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2.4. Functional analysis

MG Mengfan Guo
JL Jie Lin
XC Xiangming Cao
JZ Jieyu Zhou
SB Shuai Ben
SC Silu Chen
HC Haiyan Chu
LM Lin Miao
SL Shuwei Li
DG Dongying Gu
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The gene‐based analysis was performed by Versatile Gene‐based Association Study 2 (VEGAS2, https://vegas2.qimrberghofer.edu.au/). The CancerSplicingQTL database (http://www.cancersplicingqtl‐hust.com/#/) was used to predict the splicing of SNPs. Enhancer states of SNPs were predicted through 3DSNP v2.0 (https://omic.tech/3dsnpv2/). To explore associations between variants and various traits, we used the MRC‐IEU OpenGWAS database (https://gwas.mrcieu.ac.uk/). 29

Oncomine (https://www.oncomine.org) was used to assess gene expression in multiple tumour tissues. The differences in mRNA expression levels were calculated using the TCGA dataset, Gene Expression Omnibus (GEO) database and in‐house RNA‐Seq data.

Copyright and License information:  ©2023 The Authors. published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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