Literature DB >> 22253290

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data.

Dan Wang1, Li Yan, Qiang Hu, Lara E Sucheston, Michael J Higgins, Christine B Ambrosone, Candace S Johnson, Dominic J Smiraglia, Song Liu.   

Abstract

UNLABELLED: The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density microarray for quantifying the methylation level of over 450 000 CpG sites within human genome. Illumina Methylation Analyzer (IMA) is a computational package designed to automate the pipeline for exploratory analysis and summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. The pipeline loads the data from Illumina platform and provides user-customized functions commonly required to perform exploratory methylation analysis for individual sites as well as annotated regions. AVAILABILITY: IMA is implemented in the R language and is freely available from http://www.rforge.net/IMA.

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Year:  2012        PMID： 22253290      PMCID： PMC3289916          DOI： 10.1093/bioinformatics/bts013

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  16 in total

Review 1.  Statistical approaches for the analysis of DNA methylation microarray data.

Authors:  Kimberly D Siegmund
Journal:  Hum Genet       Date:  2011-04-26       Impact factor: 4.132

2.  Accurate genome-scale percentage DNA methylation estimates from microarray data.

Authors:  Martin J Aryee; Zhijin Wu; Christine Ladd-Acosta; Brian Herb; Andrew P Feinberg; Srinivasan Yegnasubramanian; Rafael A Irizarry
Journal:  Biostatistics       Date:  2010-09-21       Impact factor: 5.899

3.  A statistical framework for Illumina DNA methylation arrays.

Authors:  Pei Fen Kuan; Sijian Wang; Xin Zhou; Haitao Chu
Journal:  Bioinformatics       Date:  2010-09-29       Impact factor: 6.937

Review 4.  Epigenetic modifications and human disease.

Authors:  Anna Portela; Manel Esteller
Journal:  Nat Biotechnol       Date:  2010-10       Impact factor: 54.908

Review 5.  Principles and challenges of genomewide DNA methylation analysis.

Authors:  Peter W Laird
Journal:  Nat Rev Genet       Date:  2010-03       Impact factor: 53.242

6.  High density DNA methylation array with single CpG site resolution.

Authors:  Marina Bibikova; Bret Barnes; Chan Tsan; Vincent Ho; Brandy Klotzle; Jennie M Le; David Delano; Lu Zhang; Gary P Schroth; Kevin L Gunderson; Jian-Bing Fan; Richard Shen
Journal:  Genomics       Date:  2011-08-02       Impact factor: 5.736

7.  DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer.

Authors:  Carmen J Marsit; Devin C Koestler; Brock C Christensen; Margaret R Karagas; E Andres Houseman; Karl T Kelsey
Journal:  J Clin Oncol       Date:  2011-02-22       Impact factor: 44.544

8.  DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma.

Authors:  Brock C Christensen; Ashley A Smith; Shichun Zheng; Devin C Koestler; E Andres Houseman; Carmen J Marsit; Joseph L Wiemels; Heather H Nelson; Margaret R Karagas; Margaret R Wrensch; Karl T Kelsey; John K Wiencke
Journal:  J Natl Cancer Inst       Date:  2010-12-16       Impact factor: 13.506

9.  An epigenetic signature in peripheral blood predicts active ovarian cancer.

Authors:  Andrew E Teschendorff; Usha Menon; Aleksandra Gentry-Maharaj; Susan J Ramus; Simon A Gayther; Sophia Apostolidou; Allison Jones; Matthias Lechner; Stephan Beck; Ian J Jacobs; Martin Widschwendter
Journal:  PLoS One       Date:  2009-12-18       Impact factor: 3.240

10.  A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Authors:  Nuno L Barbosa-Morais; Mark J Dunning; Shamith A Samarajiwa; Jeremy F J Darot; Matthew E Ritchie; Andy G Lynch; Simon Tavaré
Journal:  Nucleic Acids Res       Date:  2009-11-18       Impact factor: 16.971
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  149 in total

