Additional file 1: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Additional file 3: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S2. Pearson correlation coefficient between the inferred bin methylation level and the RRBS da...

Additional file 2: of Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation

M. Morris (3777250)
L. Hesson (6164282)
R. Poulos (6164285)
R. Ward (3037509)
J. Wong (6164288)
N. Youngson (6164291)

December 2018

Figure S2. Quality control of ‘omics’. A Volcano plot depicting fold changes associated with differe...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

Additional file 2: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Yujie He (3068052)
Lot Witte (6708743)
Lotte Houtepen (5454887)
Danny Nispeling (6708746)
Zhida Xu (2023525)
Qiong Yu (446491)
Yaqin Yu (605430)
Elly Hol (805688)
RenĂŠ Kahn (6708749)
Marco Boks (3529895)

May 2019

Nominally associated loci of Chinese and fibroblast samples. The file contains the loci ID and p val...

Additional file 3: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Yujie He (3068052)
Lot Witte (6708743)
Lotte Houtepen (5454887)
Danny Nispeling (6708746)
Zhida Xu (2023525)
Qiong Yu (446491)
Yaqin Yu (605430)
Elly Hol (805688)
RenĂŠ Kahn (6708749)
Marco Boks (3529895)

May 2019

Permutation analysis of DMRs. The file contains the results of the permutation analysis. (DOCX 14 kb

Additional file 2: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S1. Pearson correlation coefficient of bin methylation level for the positive and negative DNA...

Additional file 2: of Comparing DNA methylation profiles in saliva and intestinal mucosa

Nerissa Hearn (6413723)
Aaron Coleman (6413726)
Vincent Ho (443227)
Christine Chiu (6413729)
Joanne Lind (3489548)

March 2019

Figure S1. Multi-dimensional scaling. A. All samples pre-normalisation samples classified by tissue ...

Additional file 1: of The associations of DNA methylation alterations in oxidative stress-related genes with cancer incidence and mortality outcomes: a population-based cohort study

Xīn Gào (6262232)
Yan Zhang (8098)
Barbara Burwinkel (146479)
Yang Xuan (419293)
Bernd Holleczek (287845)
Hermann Brenner (63649)
Ben Schöttker (300688)

January 2019

Table S1. 519 genes coding for proteins involved in pathways from oxidative stress to cancer. Table ...

Additional file 2: of DNA methylation of the promoter region of bnip3 and bnip3l genes induced by metabolic programming

Vincent Veron (154657)
Lucie Marandel (3994841)
Jingwei Liu (525202)
Emilio VĂŠlez (5755055)
Olivier Lepais (464756)
StĂŠphane Panserat (3994844)
Sandrine Skiba (5755040)
Iban Seiliez (320251)

September 2018

Table S1. Formulation and proximate composition of diet used in hypoxia stimulus [14]. Table S2. For...

Additional file 8 of Integrated analysis of DNA-methylation and gene expression using high-dimensional penalized regression: a cohort study on bone mineral density in postmenopausal women

Tonje Lien (4593184)
Ărnulf Borgan (4920787)
Sjur Reppe (152868)
Kaare Gautvik (580427)
Ingrid Glad (4920790)

March 2018

Figure S8. Distribution of p-values. The distribution of p-values from the âglobal testâ, when t...

Additional file 1: of Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation

Lucas Husquin (5864030)
Maxime Rotival (133720)
Maud Fagny (3470801)
Hélène Quach (262024)
Nora Zidane (85964)
Lisa McEwen (3968174)
Julia MacIsaac (3575030)
Michael Kobor (3470795)
Hugues Aschard (110171)
Etienne Patin (107311)
Lluis Quintana-Murci (3320199)

December 2018

Figure S1. Overview of the EvoImmunoPop experimental setting. Figure S2. Exploring the non-linear ef...

Additional file 1: Figure S1. of Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots

Nicklas Staunstrup (3470612)
Anna Starnawska (773141)
Mette Nyegaard (202075)
Lene Christiansen (158189)
Anders Nielsen (742984)
Anders BĂ¸rglum (3470615)
Ole Mors (128054)

July 2016

Number of experiments achievable per DBS by different methods. Part of a DBS necessary to meet the m...

Additional file 3: of DNA methylation patterns associated with oxidative stress in an ageing population

Åsa Hedman (59281)
Mihkel Zilmer (673181)
Johan Sundström (232655)
Lars Lind (88400)
Erik Ingelsson (232651)

November 2016

Supplemental Tables. Table S1. Methylation sites associated with TGSH (FDR <0.05). Table S2. Methyla...

Additional file 1: of Global DNA methylation changes spanning puberty are near predicted estrogen-responsive genes and enriched for genes involved in endocrine and immune processes

Emma Thompson (392865)
Jessie Nicodemus-Johnson (772733)
Kyung Kim (31555)
James Gern (3472670)
Daniel Jackson (176636)
Robert Lemanske (588802)
Carole Ober (259474)

May 2018

Scatterplot illustrating correlation between methylation beta values in all samples (Nâ=â55 pair...

Additional file 1: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Correcting CpG density bias by the normal curve and Using WGBS data for validation. (DOCX 16 kb

Additional file 3: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S2. Pearson correlation coefficient between the inferred bin methylation level and the RRBS da...

