HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas

Lian, Qiuyu; Wang, Shicheng; Zhang, Guchao; Wang, Dongfang; Luo, Guijuan; Tang, Jing; Chen, Lei; Gu, Jin

doi:10.1016/j.gpb.2018.07.003

Cited by 211 publications

(184 citation statements)

References 38 publications

Supporting

Mentioning

178

Contrasting

Order By: Relevance

“…HCCDB (http://lifeome.net/database/hccdb/home.html) is an integrated liver cancer database that currently contains information from multiple open liver cancer datasets and provides information on drugs, proteomics and literature links to third‐party databases, and also graphically display the results of computational analysis, including differential expression analysis, tissue‐specific and tumor‐specific expression analysis, survival analysis and co‐expression analysis. We downloaded liver cancer transcriptome data and clinical information (HCCDB18) from the HCCDB database, grouped according to the expression of SPAG5, performed GSEA analysis, and compared the relationship between SPAG5 expression and liver cancer risk factors, including liver cancer virus infection and alcohol.…”

Section: Methodsmentioning

confidence: 99%

Expression, immune infiltration and clinical significance of SPAG5 in hepatocellular carcinoma: A gene expression‐based study

Chen

et al. 2020

The Journal of Gene Medicine

View full text Add to dashboard Cite

Background Overexpression of sperm‐associated antigen 5 (SPAG5) is a marker of poor prognosis in numerous tumors and is recognized as an index of tumor proliferation; however, its expression in liver cancer remains unclear. Methods The Oncomine (https://www.oncomine.org) and Timer (https://cistrome.shinyapps.io/timer) databases were used to analyze the expression of SPAG5 in liver hepatocellular carcinoma (HCC) and normal liver tissues. The relationship between the expression of SPAG5 and immune infiltration of HCC was investigated using the Timer and GEPIA (http://gepia.cancer‐pku.cn) databases, and the mechanism was analyzed using Gene Set Enrichment Analysis. A Kaplan–Meier Plotter (http://kmplot.com/analysis) was used to evaluate the effect of SPAG5 on the prognosis of patients with HCC. Results The results revealed that the SPAG5 expression level was positively correlated with the infiltration levels of CD8+ T cells, macrophages, neutrophils, and especially B cells and dendritic cells. In addition, SPAG5 expression was significantly associated with T cell exhaustion. The overall survival time, progression‐free survival time, recurrence‐free survival time and disease‐specific survival time were significantly reduced for HCC patients with high SPAG5 expression (p < 0.01) and high expression of SPAG5 was significantly associated with a poor overall survival time and progression‐free survival time of grade and stage II–III HCC (p < 0.05) but not with stage I HCC (p > 0.05). Additionally, the expression of SPAG5 is related to the p53 and cell cycle signal pathways. Conclusions In conclusion, SPAG5 is not only a marker of immune infiltration and poor prognosis, but also a potential therapeutic target for liver cancer.

show abstract

Section: Methodsmentioning

confidence: 99%

Expression, immune infiltration and clinical significance of SPAG5 in hepatocellular carcinoma: A gene expression‐based study

Chen

et al. 2020

The Journal of Gene Medicine

View full text Add to dashboard Cite

show abstract

“…The HCCDB database (http://lifeome.net/database/hccdb) is a free one-stop online resource for exploring HCC gene expression with a user-friendly interface. It includes 15 datasets that cover approximately 4000 clinical samples [13]. Users can analyze the consistently differentially expressed genes across multiple datasets to establish a global differential gene expression landscape of HCC.…”

Section: Hccdbmentioning

confidence: 99%

Identification of CELSR2 as a novel prognostic biomarker for hepatocellular carcinoma

Zhu

et al. 2020

BMC Cancer

View full text Add to dashboard Cite

Background: CELSR2 is postulated to be a receptor involved in contact-mediated communication; however, the specific function of this particular member has not been determined in hepatocellular carcinoma (HCC). Methods: Here, we explored the expression and function of CELSR2 in HCC patients through data mining and examined the results using clinical samples and in vitro experiments. Results: It was found that CELSR2 mRNA and protein expression levels were significantly higher in cancerous tissue than in normal tissue. The increased mRNA expression of CELSR2 was significantly associated with overall survival (OS) in HCC patients. Moreover, the genetic alteration rate of CELSR2 gene in HCC can reach 8%, and these alterations would deeply influence its neighboring genes, then jointly affecting the occurrence and development of tumor through cell adhesion and numerous common carcinogenic pathways. Our in vitro results indicated that the depletion of CELSR2 inhibited liver cancer cell proliferation and invasion. Univariate and multivariate Cox regression analyses showed that CELSR2 could be viewed as an independent risk factor for HCC patients.Conclusions: This study demonstrated that data mining could efficiently reveal the roles of CELSR2 in HCC and its potential regulatory networks. The CELSR2 protein level may serve as a novel prognostic biomarker for HCC.

show abstract

“…The HCCDB (http://lifeome. net/database/hccdb/) (15) is an integrated molecular database of HCC with 15 HCC gene expression datasets including 3,917 samples. The HCCDB includes 13 datasets from the Gene Expression Omnibus database and 2 RNA-seq datasets from TCGA liver hepatocellular carcinoma (LIHC) and the International Cancer Genome Consortium (ICGC) databases to explore the expression levels of GNA14 mRNA in HCC.…”

Section: Integrative Molecular Database Of Hepatocellularmentioning

confidence: 99%

Downregulation of GNA14 in hepatocellular carcinoma indicates an unfavorable prognosis

Tao

Wenjing

2020

Oncol Lett

View full text Add to dashboard Cite

Guanine nucleotide-binding protein subunit α14 (GNA14) knockdown was demonstrated to inhibit the proliferation of endometrial carcinoma cells in a recent study; however, its role in hepatocellular carcinoma (HCC) is unknown. In the present study, the clinical significance of GNA14 in HCC was assessed using a dataset of patients with HCC from The Cancer Genome Atlas database. The Integrative Molecular Database of Hepatocellular Carcinoma and Oncomine databases were also used to identify the expression levels of GNA14 in HCC tissues. The association between GNA14 expression levels and clinicopathological features was assessed using the Wilcoxon signed-rank test and logistic regression analysis. Kaplan-Meier curves and Cox regression analysis were applied to evaluate the independent risk factors for clinical outcomes. The present study determined GNA14 DNA methylation levels and tumor-infiltrating immune cells, as well as used Gene Set Enrichment Analysis (GSEA) in HCC. GNA14 mRNA expression levels were lower in HCC compared with normal tissues. Downregulation of GNA14 in HCC was significantly associated with tumor grade, clinical stage and T stage. Furthermore, low expression of GNA14 was an independent predictor for survival outcomes. GNA14 expression levels were partially correlated with the infiltration of B cells and macrophages. Additionally, GSEA analysis revealed that the expression levels of GNA14 were associated with multiple signaling pathways, such as translation, DNA replication, and homologous recombination.In conclusion, low GNA14 expression may be a novel biomarker for diagnosis and prognosis prediction for patients with HCC.

show abstract

HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas

Cited by 211 publications

References 38 publications

Expression, immune infiltration and clinical significance of SPAG5 in hepatocellular carcinoma: A gene expression‐based study

Expression, immune infiltration and clinical significance of SPAG5 in hepatocellular carcinoma: A gene expression‐based study

Identification of CELSR2 as a novel prognostic biomarker for hepatocellular carcinoma

Downregulation of GNA14 in hepatocellular carcinoma indicates an unfavorable prognosis

Contact Info

Product

Resources

About