ArticleNature communications2022
Systematic characterization of cancer transcriptome at transcript resolution.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 22 citations in OpenAlex.
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- The expression landscape and clinical significance of cancer-specific RNA transcripts across human cancers.Journal of translational medicine · 2026Article
- Solid Tumors Pan Cancer Transcriptome: Tissue/Cancer specific expression groups at the Isoform-Level.bioRxiv : the preprint server for biology · 2026Article
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- Human messenger RNA harbors widespread noncoding splice isoforms.Briefings in bioinformatics · 2026Article
- Network-informed deconvolution of bulk immune gene co-expression reveals single-cell programs and spatial organization.Frontiers in immunology · 2026Article
- Long-read RNA sequencing dataset of human pancreatic cancer cell lines.Scientific data · 2025Article
- Artificial Intelligence-Driven Multi-Omics Approaches in Glioblastoma.International journal of molecular sciences · 2025Review
- Transcriptomic Analysis ofBrain sciences · 2025Article
- Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer.Nature communications · 2024Article
- Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides.Nature communications · 2024Article
- FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues.Nucleic acids research · 2024Article
- Transcriptome and metabolome analyses provide crucial insights into the adaptation of chieh-qua toFrontiers in plant science · 2024Article
- Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells.Communications biology · 2023Article
- Shining a light on the dark proteome: Non-canonical open reading frames and their encoded miniproteins as a new frontier in cancer biology.Protein science : a publication of the Protein Society · 2023Review
- Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer's disease.Frontiers in aging neuroscience · 2023Article
- Hybrid-seq deciphers the complex transcriptional profile of the humanRNA biology · 2023Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcribed RNAs undergo various regulation and modification to become functional transcripts. Notably, cancer transcriptome has not been fully characterized at transcript resolution. Herein, we carry out a reference-based transcript assembly across >1000 cancer cell lines. We identify 498,255 transcripts, approximately half of which are unannotated. Unannotated transcripts are closely associated with cancer-related hallmarks and show clinical significance. We build a high-confidence RNA binding protein (RBP)-transcript regulatory network, wherein most RBPs tend to regulate transcripts involved in cell proliferation. We identify numerous transcripts that are highly associated with anti-cancer drug sensitivity. Furthermore, we establish RBP-transcript-drug axes, wherein PTBP1 is experimentally validated to affect the sensitivity to decitabine by regulating KIAA1522-a6 transcript. Finally, we establish a user-friendly data portal to serve as a valuable resource for understanding cancer transcriptome diversity and its potential clinical utility at transcript level. Our study substantially extends cancer RNA repository and will facilitate anti-cancer drug discovery.
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