Additional file 2: of Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation

M. Morris (3777250)
L. Hesson (6164282)
R. Poulos (6164285)
R. Ward (3037509)
J. Wong (6164288)
N. Youngson (6164291)

December 2018

Figure S2. Quality control of ‘omics’. A Volcano plot depicting fold changes associated with differe...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

Additional file 2: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Yujie He (3068052)
Lot Witte (6708743)
Lotte Houtepen (5454887)
Danny Nispeling (6708746)
Zhida Xu (2023525)
Qiong Yu (446491)
Yaqin Yu (605430)
Elly Hol (805688)
RenĂŠ Kahn (6708749)
Marco Boks (3529895)

May 2019

Nominally associated loci of Chinese and fibroblast samples. The file contains the loci ID and p val...

Additional file 3: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Yujie He (3068052)
Lot Witte (6708743)
Lotte Houtepen (5454887)
Danny Nispeling (6708746)
Zhida Xu (2023525)
Qiong Yu (446491)
Yaqin Yu (605430)
Elly Hol (805688)
RenĂŠ Kahn (6708749)
Marco Boks (3529895)

May 2019

Permutation analysis of DMRs. The file contains the results of the permutation analysis. (DOCX 14 kb

Additional file 2: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S1. Pearson correlation coefficient of bin methylation level for the positive and negative DNA...

Additional file 2: of Comparing DNA methylation profiles in saliva and intestinal mucosa

Nerissa Hearn (6413723)
Aaron Coleman (6413726)
Vincent Ho (443227)
Christine Chiu (6413729)
Joanne Lind (3489548)

March 2019

Figure S1. Multi-dimensional scaling. A. All samples pre-normalisation samples classified by tissue ...

Additional file 1: of The associations of DNA methylation alterations in oxidative stress-related genes with cancer incidence and mortality outcomes: a population-based cohort study

Xīn Gào (6262232)
Yan Zhang (8098)
Barbara Burwinkel (146479)
Yang Xuan (419293)
Bernd Holleczek (287845)
Hermann Brenner (63649)
Ben Schöttker (300688)

January 2019

Table S1. 519 genes coding for proteins involved in pathways from oxidative stress to cancer. Table ...

Additional file 2: of DNA methylation of the promoter region of bnip3 and bnip3l genes induced by metabolic programming

Vincent Veron (154657)
Lucie Marandel (3994841)
Jingwei Liu (525202)
Emilio VĂŠlez (5755055)
Olivier Lepais (464756)
StĂŠphane Panserat (3994844)
Sandrine Skiba (5755040)
Iban Seiliez (320251)

September 2018

Table S1. Formulation and proximate composition of diet used in hypoxia stimulus [14]. Table S2. For...

Additional file 8 of Integrated analysis of DNA-methylation and gene expression using high-dimensional penalized regression: a cohort study on bone mineral density in postmenopausal women

Tonje Lien (4593184)
Ărnulf Borgan (4920787)
Sjur Reppe (152868)
Kaare Gautvik (580427)
Ingrid Glad (4920790)

March 2018

Figure S8. Distribution of p-values. The distribution of p-values from the âglobal testâ, when t...

Additional file 1: of Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation

Lucas Husquin (5864030)
Maxime Rotival (133720)
Maud Fagny (3470801)
Hélène Quach (262024)
Nora Zidane (85964)
Lisa McEwen (3968174)
Julia MacIsaac (3575030)
Michael Kobor (3470795)
Hugues Aschard (110171)
Etienne Patin (107311)
Lluis Quintana-Murci (3320199)

December 2018

Figure S1. Overview of the EvoImmunoPop experimental setting. Figure S2. Exploring the non-linear ef...

Additional file 1: Figure S1. of Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots

Nicklas Staunstrup (3470612)
Anna Starnawska (773141)
Mette Nyegaard (202075)
Lene Christiansen (158189)
Anders Nielsen (742984)
Anders BĂ¸rglum (3470615)
Ole Mors (128054)

July 2016

Number of experiments achievable per DBS by different methods. Part of a DBS necessary to meet the m...

Additional file 3: of DNA methylation patterns associated with oxidative stress in an ageing population

Åsa Hedman (59281)
Mihkel Zilmer (673181)
Johan Sundström (232655)
Lars Lind (88400)
Erik Ingelsson (232651)

November 2016

Supplemental Tables. Table S1. Methylation sites associated with TGSH (FDR <0.05). Table S2. Methyla...

Additional file 1: of Global DNA methylation changes spanning puberty are near predicted estrogen-responsive genes and enriched for genes involved in endocrine and immune processes

Emma Thompson (392865)
Jessie Nicodemus-Johnson (772733)
Kyung Kim (31555)
James Gern (3472670)
Daniel Jackson (176636)
Robert Lemanske (588802)
Carole Ober (259474)

May 2018

Scatterplot illustrating correlation between methylation beta values in all samples (Nâ=â55 pair...

Additional file 1: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Correcting CpG density bias by the normal curve and Using WGBS data for validation. (DOCX 16 kb

Additional file 3: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S2. Pearson correlation coefficient between the inferred bin methylation level and the RRBS da...

Additional file 2: of Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation

M. Morris (3777250)
L. Hesson (6164282)
R. Poulos (6164285)
R. Ward (3037509)
J. Wong (6164288)
N. Youngson (6164291)

December 2018

Figure S2. Quality control of ‘omics’. A Volcano plot depicting fold changes associated with differe...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

Additional file 1: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Abstract

Extracted data

Additional file 1: of DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data

Abstract

Extracted data

Related items

Related items