Additional file 9: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Additional file 7: Figure S3. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

ROC curve and waterfall plot for diagnostic model applied to an independent cohort of prostate cance...

Additional file 1: of Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients

Catarina Moreira-Barbosa (5907095)
Daniela Barros-Silva (4922425)
Pedro Costa-Pinheiro (816456)
Jorge Torres-Ferreira (3764845)
Vera Constâncio (5907098)
Rui Freitas (3764833)
Jorge Oliveira (33493)
Luís Antunes (701921)
Rui Henrique (33490)
Carmen Jerónimo (33496)

October 2018

Table S1. Primer sequences for β-Actin, miR-34b/c, and miR-193b (panel #1). Table S2. Scorpion prime...

Additional file 1: of Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

Sarah Voisin (695350)
Markus Almén (3432941)
Galina Zheleznyakova (625786)
Lina Lundberg (3557939)
Sanaz Zarei (3557936)
Sandra Castillo (218332)
Fia Eriksson (3557933)
Emil Nilsson (3557942)
Matthias Blüher (103713)
Yvonne Böttcher (103725)
Peter Kovacs (103720)
Janis Klovins (76934)
Mathias Rask-Andersen (446207)
Helgi Schiöth (3432935)

October 2015

Description of the 52 investigated SNPs. SNPs in bold are SNPs for which significant associations wi...

Additional file 8: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S6. GO molecular function analysis of promoter hypermethylated genes. GO molecular function an...

Additional file 10: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S8. Pathway enrichment analysis of the genes included in PPI networks. Pathway enrichment anal...

Additional file 12: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S10. Pathway enrichment analysis of the selected genes with multiple hypermethylated CpG sites...

Additional file 14: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S12. GO molecular function analysis of the overlapping genes. GO molecular function analyses f...

Additional file 4: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S2. Distribution of differentially methylated CpG sites in relation to the nearest gene region...

Additional file 6: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S4. Differentially methylated CpG sites located at both gene promoters and CpG islands. This t...

Additional file 2: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S1. Differentially methylated CpG sites in PPAT between obese/overweight PCa patients and norm...

Additional file 9: Figure S5. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

ROC curve and waterfall plot for the top hypermethylated CpG model in the TCGA validation cohort (a-...

Additional file 9: of Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression

Shivani Kamdar (3423416)
Ruth Isserlin (237394)
Theodorus Kwast (3423422)
Alexandre Zlotta (3423419)
Gary Bader (3423413)
Neil Fleshner (361896)
Bharati Bapat (112041)

March 2019

Table S3. Characteristics of the 61 genes exhibiting significantly increased promoter methylation an...

Additional file 1: Table S1. of Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes

Samantha Day (3560522)
Richard Coletta (3560528)
Joon Kim (510697)
Latoya Campbell (3560537)
Tonya Benjamin (3560519)
Lori Roust (3560531)
Elena De Filippis (2993133)
Valentin Dinu (801175)
Gabriel Shaibi (3560525)
Lawrence Mandarino (3505169)
Dawn Coletta (3560534)

July 2016

The 13,130 differentially methylated cytosines (DMCs; Pâ<â0.05) that were located within a promo...

Additional file 8: Figure S4. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

Boxplots of CpGs in the top diagnostic model from hypermethylated CpGs. Normal data is from benign-a...

Additional file 9: of Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

Sarah Voisin (695350)
Markus Almén (3432941)
Galina Zheleznyakova (625786)
Lina Lundberg (3557939)
Sanaz Zarei (3557936)
Sandra Castillo (218332)
Fia Eriksson (3557933)
Emil Nilsson (3557942)
Matthias Blüher (103713)
Yvonne Böttcher (103725)
Peter Kovacs (103720)
Janis Klovins (76934)
Mathias Rask-Andersen (446207)
Helgi Schiöth (3432935)

October 2015

Correlations between Illumina 450 K and pyrosequence analysis of cg15576492. Methylation at cg155764...

Additional file 7: Figure S3. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

ROC curve and waterfall plot for diagnostic model applied to an independent cohort of prostate cance...

Additional file 1: of Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients

Catarina Moreira-Barbosa (5907095)
Daniela Barros-Silva (4922425)
Pedro Costa-Pinheiro (816456)
Jorge Torres-Ferreira (3764845)
Vera Constâncio (5907098)
Rui Freitas (3764833)
Jorge Oliveira (33493)
Luís Antunes (701921)
Rui Henrique (33490)
Carmen Jerónimo (33496)

October 2018

Table S1. Primer sequences for β-Actin, miR-34b/c, and miR-193b (panel #1). Table S2. Scorpion prime...

Additional file 1: of Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

Sarah Voisin (695350)
Markus Almén (3432941)
Galina Zheleznyakova (625786)
Lina Lundberg (3557939)
Sanaz Zarei (3557936)
Sandra Castillo (218332)
Fia Eriksson (3557933)
Emil Nilsson (3557942)
Matthias Blüher (103713)
Yvonne Böttcher (103725)
Peter Kovacs (103720)
Janis Klovins (76934)
Mathias Rask-Andersen (446207)
Helgi Schiöth (3432935)

October 2015

Description of the 52 investigated SNPs. SNPs in bold are SNPs for which significant associations wi...

