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DNA methylation profiles of BM- and DF-iPSCs were similar in general, but had distinct features.

Akira Nasu (278429)
Makoto Ikeya (278430)
Takuya Yamamoto (232596)
Akira Watanabe (134585)
Yonghui Jin (278431)
Yoshihisa Matsumoto (114045)
Kazuo Hayakawa (278432)
Naoki Amano (278433)
Shingo Sato (185673)
Kenji Osafune (278434)
Tomoki Aoyama (105357)
Takashi Nakamura (8496)
Tomohisa Kato (278435)
Junya Toguchida (105365)

Publication date

January 2013

DOI

10.1371/journal.pone.0053771.g005

Abstract

<p>Hierarchical clustering using Euclidian distance with probe sets of differentially methylated regions between DFs and BMSCs.</p

Extracted data

Related items

Comparison of novel and existing methods for detecting differentially methylated regions

Samantha Lent
Hanfei Xu
Lan Wang
Zhe Wang
Chloé Sarnowski
Marie-France Hivert
Josée Dupuis

September 2018

Abstract Background Single-probe analyses in epigenome-wide association studies (EWAS) have identifi...

Diametrically opposed DNA methylation patterns in MLLr and IDH-mut AMLs.

Altuna Akalin (28028)
Francine E. Garrett-Bakelman (156647)
Matthias Kormaksson (103832)
Jennifer Busuttil (156649)
Lu Zhang (50563)
Irina Khrebtukova (156652)
Thomas A. Milne (156654)
Yongsheng Huang (156655)
Debabrata Biswas (156656)
Jay L. Hess (156657)
C. David Allis (156658)
Robert G. Roeder (156660)
Peter J. M. Valk (156662)
Bob Löwenberg (5648797)
Ruud Delwel (65976)
Hugo F. Fernandez (156665)
Elisabeth Paietta (88750)
Martin S. Tallman (156670)
Gary P. Schroth (156674)
Christopher E. Mason (152583)
Ari Melnick (88754)
Maria E. Figueroa (88744)

June 2012

<p>(A) Unsupervised analysis of DNA methylation by ERRBS using hierarchical clustering (distance = 1...

Clustering of gene expression and DNA methylation data.

Arnoud Boot (481202)
Jan Oosting (24912)
Jaap D. H. van Eendenburg (4449046)
Peter J. K. Kuppen (481206)
Hans Morreau (66216)
Tom van Wezel (24913)

September 2017

<p>To minimize overlap between cell line names, only the numbers corresponding to the cell lines wer...

Clustering analysis showing differential methylation in episomal iPS cells compared with virally induced iPS cells.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>(A) The heat map of hierarchical clustering analysis represents DNA methylation levels from compl...

Comparison of aberrant and inherited methylation in human iPSCs.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>The DMRs between ESCs and iPSCs are designated as ES-iPS-DMRs, and the DMRs between ESCs and pare...

Unsupervised clustering of samples.

Xufeng Li (602478)
Fuyou Zhou (280711)
Chunyu Jiang (602479)
Yinuo Wang (385434)
Yanqiang Lu (602480)
Fei Yang (46361)
Nengchao Wang (602481)
Haijun Yang (166821)
Yanfang Zheng (602482)
Jiren Zhang (602483)

July 2014

<p>Unsupervised hierarchical clustering on the entire DNA methylation data set showed the 2 clusters...

Heatmap of 26 highly differentially methylated loci.

Uppala Radhakrishna (804909)
Sangeetha Vishweswaraiah (429990)
Avinash M. Veerappa (429989)
Rita Zafra (5746679)
Samet Albayrak (2734897)
Prajna H. Sitharam (5746682)
Nazia M. Saiyed (5746685)
Nitish K. Mishra (589321)
Chittibabu Guda (13806)
Ray Bahado-Singh (5746688)

September 2018

DNA methylation profiling based on unsupervised hierarchical clustering identified four unique clust...

Hierarchical clustering of DNA methylation profiles.

