A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
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Transcription of alternative promoters is widespread in cancer.
“Transcription of alternative promoters is widespread in cancer19.”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [19]
A highly expressed promoter is often annotated as reference promoter, which is what we used in this study.
“a highly expressed promoter is often annotated as the reference promoter16,19, which is what we used in this study”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [19]
The retrieved passages have no section or page information and do not state that a highly expressed promoter is often annotated as the reference promoter. Searches for “reference promoter,” “highly expressed promoter,” and related terms returned URLs or garbled text, so our copy cannot verify the attribution. (LLM, conf=0.70)
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Cites
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Genome-wide analysis of mammalian promoter architecture and evolution
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1789 · Cited by 1,350 · see citing works
Genome-wide analysis of noncoding regulatory mutations in cancer
Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484 · see citing works
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Nepal, C., & Andersen, J. B. (2023) · Nature Communications · doi:10.1038/s41467-023-38272-4 · Cited by 39 · see citing works
- Authors
- Demircioğlu, D., Cukuroglu, E., Kindermans, M., Nandi, T., Calabrese, C., Fonseca, N. A., Kahles, A., Lehmann, K.-V., Stegle, O., Brazma, A., Brooks, A. N., Rätsch, G., Tan, P., & Göke, J.
- Affiliations
- National University of Singapore (SG)
- Genome Institute of Singapore (SG)
- European Bioinformatics Institute (GB)
- SIB Swiss Institute of Bioinformatics (CH)
- University of California, Santa Cruz (US)
- SingHealth (SG)
- National Cancer Centre Singapore (SG)
- Corresponding author
- Göke, Jonathan
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-09
- Volume
- 178
- Issue
- 6
- Pages
- 1465-1477.e17
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2971958993
- Cited by
- 250
- References
- 9
- Citations by year
- 2026: 35 · 2025: 40 · 2024: 33 · 2023: 40 · 2022: 40 · 2021: 44 · 2020: 16 · 2019: 1 · 2017: 1
- FWCI
- 8.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Agency for Science, Technology and Research
- National Medical Research Council (OFIRG16nov019, TCR/009-NUHS/2013, NMRC/STaR/0026/2015)
- National Research Foundation Singapore
- Singapore Ministry of Education
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- alternative promoters, promoter activity, tumor transcriptome, gene expression regulation, cancer genes, patient survival prediction, cancer diagnosis, tissue-specific gene regulation
- MeSH terms
- RNA-Seq, Humans, Neoplasms, Promoter Regions, Genetic, Gene Expression Regulation, Neoplastic, Computational Biology, Databases, Genetic, Transcriptome
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