1.  Hypomethylation within gene promoter regions and type 1 diabetes in discordant monozygotic twins.

Authors:  Emon Elboudwarej; Michael Cole; Farren B S Briggs; Alexandra Fouts; Pamela R Fain; Hong Quach; Diana Quach; Elizabeth Sinclair; Lindsey A Criswell; Julie A Lane; Andrea K Steck; Lisa F Barcellos; Janelle A Noble
Journal:  J Autoimmun       Date:  2016-01-09       Impact factor: 7.094

2.  Bayesian genome- and epigenome-wide association studies with gene level dependence.

Authors:  Eric F Lock; David B Dunson
Journal:  Biometrics       Date:  2017-01-12       Impact factor: 2.571

3.  ChAMP: 450k Chip Analysis Methylation Pipeline.

Authors:  Tiffany J Morris; Lee M Butcher; Andrew Feber; Andrew E Teschendorff; Ankur R Chakravarthy; Tomasz K Wojdacz; Stephan Beck
Journal:  Bioinformatics       Date:  2013-12-12       Impact factor: 6.937

4.  Tetanus vaccination is associated with differential DNA-methylation: Reduces the risk of asthma in adolescence.

Authors:  Vimala Devi Janjanam; Nandini Mukherjee; Gabrielle A Lockett; Faisal I Rezwan; Ramesh Kurukulaaratchy; Frances Mitchell; Hongmei Zhang; Hasan Arshad; John W Holloway; Wilfried Karmaus
Journal:  Vaccine       Date:  2016-11-17       Impact factor: 3.641

5.  DNA methylation analysis of Homeobox genes implicates HOXB7 hypomethylation as risk factor for neural tube defects.

Authors:  Anne Rochtus; Benedetta Izzi; Elise Vangeel; Sophie Louwette; Christine Wittevrongel; Diether Lambrechts; Yves Moreau; Raf Winand; Carla Verpoorten; Katrien Jansen; Chris Van Geet; Kathleen Freson
Journal:  Epigenetics       Date:  2015-01-29       Impact factor: 4.528

6.  An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays.

Authors:  Saurav Mallik; Gabriel J Odom; Zhen Gao; Lissette Gomez; Xi Chen; Lily Wang
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

Review 7.  Analysing and interpreting DNA methylation data.

Authors:  Christoph Bock
Journal:  Nat Rev Genet       Date:  2012-10       Impact factor: 53.242

8.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Authors:  Martin J Aryee; Andrew E Jaffe; Hector Corrada-Bravo; Christine Ladd-Acosta; Andrew P Feinberg; Kasper D Hansen; Rafael A Irizarry
Journal:  Bioinformatics       Date:  2014-01-28       Impact factor: 6.937

9.  Integrated genomic characterization of IDH1-mutant glioma malignant progression.

Authors:  Hanwen Bai; Akdes Serin Harmancı; E Zeynep Erson-Omay; Jie Li; Süleyman Coşkun; Matthias Simon; Boris Krischek; Koray Özduman; S Bülent Omay; Eric A Sorensen; Şevin Turcan; Mehmet Bakırcığlu; Geneive Carrión-Grant; Phillip B Murray; Victoria E Clark; A Gulhan Ercan-Sencicek; James Knight; Leman Sencar; Selin Altınok; Leon D Kaulen; Burcu Gülez; Marco Timmer; Johannes Schramm; Ketu Mishra-Gorur; Octavian Henegariu; Jennifer Moliterno; Angeliki Louvi; Timothy A Chan; Stacey L Tannheimer; M Necmettin Pamir; Alexander O Vortmeyer; Kaya Bilguvar; Katsuhito Yasuno; Murat Günel
Journal:  Nat Genet       Date:  2015-11-30       Impact factor: 38.330

10.  Association of season of birth with DNA methylation and allergic disease.

Authors:  G A Lockett; N Soto-Ramírez; M A Ray; T M Everson; C-J Xu; V K Patil; W Terry; A Kaushal; F I Rezwan; S L Ewart; U Gehring; D S Postma; G H Koppelman; S H Arshad; H Zhang; W Karmaus; J W Holloway
Journal:  Allergy       Date:  2016-03-29       Impact factor: 13.146
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