ArticleBMC systems biology2011
An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver.
Article in BMC systems biology, 2011. 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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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
18 citing papers in PubMed, 38 citations in OpenAlex.
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- Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts.PLoS biology · 2021Article
- Aberrant CpG-methylation affects genes expression predicting survival in lung adenocarcinoma.Cancer medicine · 2018Article
- HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation.Genomics, proteomics & bioinformatics · 2018Article
- Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling.Development (Cambridge, England) · 2017Article
- Computational dynamic approaches for temporal omics data with applications to systems medicine.BioData mining · 2017Review
- Gene network and familial analyses uncover a gene network involving Tbx5/Osr1/Pcsk6 interaction in the second heart field for atrial septation.Human molecular genetics · 2016Article
- Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach.International journal of molecular sciences · 2016Article
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
- Label-free proteomic methodology for the analysis of human kidney stone matrix composition.Proteome science · 2016Article
- Predominant expression of exon 7 skipped SMN mRNAs in lung based on analysis of transcriptome sequencing datasets.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2014Article
- Article
- Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.BMC systems biology · 2013Article
- SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2013Article
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- Regulation of chromatin structure in the cardiovascular system.Circulation journal : official journal of the Japanese Circulation Society · 2013Review
- From genes to networks: in systematic points of view.BMC systems biology · 2011Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMany groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression.
resultsIn this study, we have used (insert statistical method here) to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arrays and compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues.
conclusionsThis study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.
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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.