Additional file 5: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Additional file 7: of Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

Roderick Slieker (3404279)
Maarten van Iterson (184364)
RenĂŠ Luijk (3427208)
Marian Beekman (67140)
Daria Zhernakova (3404231)
Matthijs Moed (3404273)
Hailiang Mei (3404261)
Michiel van Galen (278743)
Patrick Deelen (187548)
Marc Bonder (3404252)
Alexandra Zhernakova (102388)
AndrĂŠ Uitterlinden (3404267)
Ettje Tigchelaar (3404243)
Coen Stehouwer (3404234)
Casper Schalkwijk (3404270)
Carla van der Kallen (3404258)
Albert Hofman (107303)
Diana van Heemst (28182)
Eco de Geus (763746)
Jenny van Dongen (109719)
Joris Deelen (188359)
Leonard van den Berg (437389)
Joyce van Meurs (3404240)
Rick Jansen (198642)
Peter ât Hoen (3427211)
Lude Franke (102406)
Cisca Wijmenga (32954)
Jan Veldink (187567)
Morris Swertz (383290)
Marleen van Greevenbroek (3404255)
Cornelia van Duijn (160701)
Dorret Boomsma (39586)
P. Slagboom (3404282)
Bastiaan Heijmans (3404276)

September 2016

a Correlation between DNA methylation and gene expression of PcG complex proteins. b Overlap between...

Additional file 2 of Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression

Jonkman, Thomas H.
Dekkers, Koen F.
Slieker, Roderick C.
Grant, Crystal D.
Ikram, M. Arfan
van Greevenbroek, Marleen M. J.
Franke, Lude
Veldink, Jan H.
Boomsma, Dorret I.
Slagboom, P. Eline
Consortium, B.I.O.S.
Heijmans, Bastiaan T.
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Leiden University Medical Center

January 2022

Table S1. All associations between clock CpG methylation and expression of genes in cis and in trans...

Temporal profiles of genes maintaining circadian rhythmicity in liver, muscle, adipose, and lung.

Panteleimon D. Mavroudis (4990031)
Debra C. DuBois (228956)
Richard R. Almon (228960)
William J. Jusko (228952)

May 2018

<p>Upper panel: Heatmaps showing mean expression data from 3 animals sacrificed at the same time poi...

Additional file 7: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

TOMTOM output for hyper-variable cytosines from populational neutrophil data. Motifs detected from s...

Additional file 4: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

MEME output for oscillating cytosines in neutrophil. Motif enrichment logos and characteristics for ...

Additional file 6: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

MEME output for hyper-variable cytosines from populational neutrophil data. Motif enrichment logos a...

Additional file 2: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters for all interrogated CpG positions. EVC p value, cosinor p value, mesor, acro...

Additional file 3: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Proportion of variance explained by oscillations at various EVCs thresholds. Number of total EVCs, p...

Additional file 1: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters of white blood cell fractions. Counts, fractions, and oscillation p values of...

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Oh, Gabriel
Koncevičius, Karolis
Ebrahimi, Sasha
Carlucci, Matthew
Groot, Daniel Erik
Nair, Akhil
Zhang, Aiping
Kriščiūnas, Algimantas
Oh, Edward S.
Labrie, Viviane
Wong, Albert H. C.
Gordevičius, Juozas
Jia, Peixin
Susic, Miki
Petronis, Artūras

January 2019

Background: Maintenance of physiological circadian rhythm plays a crucial role in human health. Nume...

Circadian Oscillations of the Mouse and Human Epigenome

Parayarikkal Nair, Akhil

November 2019

Circadian rhythmicity in biological processes is an evolutionary adaptation in response to Earth’s r...

Circadian Hallmarks of the Aging Epigenome

Ebrahimi, Sasha

November 2017

Circadian rhythmicity governs a remarkable array of fundamental biological functions in eukaryotes w...

Additional file 4 of Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression

Jonkman, Thomas H.
Dekkers, Koen F.
Slieker, Roderick C.
Grant, Crystal D.
Ikram, M. Arfan
van Greevenbroek, Marleen M. J.
Franke, Lude
Veldink, Jan H.
Boomsma, Dorret I.
Slagboom, P. Eline
Consortium, B.I.O.S.
Heijmans, Bastiaan T.
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Leiden University Medical Center

January 2022

Table S3. Overlap between meQTLs affecting clock CpG DNAm and eQTLs affecting trans-gene expression

Bioinformatic Analysis of Circadian Reprogramming Events

Ceglia, Nicholas Joseph

January 2018

Circadian oscillations play a fundamental role in many biological processes including cell metabolis...

Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging

Oh, Gabriel
Ebrahimi, Sasha
Carlucci, Matthew
Zhang, Aiping
Nair, Akhil
Groot, Daniel E.
Labrie, Viviane
Jia, Peixin
Oh, Edward S.
Jeremian, Richie H.
Susic, Miki
Shrestha, Tenjin C.
Ralph, Martin R.
Gordevičius, Juozas
Koncevičius, Karolis
Petronis, Artūras

January 2018

Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated...

Additional file 7: of Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

Roderick Slieker (3404279)
Maarten van Iterson (184364)
RenĂŠ Luijk (3427208)
Marian Beekman (67140)
Daria Zhernakova (3404231)
Matthijs Moed (3404273)
Hailiang Mei (3404261)
Michiel van Galen (278743)
Patrick Deelen (187548)
Marc Bonder (3404252)
Alexandra Zhernakova (102388)
AndrĂŠ Uitterlinden (3404267)
Ettje Tigchelaar (3404243)
Coen Stehouwer (3404234)
Casper Schalkwijk (3404270)
Carla van der Kallen (3404258)
Albert Hofman (107303)
Diana van Heemst (28182)
Eco de Geus (763746)
Jenny van Dongen (109719)
Joris Deelen (188359)
Leonard van den Berg (437389)
Joyce van Meurs (3404240)
Rick Jansen (198642)
Peter ât Hoen (3427211)
Lude Franke (102406)
Cisca Wijmenga (32954)
Jan Veldink (187567)
Morris Swertz (383290)
Marleen van Greevenbroek (3404255)
Cornelia van Duijn (160701)
Dorret Boomsma (39586)
P. Slagboom (3404282)
Bastiaan Heijmans (3404276)

September 2016

a Correlation between DNA methylation and gene expression of PcG complex proteins. b Overlap between...

Additional file 2 of Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression

Jonkman, Thomas H.
Dekkers, Koen F.
Slieker, Roderick C.
Grant, Crystal D.
Ikram, M. Arfan
van Greevenbroek, Marleen M. J.
Franke, Lude
Veldink, Jan H.
Boomsma, Dorret I.
Slagboom, P. Eline
Consortium, B.I.O.S.
Heijmans, Bastiaan T.
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Leiden University Medical Center

January 2022

Table S1. All associations between clock CpG methylation and expression of genes in cis and in trans...

Temporal profiles of genes maintaining circadian rhythmicity in liver, muscle, adipose, and lung.

Panteleimon D. Mavroudis (4990031)
Debra C. DuBois (228956)
Richard R. Almon (228960)
William J. Jusko (228952)

May 2018

<p>Upper panel: Heatmaps showing mean expression data from 3 animals sacrificed at the same time poi...

Additional file 7: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

TOMTOM output for hyper-variable cytosines from populational neutrophil data. Motifs detected from s...

Additional file 4: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

MEME output for oscillating cytosines in neutrophil. Motif enrichment logos and characteristics for ...

Additional file 6: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

MEME output for hyper-variable cytosines from populational neutrophil data. Motif enrichment logos a...

Additional file 2: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters for all interrogated CpG positions. EVC p value, cosinor p value, mesor, acro...

Additional file 3: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Proportion of variance explained by oscillations at various EVCs thresholds. Number of total EVCs, p...

Additional file 1: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Gabriel Oh (3448379)
Karolis Koncevičius (6173486)
Sasha Ebrahimi (3448385)
Matthew Carlucci (6173489)
Daniel Groot (6173492)
Akhil Nair (6173495)
Aiping Zhang (448556)
Algimantas Kriščiūnas (6173498)
Edward Oh (6173501)
Viviane Labrie (6173504)
Albert Wong (365470)
Juozas Gordevičius (6173507)
Peixin Jia (6173510)
Miki Susic (6173513)
Art Petronis (3448373)

January 2019

Oscillation parameters of white blood cell fractions. Counts, fractions, and oscillation p values of...

