EBV-GCR - The EBV Gastric Cancer Resource
EBV-GCR - Home Page
Description: Welcome to EBV-GCR suite of tools, which allows a wide variety of statistical comparisons for cellular miRNA and mRNA expression patterns for the gastric carcinoma (GC) dataset. The primary focus of EBV-GCR is to explore the impact of EBV status on this common human cancer type. These analysis and visualization tools are intended specifically as a resource for those working in the field of HPV dependent cancers and should not require any significant computational or bioinformatics expertise. The EBV-GCR suite consists of 6 different tools, which allow the exploration of differential mRNA/miRNA expression, gene loci methylation, overall patient survival, changes in immune landscape features, and single-cell mRNA/miRNA expression as a function of EBV status and viral miRNA expression in primary human GC.
Standalone Version: Please download the portable version at https://github.com/msaland/EBVGCR-Suite .
Source Data Resources
Level 3 miRNA and mRNA expression data from the TCGA GC cohort was downloaded from the Broad Genome Data Analysis Center’s Firehose server Link .
Level 3 Infinium HumanMethylation450 BeadChip array datasets for the TCGA GC cohorts were sourced from the Broad Genome Data Analysis Centers Firehose server Link .
The TCGA GC overall survival (OS) datasets were sourced from Liu et al, Cell 2018 (An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics) DOI: 10.1016/j.cell.2018.02.052 .
The TCGA GC immune landscape feature datasets were sourced from Thorsson et al, Immunity 2018 (The Immune Landscape of Cancer) DOI: 10.1016/j.immuni.2018.03.023 .
EBV viral mRNA expression data were sourced from Chakravorty et al, Cancer Research 2019 (Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host-Virus Interactions) DOI: 10.1158/0008-5472.CAN-19-0615 .
EBV viral miRNA expression data were sourced from Ungerleider et al, PLOS Pathogens 2021 (EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape) DOI: 10.1371/journal.ppat.1009217 .
Citing EBV-GCR: Salnikov MY, Wang E, Christensen E, Prusinkiewicz MA, Shooshtari P, Mymryk JS. The EBV Gastric Cancer Resource (EBV-GCR): A Suite of Tools for Investigating EBV-Associated Human Gastric Carcinogenesis. Viruses. 2023 Mar 27;15(4):853.
Manuscript: Link
Contact: contact.thincr@gmail.com
