Gene-set analysis is severely biased when applied to genome-wide methylation data (Q28291972)

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2 March 2020

title

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

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2 March 2020

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4

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2 March 2020

author name string

Paul Geeleher

1

1 reference

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2 March 2020

Lori Hartnett

2

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2 March 2020

Laurance J Egan

3

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2 March 2020

Raja Affendi Raja Ali

5

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2 March 2020

Cathal Seoighe

6

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2 March 2020

language of work or name

English

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publication date

3 June 2013

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2 March 2020

2 references

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2 March 2020

volume

29

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2 March 2020

issue

15

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2 March 2020

page(s)

1851-1857

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Gene ontology: tool for the unification of biology

2 March 2020

cites work

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

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Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

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Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia

21 January 2018

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

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

21 January 2018

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

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The risk of colorectal cancer in ulcerative colitis: a meta-analysis

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

21 January 2018

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Using GOstats to test gene lists for GO term association

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

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

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

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

21 January 2018

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A study of the influence of sex on genome wide methylation

21 January 2018

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GREAT improves functional interpretation of cis-regulatory regions

21 January 2018

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Methylated DNA immunoprecipitation (MeDIP).

21 January 2018

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

21 January 2018

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Transcript length bias in RNA-seq data confounds systems biology

21 January 2018

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High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer

21 January 2018

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

21 January 2018

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DNMT1 maintains progenitor function in self-renewing somatic tissue

21 January 2018

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Functional switching of TGF-beta1 signaling in liver cancer via epigenetic modulation of a single CpG site in TTP promoter

21 January 2018

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

21 January 2018

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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

21 January 2018

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

21 January 2018

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Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

21 January 2018

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

21 January 2018

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Differential DNA methylation status between human preadipocytes and mature adipocytes

21 January 2018

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Correlation between the single-site CpG methylation and expression silencing of the XAF1 gene in human gastric and colon cancers.

21 January 2018

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10.1093/BIOINFORMATICS/BTT311

21 January 2018

Identifiers

DOI

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

3328811

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23732277%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/GeeleherHEGAS13

2 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

OpenCitations bibliographic resource ID

28 January 2021

3328811

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23732277%20AND%20SRC:MED&resulttype=core&format=json