Additional file 8: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S6. GO molecular function analysis of promoter hypermethylated genes. GO molecular function an...

Additional file 10: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S8. Pathway enrichment analysis of the genes included in PPI networks. Pathway enrichment anal...

Additional file 12: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S10. Pathway enrichment analysis of the selected genes with multiple hypermethylated CpG sites...

Additional file 14: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S12. GO molecular function analysis of the overlapping genes. GO molecular function analyses f...

Additional file 4: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S2. Distribution of differentially methylated CpG sites in relation to the nearest gene region...

Additional file 6: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S4. Differentially methylated CpG sites located at both gene promoters and CpG islands. This t...

Additional file 2: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Yan Cheng (149222)
Cátia Monteiro (5113517)
Andreia Matos (5113523)
Jiaying You (5113520)
Avelino Fraga (740667)
Carina Pereira (546267)
Victoria Catalán (260177)
Amaia Rodríguez (260171)
Javier Gómez-Ambrosi (260192)
Gema Frühbeck (161466)
Ricardo Ribeiro (3705724)
Pingzhao Hu (62169)

April 2018

Table S1. Differentially methylated CpG sites in PPAT between obese/overweight PCa patients and norm...

Additional file 9: Figure S5. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

ROC curve and waterfall plot for the top hypermethylated CpG model in the TCGA validation cohort (a-...

Additional file 9: of Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression

Shivani Kamdar (3423416)
Ruth Isserlin (237394)
Theodorus Kwast (3423422)
Alexandre Zlotta (3423419)
Gary Bader (3423413)
Neil Fleshner (361896)
Bharati Bapat (112041)

March 2019

Table S3. Characteristics of the 61 genes exhibiting significantly increased promoter methylation an...

Additional file 1: Table S1. of Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes

Samantha Day (3560522)
Richard Coletta (3560528)
Joon Kim (510697)
Latoya Campbell (3560537)
Tonya Benjamin (3560519)
Lori Roust (3560531)
Elena De Filippis (2993133)
Valentin Dinu (801175)
Gabriel Shaibi (3560525)
Lawrence Mandarino (3505169)
Dawn Coletta (3560534)

July 2016

The 13,130 differentially methylated cytosines (DMCs; Pâ<â0.05) that were located within a promo...

Additional file 8: Figure S4. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

Boxplots of CpGs in the top diagnostic model from hypermethylated CpGs. Normal data is from benign-a...

Additional file 9: of Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

Sarah Voisin (695350)
Markus Almén (3432941)
Galina Zheleznyakova (625786)
Lina Lundberg (3557939)
Sanaz Zarei (3557936)
Sandra Castillo (218332)
Fia Eriksson (3557933)
Emil Nilsson (3557942)
Matthias Blüher (103713)
Yvonne Böttcher (103725)
Peter Kovacs (103720)
Janis Klovins (76934)
Mathias Rask-Andersen (446207)
Helgi Schiöth (3432935)

October 2015

Correlations between Illumina 450 K and pyrosequence analysis of cg15576492. Methylation at cg155764...

Additional file 7: Figure S3. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Marie Kirby (3928127)
Ryne Ramaker (3533108)
Brian Roberts (413821)
Brittany Lasseigne (3928124)
David Gunther (3928130)
Todd Burwell (3533105)
Nicholas Davis (3928121)
Zulfiqar Gulzar (3928133)
Devin Absher (217357)
Sara Cooper (668192)
James Brooks (160771)
Richard Myers (179413)

April 2017

ROC curve and waterfall plot for diagnostic model applied to an independent cohort of prostate cance...

Additional file 1: of Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients

Catarina Moreira-Barbosa (5907095)
Daniela Barros-Silva (4922425)
Pedro Costa-Pinheiro (816456)
Jorge Torres-Ferreira (3764845)
Vera Constâncio (5907098)
Rui Freitas (3764833)
Jorge Oliveira (33493)
Luís Antunes (701921)
Rui Henrique (33490)
Carmen Jerónimo (33496)

October 2018

Table S1. Primer sequences for β-Actin, miR-34b/c, and miR-193b (panel #1). Table S2. Scorpion prime...

Additional file 1: of Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

Sarah Voisin (695350)
Markus Almén (3432941)
Galina Zheleznyakova (625786)
Lina Lundberg (3557939)
Sanaz Zarei (3557936)
Sandra Castillo (218332)
Fia Eriksson (3557933)
Emil Nilsson (3557942)
Matthias Blüher (103713)
Yvonne Böttcher (103725)
Peter Kovacs (103720)
Janis Klovins (76934)
Mathias Rask-Andersen (446207)
Helgi Schiöth (3432935)

October 2015

Description of the 52 investigated SNPs. SNPs in bold are SNPs for which significant associations wi...

Additional file 9: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Abstract

Extracted data

Additional file 9: of Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Abstract

Extracted data

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