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Oh, Gabriel
Koncevičius, Karolis
Ebrahimi, Sasha
Carlucci, Matthew
Groot, Daniel Erik
Nair, Akhil
Zhang, Aiping
Kriščiūnas, Algimantas
Oh, Edward S.
Labrie, Viviane
Wong, Albert H. C.
Gordevičius, Juozas
Jia, Peixin
Susic, Miki
Petronis, Artūras

January 2019

Background: Maintenance of physiological circadian rhythm plays a crucial role in human health. Nume...

Circadian Oscillations of the Mouse and Human Epigenome

Parayarikkal Nair, Akhil

November 2019

Circadian rhythmicity in biological processes is an evolutionary adaptation in response to Earth’s r...

Circadian Hallmarks of the Aging Epigenome

Ebrahimi, Sasha

November 2017

Circadian rhythmicity governs a remarkable array of fundamental biological functions in eukaryotes w...

Additional file 4 of Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression

Jonkman, Thomas H.
Dekkers, Koen F.
Slieker, Roderick C.
Grant, Crystal D.
Ikram, M. Arfan
van Greevenbroek, Marleen M. J.
Franke, Lude
Veldink, Jan H.
Boomsma, Dorret I.
Slagboom, P. Eline
Consortium, B.I.O.S.
Heijmans, Bastiaan T.
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Leiden University Medical Center

January 2022

Table S3. Overlap between meQTLs affecting clock CpG DNAm and eQTLs affecting trans-gene expression

Bioinformatic Analysis of Circadian Reprogramming Events

Ceglia, Nicholas Joseph

January 2018

Circadian oscillations play a fundamental role in many biological processes including cell metabolis...

Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging

Oh, Gabriel
Ebrahimi, Sasha
Carlucci, Matthew
Zhang, Aiping
Nair, Akhil
Groot, Daniel E.
Labrie, Viviane
Jia, Peixin
Oh, Edward S.
Jeremian, Richie H.
Susic, Miki
Shrestha, Tenjin C.
Ralph, Martin R.
Gordevičius, Juozas
Koncevičius, Karolis
Petronis, Artūras

January 2018

Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated...

Additional file 7: of Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

Roderick Slieker (3404279)
Maarten van Iterson (184364)
RenĂŠ Luijk (3427208)
Marian Beekman (67140)
Daria Zhernakova (3404231)
Matthijs Moed (3404273)
Hailiang Mei (3404261)
Michiel van Galen (278743)
Patrick Deelen (187548)
Marc Bonder (3404252)
Alexandra Zhernakova (102388)
AndrĂŠ Uitterlinden (3404267)
Ettje Tigchelaar (3404243)
Coen Stehouwer (3404234)
Casper Schalkwijk (3404270)
Carla van der Kallen (3404258)
Albert Hofman (107303)
Diana van Heemst (28182)
Eco de Geus (763746)
Jenny van Dongen (109719)
Joris Deelen (188359)
Leonard van den Berg (437389)
Joyce van Meurs (3404240)
Rick Jansen (198642)
Peter ât Hoen (3427211)
Lude Franke (102406)
Cisca Wijmenga (32954)
Jan Veldink (187567)
Morris Swertz (383290)
Marleen van Greevenbroek (3404255)
Cornelia van Duijn (160701)
Dorret Boomsma (39586)
P. Slagboom (3404282)
Bastiaan Heijmans (3404276)

September 2016

a Correlation between DNA methylation and gene expression of PcG complex proteins. b Overlap between...

Additional file 2 of Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression

Jonkman, Thomas H.
Dekkers, Koen F.
Slieker, Roderick C.
Grant, Crystal D.
Ikram, M. Arfan
van Greevenbroek, Marleen M. J.
Franke, Lude
Veldink, Jan H.
Boomsma, Dorret I.
Slagboom, P. Eline
Consortium, B.I.O.S.
Heijmans, Bastiaan T.
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Leiden University Medical Center

January 2022

Table S1. All associations between clock CpG methylation and expression of genes in cis and in trans...

Temporal profiles of genes maintaining circadian rhythmicity in liver, muscle, adipose, and lung.

Panteleimon D. Mavroudis (4990031)
Debra C. DuBois (228956)
Richard R. Almon (228960)
William J. Jusko (228952)

May 2018

<p>Upper panel: Heatmaps showing mean expression data from 3 animals sacrificed at the same time poi...

Additional file 5: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Abstract

Extracted data

Additional file 5: of Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

Abstract

Extracted data

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