Additional file 5: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Additional file 1: Table S1. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

Affymetrix DNA microarray analysis of gene expression in HuH6shCTNNB1 cells in response to Dox treat...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 5: of Identification of trunk mutations in gastric carcinoma: a case study

Zhan Zhou (619006)
Shanshan Wu (348762)
Jun Lai (283485)
Yuan Shi (347224)
Chixiao Qiu (4253977)
Zhe Chen (196097)
Yufeng Wang (274657)
Xun Gu (4120)
Jie Zhou (28945)
Shuqing Chen (284288)

July 2017

Function annotation tables of 160 mutated genes, including Interpro, Gene Ontology (GO), KEGG pathwa...

Additional file 3: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Jianzhong Su (235944)
Yung-Hsin Huang (526919)
Xiaodong Cui (115533)
Xinyu Wang (341591)
Xiaotian Zhang (529088)
Yong Lei (337331)
Jianfeng Xu (80211)
Xueqiu Lin (4406707)
Kaifu Chen (116208)
Jie Lv (235936)
Margaret Goodell (4444438)
Wei Li (7081)

August 2018

Table S3. Pan-cancer differentially methylated UMRs across 7 tumor types. (XLS 15579 kb

Additional file 1: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Jianzhong Su (235944)
Yung-Hsin Huang (526919)
Xiaodong Cui (115533)
Xinyu Wang (341591)
Xiaotian Zhang (529088)
Yong Lei (337331)
Jianfeng Xu (80211)
Xueqiu Lin (4406707)
Kaifu Chen (116208)
Jie Lv (235936)
Margaret Goodell (4444438)
Wei Li (7081)

August 2018

Table S1. Data resource of WGBS, RNA-seq, and Infinium HumanMethylation 450 BeadChip data. (XLS 720 ...

Additional file 5: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S4. CDGs associated with significant genome-wide methylation changes in one cancer type. Hyper...

Additional file 4: Table S4. of Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India

Baidehi Basu (3717586)
Joyeeta Chakraborty (3717592)
Aditi Chandra (3717583)
Atul Katarkar (282856)
Jadav Baldevbhai (3717589)
Debjit Dhar Chowdhury (3717580)
Jay Ray (3717595)
Keya Chaudhuri (90539)
Raghunath Chatterjee (90538)

February 2017

Spreadsheet showing list of all unique differentially methylated probes. (XLSX 23 kb

Additional file 1: Table S1. of Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer

Tyler McInnes (3874525)
Donghui Zou (3874513)
Dasari Rao (3874516)
Francesca Munro (3874534)
Vicky Phillips (3874528)
John McCall (3874522)
Michael Black (246211)
Anthony Reeve (3874519)
Parry Guilford (3874531)

March 2017

258 genes hypermethylated in more than 90% of all CIMP-H tumours. Two-hundred fifty eight CpG island...

Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP...

Additional file 8: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S6. Number of tumor samples with mutations in each of the 21 chromatin regulator genes in list...

Additional file 2: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S2. A list of differentially hypermethylated and expressed genes identified by both EPIC array...

Additional file 7: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S5. Results from stratified analysis for the rest of the 15 cancer types (other than LGG) whos...

Additional file 4: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Figure S3. Methylation and hydroxymethylation levels distribution in different types of genomic elem...

Additional file 2: of Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma

Yu Cao (274482)
Katherine Green (5055230)
Steve Quattlebaum (5055248)
Ben Milam (5055236)
Ling Lu (53325)
Dexiang Gao (5055245)
Hui He (356808)
Ningning Li (566420)
Liwei Gao (794309)
Francis Hall (5055233)
Matthew Whinery (5055239)
Elyse Handley (5055242)
Yi Ma (167857)
Tao Xu (3537)
Feng Jin (303721)
Jing Xiao (356412)
Minjie Wei (154099)
Derek Smith (399177)
Sophia Bornstein (3515549)
Neil Gross (4425496)
Dohun Pyeon (266665)
John Song (437939)
Shi-Long Lu (1912276)

April 2018

Table S1. Relative methylation levels of mgmiRs in human HNSCC cell lines and normal head and neck c...

Additional file 2: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1: Table S1. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

Affymetrix DNA microarray analysis of gene expression in HuH6shCTNNB1 cells in response to Dox treat...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 5: of Identification of trunk mutations in gastric carcinoma: a case study

Zhan Zhou (619006)
Shanshan Wu (348762)
Jun Lai (283485)
Yuan Shi (347224)
Chixiao Qiu (4253977)
Zhe Chen (196097)
Yufeng Wang (274657)
Xun Gu (4120)
Jie Zhou (28945)
Shuqing Chen (284288)

July 2017

Function annotation tables of 160 mutated genes, including Interpro, Gene Ontology (GO), KEGG pathwa...

