Abstract
Gastric cancer (GC) is the fifth most common cancer and third leading cause of cancer-related deaths worldwide. Its lethality primarily stems from a lack of detection strategies for early stages of GC and a lack of noninvasive detection strategies for advanced stages. The development of early diagnostic biomarkers largely depends on understanding the biological pathways and regulatory mechanisms associated with putative GC genes. Unfortunately, the GC-implicated genes that have been identified thus far are scattered among thousands of published studies, and no systematic summary is available, which hinders the development of a large-scale genetic screen. To provide a publically accessible resource tool to meet this need, we constructed a literature-based database GCGene (Gastric Cancer Gene database) with comprehensive annotations supported by a user-friendly website. In the current release, we have collected 1,815 unique human genes including 1,678 protein-coding and 137 non-coding genes curated from extensive examination of 3,142 PubMed abstracts. The resulting database has a convenient web-based interface to facilitate both textual and sequence-based searches. All curated genes in GCGene are downloadable for advanced bioinformatics data mining. Gene prioritization was performed to rank the relative relevance of these genes in GC development. The 100 top-ranked genes are highly mutated according to the cohort of published studies we reviewed. By conducting a network analysis of these top-ranked GC-associated genes in the human interactome, we were able to identify strong links between 8 highly connected genes with low expression and patient survival time. GCGene is freely available to academic users at http://gcgene.bioinfo-minzhao.org/.
Highlights
Gastric cancer (GC) is the fifth most commonly diagnosed cancer (952,000 new cases diagnosed in 2012) and the third leading cause of cancerrelated deaths in both sexes worldwide [1]
Based on the systematic survey of GC-associated genes in publically available databases and literature, we developed a user-friendly web interface to make this annotated information freely available to all researchers
The database is supported by a web browser that allows researchers to explore all the GC-associated genes using chromosome and coloured KEGG pathway maps (Figure 1)
Summary
Gastric (stomach) cancer (GC) is the fifth most commonly diagnosed cancer (952,000 new cases diagnosed in 2012) and the third leading cause of cancerrelated deaths in both sexes worldwide [1]. GC has complex molecular mechanisms for uncontrolled cell growth, which could be caused by promoter methylation [3], deregulated gene expression [4], competing endogenous long non-coding RNAs [5, 6], and/or copy number alteration of tumor-suppressor genes and oncogenes [7]. The majority of GC studies to date have not focused beyond the gene level; they fail to provide the whole picture of tumorigenesis. We aimed www.impactjournals.com/oncotarget to develop the first literature-based genetic resource with extensive annotations, GCGene. This data resource can be used to prioritize genes by their GC-associated importance relevance and to identify both the common and unique cellular events at different oncogenic stages
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