Magnus Borssén (419233)
Lars Palmqvist (78127)
Kristina Karrman (419234)
Jonas Abrahamsson (419235)
Mikael Behrendtz (419236)
Jesper Heldrup (419237)
Erik Forestier (419238)
Göran Roos (285532)
Sofie Degerman (419239)

June 2013

<p>A) Unsupervised Euclidean hierarchical clustering was performed using beta values for the 1347 mo...

Pluripotent stem cells are significantly more hyper-methylated than differentiated cells.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>(A) Unsupervised hierarchical clustering analysis based on DNA methylation. (B) Principal compone...

Hierarchical Clustering of DNA methylation in 24 PA cases.

Chao Ling (418561)
Matthew Pease (499293)
Lingling Shi (275818)
Vasu Punj (15504)
Mark S. Shiroishi (556572)
Deborah Commins (556573)
Daniel J. Weisenberger (12485)
Kai Wang (21246)
Gabriel Zada (275823)

April 2014

<p>The HM450 probes (7,674) with the highest 2% of standard deviation across the set of 383,718 glob...

Overall methylation profiling of three cell types.

Anyou Wang (281729)
Ying Du (42066)
Qianchuan He (143345)
Chunxiao Zhou (281730)

February 2013

<p>All methylation sites measured by microarray were used to profile the overall methylation pattern...

Different cell types exhibit distinctive global DNA methylation patterns.

Zhenshan Liu (147780)
Rongfeng Jiang (459999)
Songtao Yuan (291486)
Na Wang (193263)
Yun Feng (193149)
Ganlu Hu (147760)
Xianmin Zhu (224947)
Kevin Huang (147764)
Jieliang Ma (538124)
Guotong Xu (466416)
Qinghuai Liu (5314640)
Zhigang Xue (147811)
Guoping Fan (147816)

March 2014

<p>DNA methylation profiles of different cell types were clustered using either unbiased hierarchica...

Visualized DMR profiles of UC and CB.

Kenichi Sakurai (6672533)
Keiko Shioda (399212)
Akifumi Eguchi (1719367)
Masahiro Watanabe (480517)
Hidenori Miyaso (6672536)
Chisato Mori (71625)
Toshi Shioda (399215)

May 2019

DNA methylation profiles of 10 UC (red) and 10 CB (blue) for the whole genome (A, B), the HOXD gene ...

General characteristics of BCC-specific DNA methylation patterns determined by MBD methylCap-seq.

Yangxing Zhao (171215)
Shicheng Guo (171219)
Jinfeng Sun (171224)
Zhaohui Huang (137665)
Tongyu Zhu (171229)
Hongyu Zhang (155876)
Jun Gu (89637)
Yinghua He (171234)
Wei Wang (17594)
Kelong Ma (171240)
Jina Wang (171246)
Jian Yu (141239)

April 2012

<p>The genomic context is defined as those found in the UCSC database. The featured differential met...

Analysis of methylation data obtained by ERRBS in oral tissues of mice treated with DBP or DMSO.

Yuan-Wan Sun (327299)
Kun-Ming Chen (589198)
Yuka Imamura Kawasawa (727177)
Anna C. Salzberg (128763)
Timothy K. Cooper (710868)
Carla Caruso (348124)
Cesar Aliaga (499854)
Junjia Zhu (638391)
Krishne Gowda (160251)
Shantu Amin (28527)
Karam El-Bayoumy (1327749)

October 2017

<p>(A) Unsupervised analysis of DNA methylation using hierarchical clustering. Distance = 1-Pearso...

Comparison of novel and existing methods for detecting differentially methylated regions

Samantha Lent
Hanfei Xu
Lan Wang
Zhe Wang
Chloé Sarnowski
Marie-France Hivert
Josée Dupuis

September 2018

Abstract Background Single-probe analyses in epigenome-wide association studies (EWAS) have identifi...

Diametrically opposed DNA methylation patterns in MLLr and IDH-mut AMLs.