Additional file 3: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Jianzhong Su (235944)
Yung-Hsin Huang (526919)
Xiaodong Cui (115533)
Xinyu Wang (341591)
Xiaotian Zhang (529088)
Yong Lei (337331)
Jianfeng Xu (80211)
Xueqiu Lin (4406707)
Kaifu Chen (116208)
Jie Lv (235936)
Margaret Goodell (4444438)
Wei Li (7081)

August 2018

Table S3. Pan-cancer differentially methylated UMRs across 7 tumor types. (XLS 15579 kb

Additional file 1: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Jianzhong Su (235944)
Yung-Hsin Huang (526919)
Xiaodong Cui (115533)
Xinyu Wang (341591)
Xiaotian Zhang (529088)
Yong Lei (337331)
Jianfeng Xu (80211)
Xueqiu Lin (4406707)
Kaifu Chen (116208)
Jie Lv (235936)
Margaret Goodell (4444438)
Wei Li (7081)

August 2018

Table S1. Data resource of WGBS, RNA-seq, and Infinium HumanMethylation 450 BeadChip data. (XLS 720 ...

Additional file 5: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S4. CDGs associated with significant genome-wide methylation changes in one cancer type. Hyper...

Additional file 4: Table S4. of Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India

Baidehi Basu (3717586)
Joyeeta Chakraborty (3717592)
Aditi Chandra (3717583)
Atul Katarkar (282856)
Jadav Baldevbhai (3717589)
Debjit Dhar Chowdhury (3717580)
Jay Ray (3717595)
Keya Chaudhuri (90539)
Raghunath Chatterjee (90538)

February 2017

Spreadsheet showing list of all unique differentially methylated probes. (XLSX 23 kb

Additional file 1: Table S1. of Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer

Tyler McInnes (3874525)
Donghui Zou (3874513)
Dasari Rao (3874516)
Francesca Munro (3874534)
Vicky Phillips (3874528)
John McCall (3874522)
Michael Black (246211)
Anthony Reeve (3874519)
Parry Guilford (3874531)

March 2017

258 genes hypermethylated in more than 90% of all CIMP-H tumours. Two-hundred fifty eight CpG island...

Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP...

Additional file 8: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S6. Number of tumor samples with mutations in each of the 21 chromatin regulator genes in list...

Additional file 2: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Table S2. A list of differentially hypermethylated and expressed genes identified by both EPIC array...

Additional file 7: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S5. Results from stratified analysis for the rest of the 15 cancer types (other than LGG) whos...

Additional file 4: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Yimin Zhu (101874)
Hanlin Lu (2925378)
Dandan Zhang (228849)
Meiyan Li (441468)
Xiaohui Sun (520181)
Ledong Wan (1947580)
Dan Yu (214174)
Yiping Tian (4908259)
Hongchuan Jin (194460)
Aifen Lin (3504350)
Fei Gao (29262)
Maode Lai (15338)

March 2018

Figure S3. Methylation and hydroxymethylation levels distribution in different types of genomic elem...

Additional file 2: of Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma

Yu Cao (274482)
Katherine Green (5055230)
Steve Quattlebaum (5055248)
Ben Milam (5055236)
Ling Lu (53325)
Dexiang Gao (5055245)
Hui He (356808)
Ningning Li (566420)
Liwei Gao (794309)
Francis Hall (5055233)
Matthew Whinery (5055239)
Elyse Handley (5055242)
Yi Ma (167857)
Tao Xu (3537)
Feng Jin (303721)
Jing Xiao (356412)
Minjie Wei (154099)
Derek Smith (399177)
Sophia Bornstein (3515549)
Neil Gross (4425496)
Dohun Pyeon (266665)
John Song (437939)
Shi-Long Lu (1912276)

April 2018

Table S1. Relative methylation levels of mgmiRs in human HNSCC cell lines and normal head and neck c...

Additional file 2: of A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Ahrim Youn (4606252)
Kyung In Kim (47502)
Raul Rabadan (88130)
Benjamin Tycko (237065)
Yufeng Shen (239573)
Shuang Wang (46453)

November 2018

Table S2. A. Number of CDGs mutated in at least 5 samples with methylation data in one tumor type; B...

Additional file 1: Table S1. of A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1

Frédéric Canal (3179895)
Elodie Anthony (3461654)
Aurianne Lescure (310453)
Elaine Del Nery (310455)
Jacques Camonis (49694)
Franck Perez (259284)
Bruno Ragazzon (140444)
Christine Perret (365234)

December 2015

Affymetrix DNA microarray analysis of gene expression in HuH6shCTNNB1 cells in response to Dox treat...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 5: of Identification of trunk mutations in gastric carcinoma: a case study

Zhan Zhou (619006)
Shanshan Wu (348762)
Jun Lai (283485)
Yuan Shi (347224)
Chixiao Qiu (4253977)
Zhe Chen (196097)
Yufeng Wang (274657)
Xun Gu (4120)
Jie Zhou (28945)
Shuqing Chen (284288)

July 2017

Function annotation tables of 160 mutated genes, including Interpro, Gene Ontology (GO), KEGG pathwa...

Additional file 5: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Abstract

Extracted data

Additional file 5: of Homeobox oncogene activation by pan-cancer DNA hypermethylation

Abstract

Extracted data

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