ArticleBreast cancer research and treatment2015
Genome-wide analysis of alternative transcripts in human breast cancer.
Article in Breast cancer research and treatment, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed, 35 citations in OpenAlex.
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- Roles of KHDRBS2 and KHDRBS3 in prostate cancer progression and AR-V7 regulation.Discover oncology · 2025Article
- RNA-binding protein quaking: a multifunctional regulator in tumour progression.Annals of medicine · 2025Review
- Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Functions of the Muscleblind-like protein family and their role in disease.Cell communication and signaling : CCS · 2025Review
- PTBP1 as a potential regulator of disease.Molecular and cellular biochemistry · 2024Review
- Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes.Communications biology · 2023Article
- Hybrid-seq deciphers the complex transcriptional profile of the humanRNA biology · 2023Article
- T-Cell Intracellular Antigen 1-Like Protein in Physiology and Pathology.International journal of molecular sciences · 2022Review
- Role of Nucleolin in Endometrial Precancerous Hyperplasia and Carcinogenesis: Ex Vivo and In Silico Study.International journal of molecular sciences · 2022Article
- Landscape of Alternative Splicing Events Related to Prognosis and Immune Infiltration in Glioma: A Data Analysis and Basic Verification.Journal of immunology research · 2022Article
- The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells.Cancers · 2021Article
- Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines.Genomics, proteomics & bioinformatics · 2021Article
- Alternatively spliced ANLN isoforms synergistically contribute to the progression of head and neck squamous cell carcinoma.Cell death & disease · 2021Article
- The emerging role of RNA N6-methyladenosine methylation in breast cancer.Biomarker research · 2021Review
- Article
- Alternative splicing modulates cancer aggressiveness: role in EMT/metastasis and chemoresistance.Molecular biology reports · 2021Review
- RNA-binding protein KHSRP promotes tumor growth and metastasis in non-small cell lung cancer.Journal of experimental & clinical cancer research : CR · 2019Article
- Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Transcript variants play a critical role in diversifying gene expression. Alternative splicing is a major mechanism for generating transcript variants. A number of genes have been implicated in breast cancer pathogenesis with their aberrant expression of alternative transcripts. In this study, we performed genome-wide analyses of transcript variant expression in breast cancer. With RNA-Seq data from 105 patients, we characterized the transcriptome of breast tumors, by pairwise comparison of gene expression in the breast tumor versus matched healthy tissue from each patient. We identified 2839 genes, ~10 % of protein-coding genes in the human genome, that had differential expression of transcript variants between tumors and healthy tissues. The validity of the computational analysis was confirmed by quantitative RT-PCR assessment of transcript variant expression from four top candidate genes. The alternative transcript profiling led to classification of breast cancer into two subgroups and yielded a novel molecular signature that could be prognostic of patients' tumor burden and survival. We uncovered nine splicing factors (FOX2, MBNL1, QKI, PTBP1, ELAVL1, HNRNPC, KHDRBS1, SFRS2, and TIAR) that were involved in aberrant splicing in breast cancer. Network analyses for the coordinative patterns of transcript variant expression identified twelve "hub" genes that differentiated the cancerous and normal transcriptomes. Dysregulated expression of alternative transcripts may reveal novel biomarkers for tumor development. It may also suggest new therapeutic targets, such as the "hub" genes identified through the network analyses of transcript variant expression, or splicing factors implicated in the formation of the tumor transcriptome.
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Registered trials
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