Altuna Akalin (28028)
Francine E. Garrett-Bakelman (156647)
Matthias Kormaksson (103832)
Jennifer Busuttil (156649)
Lu Zhang (50563)
Irina Khrebtukova (156652)
Thomas A. Milne (156654)
Yongsheng Huang (156655)
Debabrata Biswas (156656)
Jay L. Hess (156657)
C. David Allis (156658)
Robert G. Roeder (156660)
Peter J. M. Valk (156662)
Bob Löwenberg (5648797)
Ruud Delwel (65976)
Hugo F. Fernandez (156665)
Elisabeth Paietta (88750)
Martin S. Tallman (156670)
Gary P. Schroth (156674)
Christopher E. Mason (152583)
Ari Melnick (88754)
Maria E. Figueroa (88744)

June 2012

<p>(A) Unsupervised analysis of DNA methylation by ERRBS using hierarchical clustering (distance = 1...

Clustering of gene expression and DNA methylation data.

Arnoud Boot (481202)
Jan Oosting (24912)
Jaap D. H. van Eendenburg (4449046)
Peter J. K. Kuppen (481206)
Hans Morreau (66216)
Tom van Wezel (24913)

September 2017

<p>To minimize overlap between cell line names, only the numbers corresponding to the cell lines wer...

Clustering analysis showing differential methylation in episomal iPS cells compared with virally induced iPS cells.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>(A) The heat map of hierarchical clustering analysis represents DNA methylation levels from compl...

Comparison of aberrant and inherited methylation in human iPSCs.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>The DMRs between ESCs and iPSCs are designated as ES-iPS-DMRs, and the DMRs between ESCs and pare...

Unsupervised clustering of samples.

Xufeng Li (602478)
Fuyou Zhou (280711)
Chunyu Jiang (602479)
Yinuo Wang (385434)
Yanqiang Lu (602480)
Fei Yang (46361)
Nengchao Wang (602481)
Haijun Yang (166821)
Yanfang Zheng (602482)
Jiren Zhang (602483)

July 2014

<p>Unsupervised hierarchical clustering on the entire DNA methylation data set showed the 2 clusters...

Heatmap of 26 highly differentially methylated loci.

Uppala Radhakrishna (804909)
Sangeetha Vishweswaraiah (429990)
Avinash M. Veerappa (429989)
Rita Zafra (5746679)
Samet Albayrak (2734897)
Prajna H. Sitharam (5746682)
Nazia M. Saiyed (5746685)
Nitish K. Mishra (589321)
Chittibabu Guda (13806)
Ray Bahado-Singh (5746688)

September 2018

DNA methylation profiling based on unsupervised hierarchical clustering identified four unique clust...

Hierarchical clustering of DNA methylation profiles.

Magnus Borssén (419233)
Lars Palmqvist (78127)
Kristina Karrman (419234)
Jonas Abrahamsson (419235)
Mikael Behrendtz (419236)
Jesper Heldrup (419237)
Erik Forestier (419238)
Göran Roos (285532)
Sofie Degerman (419239)

June 2013

<p>A) Unsupervised Euclidean hierarchical clustering was performed using beta values for the 1347 mo...

Pluripotent stem cells are significantly more hyper-methylated than differentiated cells.

WenYin He (5660608)
XiangJin Kang (286621)
HongZi Du (3397691)
Bing Song (155375)
ZhenYu Lu (633884)
Yuling Huang (633885)
Ding Wang (191462)
Xiaofang Sun (402841)
Yang Yu (4292)
Yong Fan (212624)

September 2014

<p>(A) Unsupervised hierarchical clustering analysis based on DNA methylation. (B) Principal compone...

Hierarchical Clustering of DNA methylation in 24 PA cases.

Chao Ling (418561)
Matthew Pease (499293)
Lingling Shi (275818)
Vasu Punj (15504)
Mark S. Shiroishi (556572)
Deborah Commins (556573)
Daniel J. Weisenberger (12485)
Kai Wang (21246)
Gabriel Zada (275823)

April 2014

<p>The HM450 probes (7,674) with the highest 2% of standard deviation across the set of 383,718 glob...

Overall methylation profiling of three cell types.

