PrognoScan: a new database for meta-analysis of the prognostic value of genes

Mizuno, Hideaki; Kitada, Koji; Nakai, Katsunori; Sarai, Akinori

doi:10.1186/1755-8794-2-18

Cited by 826 publications

(811 citation statements)

References 59 publications

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“…Univariate and multivariate analyses were used to determine patient prognosis and were performed by Cox regression analysis with a backward stepwise model. Based on the levels of ZNF750 mRNA expression in the Kyushu and the TCGA datasets, patients were divided into two groups using the minimum P-value approach, a comprehensive method that determines the optimal risk separation cutoff point in continuous gene expression measurement (19). The cutoff values for high and low ZNF750 expression groups were 8.34 (ZNF750/GAPDH expression) in the Kyushu dataset and 2.75 (log2 expression) in the TCGA dataset.…”

Section: Cancer Cell Line Encyclopedia (Ccle) Data Analysismentioning

confidence: 99%

Clinical significance of ZNF750 gene expression, a novel tumor suppressor gene, in esophageal squamous cell carcinoma

et al. 2017

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Abstract. The present authors previously identified a novel candidate tumor suppressor gene, zinc finger protein 750 (ZNF750), in esophageal squamous cell carcinoma (ESCC) (1). The present study aimed to clarify the clinical significance of ZNF750 expression in ESCC. The association between ZNF750 DNA mutation status and the mRNA expression was examined by whole exome sequence analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR). The expression of ZNF750 in 76 patients with ESCC (Kyushu University Beppu Hospital) was measured using immunohistochemistry and RT-qPCR. Using this dataset, the association between ZNF750 mRNA expression and clinicopathological factors was examined. Additionally, survival analysis was performed using datasets from the Kyushu University Beppu Hospital and The Cancer Genome Atlas (TCGA). The biological effects of ZNF750 expression were explored using gene set enrichment analysis (GSEA) and were validated using datasets from the Cancer Cell Line Encyclopedia (CCLE) and the Kyushu University Beppu Hospital. ZNF750 expression analyses demonstrated that ZNF750 mRNA expression was lower in patients with the DNA mutations compared with those without the mutations (P<0.05), and ZNF750 expression was downregulated in tumor tissues compared with normal tissues (P<0.00005). In the clinicopathological analysis, the low ZNF750 expression group exhibited a higher incidence of undifferentiated histology (P<0.05) compared with the high expression group. The low ZNF750 expression group exhibited a poorer prognosis in the Kyushu and TCGA datasets (P<0.0005 and P<0.05, respectively). GSEA indicated that ZNF750 expression was significantly correlated with epithelial differentiation in ESCC. This was confirmed using the datasets from CCLE and the Kyushu University Beppu Hospital by analyzing the levels of small proline rich protein 1A mRNA, an epithelial differentiation-associated gene. In conclusion, the results of the present study suggested that ZNF750 serves a role as a tumor suppressor; potentially via regulating epithelial differentiation and that it may be a promising biomarker of poor outcomes in ESCC.

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Section: Cancer Cell Line Encyclopedia (Ccle) Data Analysismentioning

confidence: 99%

Clinical significance of ZNF750 gene expression, a novel tumor suppressor gene, in esophageal squamous cell carcinoma

et al. 2017

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“…A database named 'PrognoScan' has been developed (30). This is i) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as ii) a tool for assessing the biological relationship between gene expression and prognosis.…”

Section: Identificationmentioning

confidence: 99%

Integrative genomic analyses of the histamine H1 receptor and its role in cancer prediction

