Identification of hub genes and functional modules in colon adenocarcinoma based on public databases by bioinformatics analysis

Zhang, Zhipeng; Luo, Aihong; Zeng, Zhijun; Zhou, Yikai; Wu, Wei

doi:10.21037/jgo-21-415

Cited by 3 publications

(1 citation statement)

References 39 publications

(34 reference statements)

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“…The genes co-expressed with SH2D1A were obtained using correlation analysis and were defined as genes whose expression was strongly correlated with that of SH2D1A (a correlation coefficient of 0.4 and P < 0.001) [ 2 , 8 ]. The gene ontology annotations include biological processes, molecular functions, and cellular components [ 9 ]. The functions and pathways associated with the 567 co-expressed genes of SH2D1A were identified through gene ontology (GO) and KEGG analysis, and the filtering standard was set to adjusted P < 0.05.…”

Section: Methodsmentioning

confidence: 99%

Overexpression of SH2D1A promotes cancer progression and is associated with immune cell infiltration in hepatocellular carcinoma via bioinformatics and in vitro study

Xiang,

Jiang,

Liu

et al. 2023

BMC Cancer

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Background SH2 domain containing 1A (SH2D1A) expression has been linked to cancer progression. However, the functions of SH2D1A in hepatocellular carcinoma (HCC) have not been reported. Methods The effects of SH2D1A on the proliferation, migration, and invasion of HCC cells and the related pathways were re-explored in cell models with SH2D1A overexpression using the CCK-8, migration and invasion assays and western blotting. The functions and mechanisms of genes co-expressed with SH2D1A were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The relationship between SH2D1A expression and immune microenvironment features in HCC was explored. Results Elevated SH2D1A expression promoted cell proliferation, migration, and invasion, which was related to the overexpression of p-Nf-κB and BCL2A1 protein levels in HCC. SH2D1A expression was related to the immune, stromal, and ESTIMATE scores, and the abundance of immune cells, such as B cells, CD8+ T cells, and T cells. SH2D1A expression was significantly related to the expression of immune cell markers, such as PDCD1, CD8A, and CTLA4 in HCC. Conclusion SH2D1A overexpression was found to promote cell growth and metastasis via the Nf-κB signaling pathway and may be related to the immune microenvironment in HCC. The findings indicate that SH2D1A can function as a biomarker in HCC.

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Section: Methodsmentioning

confidence: 99%

Overexpression of SH2D1A promotes cancer progression and is associated with immune cell infiltration in hepatocellular carcinoma via bioinformatics and in vitro study

Xiang,

Jiang,

Liu

et al. 2023

BMC Cancer

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Prognosis-related metabolic genes in the development of colorectal cancer progress and perspective

Miao

Quan

Dong

et al. 2023

Gene

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Gradient boosting reveals spatially diverse cholesterol gene signatures in colon cancer

Yang,

Chatterjee,

Couetil

et al. 2024

Front. Genet.

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Colon cancer (CC) is the second most common cause of cancer deaths and the fourth most prevalent cancer in the United States. Recently cholesterol metabolism has been identified as a potential therapeutic avenue due to its consistent association with tumor treatment effects and overall prognosis. We conducted differential gene analysis and KEGG pathway analysis on paired tumor and adjacent-normal samples from the TCGA Colon Adenocarcinoma project, identifying that bile secretion was the only significantly downregulated pathway. To evaluate the relationship between cholesterol metabolism and CC prognosis, we used the genes from this pathway in several statistical models like Cox proportional Hazard (CPH), Random Forest (RF), Lasso Regression (LR), and the eXtreme Gradient Boosting (XGBoost) to identify the genes which contributed highly to the predictive ability of all models, ADCY5, and SLC2A1. We demonstrate that using cholesterol metabolism genes with XGBoost models improves stratification of CC patients into low and high-risk groups compared with traditional CPH, RF and LR models. Spatial transcriptomics (ST) revealed that SLC2A1 (glucose transporter 1, GLUT1) colocalized with small blood vessels. ADCY5 localized to stromal regions in both the ST and protein immunohistochemistry. Interestingly, both these significant genes are expressed in tissues other than the tumor itself, highlighting the complex interplay between the tumor and microenvironment, and that druggable targets may be found in the ability to modify how “normal” tissue interacts with tumors.

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Identification of hub genes and functional modules in colon adenocarcinoma based on public databases by bioinformatics analysis

Cited by 3 publications

References 39 publications

Overexpression of SH2D1A promotes cancer progression and is associated with immune cell infiltration in hepatocellular carcinoma via bioinformatics and in vitro study

Overexpression of SH2D1A promotes cancer progression and is associated with immune cell infiltration in hepatocellular carcinoma via bioinformatics and in vitro study

Prognosis-related metabolic genes in the development of colorectal cancer progress and perspective

Gradient boosting reveals spatially diverse cholesterol gene signatures in colon cancer

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