Anyou Wang (281729)
Ying Du (42066)
Qianchuan He (143345)
Chunxiao Zhou (281730)

February 2013

<p>All methylation sites measured by microarray were used to profile the overall methylation pattern...

Different cell types exhibit distinctive global DNA methylation patterns.

Zhenshan Liu (147780)
Rongfeng Jiang (459999)
Songtao Yuan (291486)
Na Wang (193263)
Yun Feng (193149)
Ganlu Hu (147760)
Xianmin Zhu (224947)
Kevin Huang (147764)
Jieliang Ma (538124)
Guotong Xu (466416)
Qinghuai Liu (5314640)
Zhigang Xue (147811)
Guoping Fan (147816)

March 2014

<p>DNA methylation profiles of different cell types were clustered using either unbiased hierarchica...

Visualized DMR profiles of UC and CB.

Kenichi Sakurai (6672533)
Keiko Shioda (399212)
Akifumi Eguchi (1719367)
Masahiro Watanabe (480517)
Hidenori Miyaso (6672536)
Chisato Mori (71625)
Toshi Shioda (399215)

May 2019

DNA methylation profiles of 10 UC (red) and 10 CB (blue) for the whole genome (A, B), the HOXD gene ...

General characteristics of BCC-specific DNA methylation patterns determined by MBD methylCap-seq.

Yangxing Zhao (171215)
Shicheng Guo (171219)
Jinfeng Sun (171224)
Zhaohui Huang (137665)
Tongyu Zhu (171229)
Hongyu Zhang (155876)
Jun Gu (89637)
Yinghua He (171234)
Wei Wang (17594)
Kelong Ma (171240)
Jina Wang (171246)
Jian Yu (141239)

April 2012

<p>The genomic context is defined as those found in the UCSC database. The featured differential met...

Analysis of methylation data obtained by ERRBS in oral tissues of mice treated with DBP or DMSO.

Yuan-Wan Sun (327299)
Kun-Ming Chen (589198)
Yuka Imamura Kawasawa (727177)
Anna C. Salzberg (128763)
Timothy K. Cooper (710868)
Carla Caruso (348124)
Cesar Aliaga (499854)
Junjia Zhu (638391)
Krishne Gowda (160251)
Shantu Amin (28527)
Karam El-Bayoumy (1327749)

October 2017

<p>(A) Unsupervised analysis of DNA methylation using hierarchical clustering. Distance = 1-Pearso...

Comparison of novel and existing methods for detecting differentially methylated regions

Samantha Lent
Hanfei Xu
Lan Wang
Zhe Wang
Chloé Sarnowski
Marie-France Hivert
Josée Dupuis

September 2018

Abstract Background Single-probe analyses in epigenome-wide association studies (EWAS) have identifi...

Diametrically opposed DNA methylation patterns in MLLr and IDH-mut AMLs.

Altuna Akalin (28028)
Francine E. Garrett-Bakelman (156647)
Matthias Kormaksson (103832)
Jennifer Busuttil (156649)
Lu Zhang (50563)
Irina Khrebtukova (156652)
Thomas A. Milne (156654)
Yongsheng Huang (156655)
Debabrata Biswas (156656)
Jay L. Hess (156657)
C. David Allis (156658)
Robert G. Roeder (156660)
Peter J. M. Valk (156662)
Bob Löwenberg (5648797)
Ruud Delwel (65976)
Hugo F. Fernandez (156665)
Elisabeth Paietta (88750)
Martin S. Tallman (156670)
Gary P. Schroth (156674)
Christopher E. Mason (152583)
Ari Melnick (88754)
Maria E. Figueroa (88744)

June 2012

<p>(A) Unsupervised analysis of DNA methylation by ERRBS using hierarchical clustering (distance = 1...

Clustering of gene expression and DNA methylation data.

Arnoud Boot (481202)
Jan Oosting (24912)
Jaap D. H. van Eendenburg (4449046)
Peter J. K. Kuppen (481206)
Hans Morreau (66216)
Tom van Wezel (24913)

September 2017

<p>To minimize overlap between cell line names, only the numbers corresponding to the cell lines wer...