ArticleBMC genomics2011
Alu distribution and mutation types of cancer genes.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 83 citations in OpenAlex.
- The role of Alu elements in causing BRCA1 structural variation and breast cancer susceptibility.Genes & genomics · 2026Review
- Exploring transposable elements: new horizons in cancer diagnostics and therapeutics.Mobile DNA · 2025Review
- Current smartphone-assisted point-of-care cancer detection: Towards supporting personalized cancer monitoring.Trends in analytical chemistry : TRAC · 2024Article
- [Molecular pathological analysis through the ages].Pathologie (Heidelberg, Germany) · 2024Review
- AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization.Cells · 2022Article
- Article
- Human rDNA and Cancer.Cells · 2021Review
- More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation.Journal of biomedical science · 2021Review
- Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice.Cell reports · 2021Article
- The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity.Molecular biology reports · 2021Review
- A single mutation in the ACTR8 gene associated with lineage-specific expression in primates.BMC evolutionary biology · 2020Article
- Aberrant Expression of RAD52, Its Prognostic Impact in Rectal Cancer and Association with Poor Survival of Patients.International journal of molecular sciences · 2020Article
- Emerging Role of Migration and Invasion Enhancer 1 (MIEN1) in Cancer Progression and Metastasis.Frontiers in oncology · 2019Review
- AberrantGenome research · 2018Article
- Telomere uncapping and vascular aging.American journal of physiology. Heart and circulatory physiology · 2018Review
- Prognostic value of the DNA integrity index in patients with malignant lung tumors.Oncotarget · 2018Article
- Frequency of Alu insertions within the ACE and PR loci in Northwestern Mexicans.BMC research notes · 2017Article
- Transposable Elements in Human Cancer: Causes and Consequences of Deregulation.International journal of molecular sciences · 2017Review
- MIEN1 is tightly regulated by SINE Alu methylation in its promoter.Oncotarget · 2016Article
- Regulation of Single-Strand Annealing and its Role in Genome Maintenance.Trends in genetics : TIG · 2016Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundAlu elements are the most abundant retrotransposable elements comprising ~11% of the human genome. Many studies have highlighted the role that Alu elements have in genetic instability and how their contribution to the assortment of mutagenic events can lead to cancer. As of yet, little has been done to quantitatively assess the association between Alu distribution and genes that are causally implicated in oncogenesis.
resultsWe have investigated the effect of various Alu densities on the mutation type based classifications of cancer genes. In order to establish the direct relationship between Alus and the cancer genes of interest, genome wide Alu-related densities were measured using genes rather than the sliding windows of fixed length as the units. Several novel genomic features, such as the density of the adjacent Alu pairs and the number of Alu-Exon-Alu triplets, were developed in order to extend the investigation via the multivariate statistical analysis toward more advanced biological insight. In addition, we characterized the genome-wide intron Alu distribution with a mixture model that distinguished genes containing Alu elements from those with no Alus, and evaluated the gene-level effect of the 5'-TTAAAA motif associated with Alu insertion sites using a two-step regression analysis method.
conclusionsThe study resulted in several novel findings worthy of further investigation. They include: (1) Recessive cancer genes (tumor suppressor genes) are enriched with Alu elements (p < 0.01) compared to dominant cancer genes (oncogenes) and the entire set of genes in the human genome; (2) Alu-related genomic features can be used to cluster cancer genes into biological meaningful groups; (3) The retention of exon Alus has been restricted in the human genome development, and an upper limit to the chromosome-level exon Alu densities is suggested by the distribution profile; (4) For the genes with at least one intron Alu repeat in individual chromosomes, the intron Alu densities can be well fitted by a Gamma distribution; (5) The effect of the 5'-TTAAAA motif on Alu densities varies across different chromosomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.