CAFuncAPA: a Knowledgebase for Systematic Functional Annotations of APA Events in Human Cancers

Overview

Journal NAR Cancer

Publisher Oxford University Press

Specialty Oncology

Date 2023 Jan 25

PMID 36694725

Authors

Kexin Huang

Sijia Wu

Xiaotong Yang

Tiangang Wang

Xi Liu

Xiaobo Zhou

Liyu Huang

Affiliations

Soon will be listed here.

Abstract

Alternative polyadenylation (APA) is a widespread posttranscriptional regulation process. APA generates diverse mRNA isoforms with different 3' UTR lengths, affecting mRNA expression, miRNA binding regulation and alternative splicing events. Previous studies have demonstrated the important roles of APA in tumorigenesis and cancer progression through diverse aspects. Thus, a comprehensive functional landscape of diverse APA events would aid in a better understanding of the underlying mechanisms related to APA in human cancers. Here, we built CAFuncAPA (https://relab.xidian.edu.cn/CAFuncAPA/) to systematically annotate the functions of 15478 APA events in human pan-cancers. Specifically, we first identified APA events associated with cancer survival and tumor progression. We annotated the potential downstream effects of APA on genes/isoforms expression, regulation of miRNAs, RNA binding proteins (RBPs) and alternative splicing events. Moreover, we also identified up-regulators of APA events, including the effects of genetic variants on poly(A) sites and RBPs, as well as the effect of methylation phenotypes on APA events. These findings suggested that CAFuncAPA can be a helpful resource for a better understanding of APA regulators and potential functions in cancer biology.

Citing Articles

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Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA.

Li Y, Gong J, Sun Q, Vong E, Cheng X, Wang B Am J Hum Genet. 2024; 111(3):562-583.

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