiling. Altogether, 25 tissues have been analyzed with single cell transcriptomics resulting in genome-wide expression in 444 single cell types using a strategy involving pooling data from individual cells to obtain genome-wide expression profiles of individual cell type. We introduce a new genome-wide classification tool based on clustering of similar expression profiles across single cell types, which can be visualized using dimensional reduction maps (UMAP). The clustering classification is integrated with a new “tau” score classification for all protein-coding genes, resulting in a measure of single cell specificity across all cell types for all individual genes. The analysis has allowed us to annotate all human protein-coding genes with regards to function and spatial distribution across individual cell types across all major tissues and organs in the human body. A new version of the open access Human Protein Atlas (www.proteinatlas.org) has been launched to enable researchers to explore the new genome-wide annotation on an individual gene level.

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Section: Resultsmentioning

confidence: 99%

Genome-wide single cell annotation of the human protein-coding genes

Karlsson

Álvez

Shi

et al. 2022

Preprint

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“…To investigate the connection between CRC and hypercholesterolemia, 13 common targets were selected for further analysis through GO and KEGG pathway enrichment studies. GO mainly comprises three parts, including biological process (BP), cellular component (CC), and molecular function (MF) (Kuang and Liu 2022). In BP, the G-protein coupled receptor signaling pathway, signal transduction, inflammatory response, immune response, and negative regulation of gene expression were enriched.…”

Section: Discussionmentioning

confidence: 99%

Identification of EDNRA as the Key Biomarker for Hypercholesterolemia and Colorectal Cancer

Han,

He,

Liu

et al. 2024

Tohoku J. Exp. Med.

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Some studies have investigated the role of cholesterol in the progression of colorectal cancer (CRC). However, the underlying mechanism of action is not clear. In this study, we used bioinformatics tools to elucidate the molecular mechanisms involved. We initially obtained CRC datasets from the Gene Expression Omnibus (GEO) database and hypercholesterolemia data from GeneCards and DisGeNE. Common differentially expressed genes (DEGs) were determined by using Venn diagram web tools. Next, we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The hub gene was identified through common expression pattern analysis and survival analysis. Finally, we conducted an immune regulatory point analysis and predicted target drugs based on the hub gene. The results of our analysis revealed 13 common DEGs, with endothelin receptor type A (EDNRA) identified as the hub gene linking hypercholesterolemia and CRC. The results of the GO analysis showed that the common DEGs were primarily associated with the Gprotein coupled receptor signaling pathway, extracellular space, and receptor binding.The results of the KEGG pathway enrichment analysis indicated enrichment in pathways related to cancer and the phospholipase D signaling pathway. Additionally, we identified potential target drugs, including Podocarpus montanus, Diospyros kaki, Herba Salviae japoniae, sitaxentan, and ambrisentan. We found that EDNRA might be an underlying biomarker for both hypercholesterolemia and CRC. The predicted target drugs provide new strategies for treating CRC.

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Mining the Biomarkers and Associated-Drugs for Esophageal Squamous Cell Carcinoma by Bioinformatic Methods

Cited by 2 publications

References 41 publications

Genome-wide single cell annotation of the human protein-coding genes

Genome-wide single cell annotation of the human protein-coding genes

Identification of EDNRA as the Key Biomarker for Hypercholesterolemia and Colorectal Cancer

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