ArticleNucleic acids research2013
Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed, 35 citations in OpenAlex.
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- Exploring objective feature sets in constructing the evolution relationship of animal genome sequences.BMC genomics · 2023Article
- TahcoRoll: fast genomic signature profiling via thinned automaton and rolling hash.Medical review (2021) · 2021Article
- Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.BMC evolutionary biology · 2020Article
- The Nubeam reference-free approach to analyze metagenomic sequencing reads.Genome research · 2020Article
- Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions.Genes & genomics · 2018Article
- Epigenetics and bone diseases.Genetics research · 2018Review
- Machine learning for epigenetics and future medical applications.Epigenetics · 2017Review
- Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2017Article
- Article
- Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines.BMC systems biology · 2016Article
- Determining the quality and complexity of next-generation sequencing data without a reference genome.Genome biology · 2014Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
CpG islands are GC-rich regions often located in the 5' end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative analysis of all CpG island sequences in 10 mammalian genomes. As sequence similarity methods and character composition techniques such as information theory are particularly difficult to conduct, we used exact patterns in CpG island sequences and single character discrepancies to identify differences in CpG island sequences. First, by calculating genome distance based on rank correlation tests, we show that k-mer and k-flank patterns around CpG sites can be used to correctly reconstruct the phylogeny of 10 mammalian genomes. Further, we used various machine learning algorithms to demonstrate that CpG islands sequences can be characterized using k-mers. In addition, by testing a human model on the nine different mammalian genomes, we provide the first evidence that k-mer signatures are consistent with evolutionary history.
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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.