Wang

Wei

Shi

et al. 2014

International Journal of Molecular Medicine

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Abstract. The human histamine receptor H1 (HRH1) gene is located on chromosome 3p25 and encodes for a 487 amino acid G protein-coupled receptor (GPCR) with a long third intracellular loop (IL3). The HRH1 predominantly couples to Gα q/11 proteins, leading to the activation of phospholipase C (PLC) and subsequent release of the second messengers inositol trisphosphate (IP 3 ) and diacylglycerol (DAG) followed by the activation of PKC and the release of [Ca 2+ ] i . In the present study, we identified HRH1 genes from 14 vertebrate genomes and found that HRH1 exists in all types of vertebrates including fish, amphibians, birds and mammals. We identified 88 SNPs including 4 available alleles disrupting an existing exonic splicing enhancer and 84 SNPs causing missense mutation, which may impact the effect of histamine on the HRH1 protein. We found that the human HRH1 gene was expressed in many tissues or organs, and predominant expression of HRH1 was shown in the bone marrow, whole blood, lymph node, thymus, brain, cerebellum, retina, spinal cord, heart, smooth muscle, skeletal muscle, small intestine, colon, adipocytes, kidney, liver, lung, pancreas, thyroid salivary gland, skin, ovary, uterus, placenta, prostate and testis. When searched in the PrognoScan database, human HRH1 was also found to be expressed in bladder cancer, blood cancer, brain cancer, breast cancer, colorectal cancer, eye cancer, head and neck cancer, lung cancer, ovarian cancer, skin cancer and soft tissue cancer tissues. The relationship between the expression of HRH1 and prognosis was found to vary in different types of cancers, even in the same cancer from different databases. This implies that the function of HRH1 in these tumors may be multidimensional. GR, STAT5A and c-Myb regulatory transcription factor binding sites were identified in the HRH1 gene upstream (promoter) region, which may be involved in the effect of HRH1 in tumors.

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“…A database named 'PrognoScan' has been developed (37). This is i) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as ii) a tool for assessing the biological relationship between gene expression and prognosis.…”

Section: Meta-analysis Of the Prognostic Value Of Il28ra Gene In Cancermentioning

confidence: 99%

Integrative genomic analyses on IL28RA, the common receptor of interferon-λ1, -λ2 and -λ3

Yang

Luo²,

Wei³

et al. 2010

Int J Mol Med

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Abstract. Interferon (IFN)-Ïs, including INF-Ï1, -Ï2, and -Ï3, are a newly described group of cytokines distantly related to the type I IFNs and IL-10 family members. IFN-Ï1, -Ï2, and -Ï3 bind to the same receptor (known as IL28RA) to exert their antiviral, antitumor and immunomodulatory effects. Here, we identified IL28RA genes from the genome of human, chimpanzee, macaque, orangutan, mouse, horse, rat, dog, chicken, and found that only one IL28RA existed in each genome. All the identified IL28RAs are single-pass type I membrane proteins except chicken IL28RA. They belong to the type II cytokine receptor family and contain one fibronectin type-III domain. We found human IL28RA was expressed in lymphs, testes, lymphoma, teratocarcinoma, pediatric pre-B cell acute lymphoblastic leukemia, germinal center B cells, embryonic stem cells, fetal lung, and also expressed in bladder, blood and breast cancers, glioma, head and neck cancer and lung cancer tissues. Three tumor-related transcriptional factor binding sites (AP-2, c-Jun and P53) were identified within the 1.0-kb regions upstream of the transcriptional start site of human IL28RA. Meta-analysis of the prognostic value of IL28RA genes in various cancers found that the expression of IL28RA was indeed related to the cancer prognosis in certain cancers. The STAT1 binding sites in the promoter region of IL28RA implied a specific mechanism for the amplifying effects of IFN-Ïs. The LyF-1 binding sites in the promoter region of IL28RA imply that IFN-Ïs were involved in the differentiation of early B and T cells.

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PrognoScan: a new database for meta-analysis of the prognostic value of genes

Cited by 826 publications

References 59 publications

Clinical significance of ZNF750 gene expression, a novel tumor suppressor gene, in esophageal squamous cell carcinoma

Clinical significance of ZNF750 gene expression, a novel tumor suppressor gene, in esophageal squamous cell carcinoma

Integrative genomic analyses of the histamine H1 receptor and its role in cancer prediction

Integrative genomic analyses on IL28RA, the common receptor of interferon-λ1, -λ2 and -λ3

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