Gene-set analysis is severely biased when applied to genome-wide methylation data

Differential DNA Methylation Status Between Human Preadipocytes and Mature Adipocytes

(2012) Jin-gai Zhu et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

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Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

(2012) Duncan Sproul et al.   GENOME BIOLOGY

Large-scale methylation domains mark a functional subset of neuronally expressed genes

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DNA hypermethylation in lung cancer is targeted at differentiation-associated genes

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DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

A Genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers

(2010) Thomas Dunwell et al.   Molecular Cancer

DNMT1 maintains progenitor function in self-renewing somatic tissue

(2010) George L. Sen et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

A Study of the Influence of Sex on Genome Wide Methylation

(2010) Jingyu Liu et al.   PLoS One

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Functional Switching of TGF-β1 Signaling in Liver Cancer via Epigenetic Modulation of a Single CpG Site in TTP Promoter

(2009) Bo Hwa Sohn et al.   GASTROENTEROLOGY

The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands

(2009) H. Takeshima et al.   GENOME RESEARCH

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

(2009) Mayumi Oda et al.   NUCLEIC ACIDS RESEARCH

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

(2009) N. Elango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH