GCGene: a gene resource for gastric cancer with literature evidence

Min Zhao; Luming Chen; Yining Liu; Hong Qu

doi:10.18632/oncotarget.9030

Back

GCGene: a gene resource for gastric cancer with literature evidence

Journal article

Open access

Peer reviewed

GCGene: a gene resource for gastric cancer with literature evidence

Min Zhao, Luming Chen, Yining Liu and Hong Qu

Oncotarget, Vol.7(23), pp.33983-33993

2016

DOI: https://doi.org/10.18632/oncotarget.9030

Files and links (2)

pdf

PDF - Published Version (Open Access)5.59 MBDownload View

Published VersionPDF - Published Version (Open Access)CC BY V3.0, Open Access

url

https://doi.org/10.18632/oncotarget.9030View

Published Version

Abstract

gastric cancer

database

cancer genomics

functional analysis

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 noncoding 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/.

Details

Title: GCGene: a gene resource for gastric cancer with literature evidence
Authors: Min Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Luming Chen (Author) - Peking University, China
Yining Liu (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Hong Qu (Author) - Peking University, China
Publication details: Oncotarget, Vol.7(23), pp.33983-33993
Publisher: Impact Journals LLC
Date published: 2016
DOI: 10.18632/oncotarget.9030
ISSN: 1949-2553
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450234802621
Output Type: Journal article

Metrics

30 File views/ downloads

580 Record Views

3 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Cell Biology; Oncology

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites