Abstract:
AIM:Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. MATERIALS & METHODS:Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms. This study proposes a three-step feature selection algorithm, TriVote, to detect a subset of transcriptomic or methylomic residues with highly accurate binary classification performance. RESULTS & CONCLUSION:TriVote outperforms both filter and wrapper feature selection algorithms with both higher classification accuracy and smaller feature number on 17 transcriptomes and two methylomes. Biological functions of the methylome biomarkers detected by TriVote were discussed for their disease associations. An easy-to-use Python package is also released to facilitate the further applications.
journal_name
Epigenomicsjournal_title
Epigenomicsauthors
Xu C,Liu J,Yang W,Shu Y,Wei Z,Zheng W,Feng X,Zhou Fdoi
10.2217/epi-2017-0097subject
Has Abstractpub_date
2018-04-01 00:00:00pages
335-347issue
4eissn
1750-1911issn
1750-192Xjournal_volume
10pub_type
杂志文章相关文献
Epigenomics文献大全abstract::Currently, the incidence of colorectal cancer (CRC) is increasing across the world. The cancer stroma exerts an impact on the spread, invasion and chemoresistance of CRC. The tumor microenvironment involves a complex interaction between cancer cells and stromal cells, for example, cancer-associated fibroblasts (CAFs)....
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi-2019-0110
更新日期:2019-11-01 00:00:00
abstract::Aim: This study aimed to identify novel miRNAs (miRs) as regulators of UGT1A gene expression and to evaluate them as potential risk factors for the development of liver fibrosis/cirrhosis. Materials & methods: miRNA target sites in UDP-glucuronosyltransferase 1A (UGT1A) 3'-UTR were predicted and confirmed by luciferas...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0244
更新日期:2021-01-12 00:00:00
abstract:AIM:To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS:Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. Th...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2016-0052
更新日期:2016-10-01 00:00:00
abstract::For the first time, the development of next-generation sequencing technologies has brought about tools to investigate epigenetic alterations in an unbiased, yet genome-wide approach. The importance of this innovative technology is undeniable since it has already been established that changes in DNA methylation play an...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.09.50
更新日期:2010-04-01 00:00:00
abstract::Proper immune function is the result of multiple cell commitment and differentiation steps, and adequate control of activation mechanisms. Deregulation of transcriptional programs in immune cells leads to the development of hematological malignancies, autoimmune diseases or immunodeficiencies. In this sense, epigeneti...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.11.99
更新日期:2011-12-01 00:00:00
abstract::The ability to culture pluripotent stem cells and direct their differentiation into specific cell types in vitro provides a valuable experimental system for modeling pluripotency, development and cellular differentiation. High-throughput profiling of the transcriptomes and epigenomes of pluripotent stem cells and thei...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.13.80
更新日期:2014-02-01 00:00:00
abstract:AIM:To identify differentially methylated probes (DMPs) and regions (DMRs) in relation to chronic obstructive pulmonary disease (COPD) and lung function traits. METHODS:We performed an epigenome-wide association study of COPD and spirometric parameters, including forced expiratory volume in 1 s (FEV1), forced vital ca...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2017-0002
更新日期:2017-07-01 00:00:00
abstract::Histone deacetylase (HDAC)6 is a member of the class IIb HDAC family. This enzyme is zinc-dependent and mainly localized in the cytoplasm. HDAC6 is a unique isoenzyme with two functional catalytic domains and specific physiological roles. Indeed, HDAC6 deacetylates various substrates including α-tubulin and HSP90α, an...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.14.69
更新日期:2015-01-01 00:00:00
abstract::Aim: This study aims to examine the DNA methylation (DNAm) and expression patterns of genes associated with placental angiogenesis in preeclampsia. Materials & methods: DNAm and expression were examined in normotensive (n = 100) and preeclampsia (n = 100) women using pyrosequencing and quantitative real-time PCR respe...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0318
更新日期:2021-01-20 00:00:00
abstract::Arsenic is a nonmutagenic human carcinogen that induces tumors through unknown mechanisms. A growing body of evidence suggests that its carcinogenicity results from epigenetic changes, particularly in DNA methylation. Changes in gene methylation status, mediated by arsenic, have been proposed to activate oncogene expr...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.09.45
更新日期:2010-02-01 00:00:00
abstract::Aim: The contribution of miRNAs as epigenetic regulators of sexually dimorphic gene expression in the placenta is unknown. Materials & methods: 382 placentas from the extremely low gestational age newborns (ELGAN) cohort were evaluated for expression levels of 37,268 mRNAs and 2,102 miRNAs using genome-wide RNA-sequen...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0062
更新日期:2020-09-01 00:00:00
abstract::Aim: Myotonic dystrophy type 1 (DM1) is caused by an unstable trinucleotide (CTG) expansion at the DMPK gene locus. Cognitive dysfunctions are often observed in the condition. We investigated the association between DMPK blood DNA methylation (DNAm) and cognitive functions in DM1, considering expansion length and vari...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0328
更新日期:2020-12-01 00:00:00
abstract::Aim: To assess isorhamnetin efficacy for diabetic kidney disease in a Type 2 diabetes mellitus rat model, through investigating its effect at the epigenetic, mRNA and protein levels. Materials & methods: Type 2 diabetes mellitus was induced in rats by streptozotocin and high-fat diet. Rats were treated with isorhamnet...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0353
更新日期:2021-01-07 00:00:00
abstract:AIM:This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS:A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS:A total of 964 retrocopies ...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2017-0071
更新日期:2018-02-01 00:00:00
