Identification of genes associated with gastric cancer survival and construction of a nomogram to improve risk stratification for patients with gastric cancer

Oncology Letters
Yongfeng DingLisong Teng

Abstract

The present study aimed to identify genes associated with gastric cancer survival and improve risk stratification for patients with gastric cancer. Transcriptomic and clinicopathological data from 443 gastric cancer samples were retrieved from The Cancer Genome Atlas database. The DESeq R package was applied to screen for differentially expressed genes between Tumor-Node-Metastasis (TNM) stage (I vs. IV) and histological grade (G3 vs. G1 and G2). A total of seven genes were common to both comparisons; spondin 1 (SPON1); thrombospondin 4 (THBS4); Sushi, Von Willebrand factor type A, EGF and pentraxin domain containing 1 (SVEP1); prickle planar cell polarity protein 1 (PRICKLE1); ATP binding cassette subfamily A member 8 (ABCA8); Slit guidance ligand 2 (SLIT2); and EGF containing fibulin extracellular matrix protein 1 (EFEMP1), were selected as candidate survival-associated genes for further analysis. The prognostic value of these genes was assessed according to a literature review and Kaplan-Meier survival analysis. In addition, a multivariate Cox regression analysis revealed PRICKLE1 expression to be an independent prognostic factor for patients with gastric cancer. Furthermore, a predictive nomogram was generated using PRICKLE...Continue Reading

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Citations

Dec 21, 2021·Frontiers in Cell and Developmental Biology·Jianwen HuYucun Liu

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Methods Mentioned

BETA
surgical resection
RNA-seq
xenograft

Software Mentioned

R package DESeq
DESeq R package
Assembler
tile
R
TCGA
SAS
- Assembler
cBioPortal
rms

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