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

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 Software Library for Circadian Analysis

Ceglia, Nicholas Joseph

January 2018

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

Expanding circadian input, output, and the clock through genomic screens

Atwood, Ann Margaret

January 2011

Many aspects of mammalian physiology display circadian--or once daily--rhythms, such as heart rate, ...

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 5: 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 oscillating cytosines in neutrophil. Motifs detected from sequences flanking osc-m...

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 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...

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...

Bioinformatic Analysis of Circadian Reprogramming Events

Ceglia, Nicholas Joseph

January 2018

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

Additional file 4: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S4. Circadian clocks in breast tissue. Left - representative Per2::Luc traces from cultures o...

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 Software Library for Circadian Analysis

Ceglia, Nicholas Joseph

January 2018

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

Expanding circadian input, output, and the clock through genomic screens

Atwood, Ann Margaret

January 2011

Many aspects of mammalian physiology display circadian--or once daily--rhythms, such as heart rate, ...

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 5: 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 oscillating cytosines in neutrophil. Motifs detected from sequences flanking osc-m...

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 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...

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...

Bioinformatic Analysis of Circadian Reprogramming Events

Ceglia, Nicholas Joseph

January 2018

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

Additional file 4: of Disrupted circadian clocks and altered tissue mechanics in primary human breast tumours

Eleanor Broadberry (5881016)
James McConnell (3487649)
Jack Williams (52430)
Nan Yang (305078)
Egor Zindy (2656738)
Angela Leek (3487679)
Rachel Waddington (5881019)
Leena Joseph (180330)
Miles Howe (3487661)
Qing-Jun Meng (179045)
Charles Streuli (3487652)

October 2018

Figure S4. Circadian clocks in breast tissue. Left - representative Per2::Luc traces from cultures o...

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 Software Library for Circadian Analysis

Ceglia, Nicholas Joseph

January 2018

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

Expanding circadian input, output, and the clock through genomic screens

Atwood, Ann Margaret

January 2011

Many aspects of mammalian physiology display circadian--or once daily--rhythms, such as heart rate, ...

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

Abstract

Extracted data

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

Abstract

Extracted data

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