GENT: Gene Expression Database of Normal and Tumor Tissues

Abstract

Background:Some oncogenes such as ERBB2 and EGFR are over-expressed in only a subset of patients. Cancer outlier profile analysis is one of computational approaches to identify outliers in gene expression data. A database with a large sample size would be a great advantage when searching for genes over-expressed in only a subset of patients.Description:GENT (Gene Expression database of Normal and Tumor tissues) is a web-accessible database that provides gene expression patterns across diverse human cancer and normal tissues. More than 40000 samples, profiled by Affymetrix U133A or U133plus2 platforms in many different laboratories across the world, were collected from public resources and combined into two large data sets, helping the identification of cancer outliers that are over-expressed in only a subset of patients. Gene expression patterns in nearly 1000 human cancer cell lines are also provided. In each tissue, users can retrieve gene expression patterns classified by more detailed clinical information.Conclusions:The large samples size (>24300 for U133plus2 and >16400 for U133A) of GENT provides an advantage in identifying cancer outliers. A cancer cell line gene expression database is useful for target validation by in vitro experiment. We hope GENT will be a useful resource for cancer researchers in many stages from target discovery to target validation. GENT is available at http://medicalgenome.kribb.re.kr/GENT/ or http://genome.kobic.re.kr/GENT/.

SH3BGRL3 Protein as a Potential Prognostic Biomarker for Urothelial Carcinoma: A Novel Binding Partner of Epidermal Growth Factor Receptor

“…Although SH3BGRL3 may be derived from blood incursion as a serum protein, our data are consistent with the GENT database (gene expression across normal and tumor tissue; ref. 17), showing a higher level of SH3BGRL3 mRNA in urothelial carcinoma than in normal tissue (Supplementary Fig. S1B).…”

CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia

“…Interestingly, CLIC5 expression has been associated with poor prognosis in breast cancer, 44 and expression arrays of a broad range of normal and tumoral tissues obtained through the GENT database 45 showed an overexpression of CLIC5 in ovarian cancers (Online Supplementary Figure S8). Based on our results, and given the importance of oxidative stress resistance in these solid tumors that require angiogenesis to promote growth, it suggests that CLIC5A protection against oxidative stress may not be limited to pre-B cell leukemia.…”

Natural variation in the histone demethylase, KDM4C, influences expression levels of specific genes including those that affect cell growth

“…Amplification of the chromosomal region 9p24, which includes KDM4C, has been observed in a variety of cancers, including pancreatic tumors (Cloos et al 2006;Rui et al 2010;Zhang et al 2011). We next used the Gene Expression Database of Normal and Tumor Tissues (GENT) (Shin et al 2011) to validate the increased KDM4C expression in cancer. Data from GENT show that KDM4C expression is higher in six of the seven cancer types that we found to show at least 20% higher KDM4C expression than their matching normal controls (Fig.…”

“…The Gene Expression in Normal and Tumor Tissues Database (Shin et al 2011) is a collection of data microarray experiments. Fifteen of the 18 tissues that we investigated by qRT-PCR were represented in this database.…”