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Literature DB >> 29129922

Statistical and integrative system-level analysis of DNA methylation data.

Andrew E Teschendorff^1,2,3, Caroline L Relton⁴.

Abstract

Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information.

Entities: Chemical

Mesh：

Year: 2017 PMID： 29129922 DOI： 10.1038/nrg.2017.86

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 53.242

208 in total

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Journal: Nat Clin Pract Oncol Date: 2005-12

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Authors: Rosa Karlić; Ho-Ryun Chung; Julia Lasserre; Kristian Vlahovicek; Martin Vingron
Journal: Proc Natl Acad Sci U S A Date: 2010-02-01 Impact factor: 11.205

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Authors: Yinming Jiao; Martin Widschwendter; Andrew E Teschendorff
Journal: Bioinformatics Date: 2014-05-02 Impact factor: 6.937

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Journal: Ann Appl Stat Date: 2013-03-01 Impact factor: 2.083

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Journal: Proc Natl Acad Sci U S A Date: 2005-09-30 Impact factor: 11.205

6. Identification of tissue-specific cell death using methylation patterns of circulating DNA.

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Journal: Proc Natl Acad Sci U S A Date: 2016-03-14 Impact factor: 11.205

7. Increased methylation variation in epigenetic domains across cancer types.

Authors: Kasper Daniel Hansen; Winston Timp; Héctor Corrada Bravo; Sarven Sabunciyan; Benjamin Langmead; Oliver G McDonald; Bo Wen; Hao Wu; Yun Liu; Dinh Diep; Eirikur Briem; Kun Zhang; Rafael A Irizarry; Andrew P Feinberg
Journal: Nat Genet Date: 2011-06-26 Impact factor: 38.330

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Authors: Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal: Nature Date: 2015-02-19 Impact factor: 69.504

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Authors: Sebastian Moran; Carles Arribas; Manel Esteller
Journal: Epigenomics Date: 2015-12-17 Impact factor: 4.778

10. DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.

Authors: Andrew E Teschendorff; Yang Gao; Allison Jones; Matthias Ruebner; Matthias W Beckmann; David L Wachter; Peter A Fasching; Martin Widschwendter
Journal: Nat Commun Date: 2016-01-29 Impact factor: 14.919

94 in total

Review 1. Origins of human disease: the chrono-epigenetic perspective.

Authors: Edward Saehong Oh; Art Petronis
Journal: Nat Rev Genet Date: 2021-04-26 Impact factor: 53.242

Review 2. Outlook and future of inner ear therapy.

Authors: Jenna Devare; Samuel Gubbels; Yehoash Raphael
Journal: Hear Res Date: 2018-05-17 Impact factor: 3.208

3. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Authors: Marinka Zitnik; Francis Nguyen; Bo Wang; Jure Leskovec; Anna Goldenberg; Michael M Hoffman
Journal: Inf Fusion Date: 2018-09-21 Impact factor: 12.975

4. Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease.

Authors: Xin Sheng; Chengxiang Qiu; Hongbo Liu; Caroline Gluck; Jesse Y Hsu; Jiang He; Chi-Yuan Hsu; Daohang Sha; Matthew R Weir; Tamara Isakova; Dominic Raj; Hernan Rincon-Choles; Harold I Feldman; Raymond Townsend; Hongzhe Li; Katalin Susztak
Journal: Proc Natl Acad Sci U S A Date: 2020-11-03 Impact factor: 11.205

5. Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes.

Authors: Chong Wu; Wei Pan
Journal: Bioinformatics Date: 2019-10-01 Impact factor: 6.937

6. Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth.

Authors: Timothy P York; Shawn J Latendresse; Colleen Jackson-Cook; Dana M Lapato; Sara Moyer; Aaron R Wolen; Roxann Roberson-Nay; Elizabeth K Do; Susan K Murphy; Catherine Hoyo; Bernard F Fuemmeler; Jerome F Strauss
Journal: Epigenetics Date: 2020-05-24 Impact factor: 4.528