ArticleNucleic acids research2010
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 49 citations in OpenAlex.
- Developmental modulation of schizophrenia risk gene methylation in offspring exhibiting cognitive deficits following maternal immune activation.Molecular psychiatry · 2026Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes.Journal, genetic engineering & biotechnology · 2024Article
- PCGIMA: developing the web server for human position-defined CpG islands methylation analysis.Frontiers in genetics · 2024Article
- Methylation Status ofCell journal · 2021Article
- A review of computational algorithms for CpG islands detection.Journal of biosciences · 2019Review
- Article
- Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.BMC bioinformatics · 2014Article
- CpG domains downstream of TSSs promote high levels of gene expression.Nucleic acids research · 2014Article
- DevMouse, the mouse developmental methylome database and analysis tools.Database : the journal of biological databases and curation · 2014Article
- Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis.Frontiers in genetics · 2014Article
- Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.Nucleic acids research · 2013Article
- An analysis and prediction of nucleosome positioning based on information content.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2013Article
- CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.Nucleic acids research · 2013Article
- Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.Molecular biology reports · 2012Article
- Mutations in the mitochondrial methionyl-tRNA synthetase cause a neurodegenerative phenotype in flies and a recessive ataxia (ARSAL) in humans.PLoS biology · 2012Article
- DiseaseMeth: a human disease methylation database.Nucleic acids research · 2012Article
- Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations.Journal of translational medicine · 2011Article
- QDMR: a quantitative method for identification of differentially methylated regions by entropy.Nucleic acids research · 2011Article
- In vivo, in vitro, and in silico analysis of methylation of the HIV-1 provirus.Methods (San Diego, Calif.) · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CpG islands (CGIs) are CpG-rich regions compared to CpG-depleted bulk DNA of mammalian genomes and are generally regarded as the epigenetic regulatory regions in association with unmethylation, promoter activity and histone modifications. Accurate identification of CpG islands with epigenetic regulatory function in bulk genomes is of wide interest. Here, the common features of functional CGIs are identified using an average mutual information method to differentiate functional CGIs from the remaining CGIs. A new approach (CpG mutual information, CpG_MI) was further explored to identify functional CGIs based on the cumulative mutual information of physical distances between two neighboring CpGs. Compared to current approaches, CpG_MI achieved the highest prediction accuracy. This approach also identified new functional CGIs overlapping with gene promoter regions which were missed by other algorithms. Nearly all CGIs identified by CpG_MI overlapped with histone modification marks. CpG_MI could also be used to identify potential functional CGIs in other mammalian genomes, as the CpG dinucleotide contents and cumulative mutual information distributions are almost the same among six mammalian genomes in our analysis. It is a reliable quantitative tool for the identification of functional CGIs from bulk genomes and helps in understanding the relationships between genomic functional elements and epigenomic modifications.
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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.