ArticleTranslational cancer research2020
Collagen family genes and related genes might be associated with prognosis of patients with gastric cancer: an integrated bioinformatics analysis and experimental validation.
Article in Translational cancer research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 19 citations in OpenAlex.
- Comprehensive analysis of the expression, prognostic, and immune infiltration for COL4s in stomach adenocarcinoma.BMC medical genomics · 2024Article
- Exploring the impact of TGF-β family gene mutations and expression on skin wound healing and tissue repair.International wound journal · 2024Article
- Large-Scale Machine Learning Analysis Reveals DNA Methylation and Gene Expression Response Signatures for Gemcitabine-Treated Pancreatic Cancer.Health data science · 2024Article
- Uneven Expression of 20 Human Papillomavirus Genes Associated with Oropharyngeal Carcinoma.Rambam Maimonides medical journal · 2023Article
- Jian Yun Qing Hua Decoction inhibits malignant behaviors of gastric carcinoma cells via COL12A1 mediated ferroptosis signal pathway.Chinese medicine · 2023Article
- ENTPD1-AS1-miR-144-3p-mediated high expression ofWorld journal of gastrointestinal oncology · 2023Article
- Galectin-1 promotes gastric cancer peritoneal metastasis through peritoneal fibrosis.BMC cancer · 2023Article
- Hub genes and pathways in gastric cancer: A comparison between studies that used normal tissues adjacent to the tumour and studies that used healthy tissues as calibrator.IET systems biology · 2023Article
- Collagen Family as Promising Biomarkers and Therapeutic Targets in Cancer.International journal of molecular sciences · 2022Review
- Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer.American journal of cancer research · 2022Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGastric cancer (GC) is disease with a high morbidity. The purpose of this study was to identify genes essential to GC development in patients and to reveal the underlying mechanisms of progression.
methodsBioinformatics analysis is an effective tool for discovering essential genes of different disease states. We used the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs), the DAVID online tool to perform Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs, the STRING database to construct the protein-protein interaction (PPI) network of DEGs, the Oncomine and the Cancer Genome Atlas-Stomach Adenocarcinoma (TCGA-STAD) databases to analyze the gene expression differences, the Human pan-Cancer Methylation database (MethHC) to compare the DNA methylation of genes, and the Kaplan-Meier plotter to show the survival analysis of DEGs. We performed Real-Time quantitative PCR (RT-qPCR) experiment to confirm our analysis results.
resultsAfter the integration of four Gene Expression Series (GSEs), we identified 407 DEGs. GO and KEGG pathway analysis indicated that the upregulated DEGs were significantly enriched in Extracellular Matrix (ECM) related functions and pathways. The main DEGs were collagens (COLs). Moreover, the downregulated DEGs were enriched in ethanol oxidation. Several groups of DEGs, such as insulin-like growth factor binding protein (IGFBP), collagen (COL) and serpin peptidase inhibitors (SERPIN) gene families, constituted several PPI networks. In the Oncomine database, all of the collagen genes were highly expressed in breast cancer, esophageal cancer, GC, head and neck cancer and pancreatic cancer, compared with normal tissues. Consistently, from the TCGA-STAD database, most of the collagens (COLs) were highly expressed and exhibited methylated variation in GC patients. In GC patients, some of these collagen (COL) genes related to worse prognosis, as evidenced by the results from the Kaplan-Meier plotter database analysis. Our RT-qPCR results showed that collagen type III α1 chain (COL3A1) was highly expressed in GC cells. Collagen type V α1 chain (COL5A1) was highly expressed, except in AGS cells, which was consistent with our analysis.
conclusionsCollagen (COL) family genes might serve as progression and prognosis markers of GC.
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