abstract::Aim: The hygiene hypothesis states that a lack of infection in early-life suppresses immune system development, and is linked to respiratory allergy (RA) and childhood acute lymphoblastic leukemia (ALL) risk. Little is known about underlying mechanisms, but DNA methylation is altered in RA and ALL, and in response to ...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2019-0052
更新日期:2019-10-01 00:00:00
abstract::A striking feature of mammalian genomes is the paucity of the CG dinucleotide. There are approximately 20,000 regions termed CpG islands where CGs cluster. This represents 5% of all CGs and 1% of the genome. CpG islands are typically unmethylated and are often promoters for housekeeping genes. The remaining 95% of CG ...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.12.55
更新日期:2012-12-01 00:00:00
abstract::DNA methylation is widely studied in the context of cancer. However, the rediscovery of 5-hydroxymethylation of DNA adds a new layer of complexity to understanding the epigenetic basis of development and disease, including carcinogenesis. There have been significant advances in techniques for the detection of 5-hydrox...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.13.69
更新日期:2013-12-01 00:00:00
abstract::Histone modifications regulate the structural status of chromatin and thereby influence the transcriptional status of genes. These processes are controlled by the recruitment of different enzymes to a specific genomic site. Furthermore, obtaining an understanding of these mechanisms could help delineate alternative tr...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi-2018-0081
更新日期:2019-02-01 00:00:00
abstract::Fibrosis is the excess deposition of extracellular matrix components which occur in multiple organs and ultimately leads to organ failure. Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs longer than approximately 200 nucleotides with no protein-encoding capacity. A growing body of evidence suggests that lnc...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi-2017-0020
更新日期:2017-09-01 00:00:00
abstract::Aberrant epigenomic programming is a hallmark of acute myeloid leukemia. This is partially due to somatic mutations that perturb cytosine methylation, histone post-translational modifications and transcription factors. Remarkably, mutations in the IDH1 and IDH2 genes perturb the epigenome through all three of these me...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi-2016-0008
更新日期:2016-07-01 00:00:00
abstract::This article focuses on the epigenetic alterations of aberrant promoter hypermethylation of genes, and histone modifications or RNA interference in cancer cells. Current knowledge of the hypermethylation of allele(s) in classical tumor suppressor genes in inherited and sporadic cancer, candidate tumor suppressor and o...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.10.64
更新日期:2011-02-01 00:00:00
abstract:AIM:Disclosing the mechanisms that regulate reprogramming memory. MATERIALS & METHODS:We established computational procedure to find DNA methylation somatic memory sites (SMSs) at single CpGs and integrated them with genomics, epigenomics, transcriptomics and imprinting information. RESULTS & CONCLUSION:Reprogramming...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2017-0098
更新日期:2018-02-01 00:00:00
abstract::Alzheimer's disease (AD) and Parkinson's disease (PD) are two common neurodegenerative diseases that result in the progressive damage or death of neurons. Environmental agents have the potential to damage the developing and mature nervous system, resulting in neurodegenerative diseases. Heritable changes in gene expre...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.10.43
更新日期:2010-10-01 00:00:00
abstract::Manipulation of chromatin, in which genomic DNA is packaged, is a fundamental requirement for all DNA-based metabolic processes in eukayotic cells. Histone variant incorporation, histone post-translational modifications, and ATP-dependent chromatin remodeling are three major strategies for chromatin manipulation, and ...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi.11.14
更新日期:2011-06-01 00:00:00
abstract::This study aimed to unveil the functional roles of LINC00221 in hepatocellular carcinoma (HCC). A discovery cohort and a validation cohort were respectively used to identify and verify the clinical value of LINC00221 in HCC. Bioinformatics analysis was performed to explore its potential mechanisms. LINC00221 was upreg...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2020-0363
更新日期:2021-01-07 00:00:00
abstract::Aim: To identify pregnancy-associated changes in cervical noncoding RNA (ncRNA), including miRNA and long noncoding RNA (lncRNA), and their potential effects on biologic processes. Materials & methods: We enrolled 21 pregnant women with term deliveries (≥37 weeks' gestation) in a prospective cohort and collected cervi...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2019-0231
更新日期:2020-06-01 00:00:00
abstract::Aim: To examine the impact of 4-nonylphenol (4-NP), on the expression of polycomb repressive complexes and cellular proliferation. Materials & methods: Cell proliferation assays, quantitative PCR, Western blotting, luciferase reporter assay, chromatin immunoprecipitation-quantitative PCR were used for the study. Resul...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2018-0175
更新日期:2019-06-01 00:00:00
abstract::Aim: The goal of this study was to comprehensively interrogate and map DNA methylation across 16 CpG-dense regions previously associated with oral and pharyngeal squamous cell carcinoma (OPSCC). Materials & methods: Targeted multiplex bisulfite amplicon sequencing was performed on four OPSCC cell lines and primary non...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2018-0172
更新日期:2019-07-01 00:00:00
abstract::Until recently, drug development in oncology was focused on treating most patients for a specific cancer type without taking in account the heterogeneity between these patients in term of response to treatment. Therefore, this type of broad treatment approach excludes the treatment of patient not responding to disease...
journal_title:Epigenomics
pub_type: 杂志文章
doi:10.2217/epi-2019-0169
更新日期:2020-01-01 00:00:00
abstract::Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used for mapping histone modifications, histone proteins, chromatin regulators, transcription factors and other DNA-binding proteins. It has played a significant role in our understanding of disease mechanisms and in exploring epigenetic changes...
journal_title:Epigenomics
pub_type: 杂志文章,评审
doi:10.2217/epi-2016-0053
更新日期:2016-09-01 00:00:00