ArticleNeoplasia (New York, N.Y.)2017
Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer.
Article in Neoplasia (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.RNA biology · 2025Article
- Identification of rare and pathogenic TAL2 gene mutations in B-lineage acute lymphoblastic leukemia (B-ALL) using mutational screening and comprehensive bioinformatics analysis.Molecular biology reports · 2025Article
- CSTF3 contributes to platinum resistance in ovarian cancer through alternative polyadenylation of lncRNA NEAT1 and generating the short isoform NEAT1_1.Cell death & disease · 2024Article
- Article
- Comprehensive Analysis of Alternative Polyadenylation Events Associated with the Tumor Immune Microenvironment in Colon Adenocarcinoma.Current genomics · 2023Article
- A Novel apaQTL-SNP for the Modification of Non-Small-Cell Lung Cancer Susceptibility across Histological Subtypes.Cancers · 2022Article
- Shortening of the KHDRBS1 3'UTR by alternative cleavage and polyadenylation alters miRNA-mediated regulation and promotes gastric cancer progression.American journal of translational research · 2022Article
- Identification of an mRNA isoform switch for HNRNPA1 in breast cancers.Scientific reports · 2021Article
- Could MicroRNAs Be Useful Tools to Improve the Diagnosis and Treatment of Rare Gynecological Cancers? A Brief Overview.International journal of molecular sciences · 2021Review
- RNA-biology ruling cancer progression? Focus on 3'UTRs and splicing.Cancer metastasis reviews · 2020Review
- Supervised Machine Learning in Oncology: A Clinician's Guide.Digestive disease interventions · 2020Article
- IMP1 3' UTR shortening enhances metastatic burden in colorectal cancer.Carcinogenesis · 2019Article
- Alternative polyadenylation of single cells delineates cell types and serves as a prognostic marker in early stage breast cancer.PloS one · 2019Article
- NUDT21 inhibits bladder cancer progression through ANXA2 and LIMK2 by alternative polyadenylation.Theranostics · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA), a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A) signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian) compared to normal tissues. Using machine-learning techniques, we further defined specific subsets of APA events to efficiently classify cancer types. Furthermore, APA patterns were associated with altered protein levels in patients, revealed by antibody-based profiling data, suggesting functional significance. Overall, our study offers a computational approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches.
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