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

Additional file 1: of A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer

Fang Zhao (11980)
Ekaterina Olkhov-Mitsel (1975102)
Shivani Kamdar (3423416)
Renu Jeyapala (6005801)
Julia Garcia (6005807)
Rachel Hurst (227017)
Marcelino Hanna (6005813)
Robert Mills (6005816)
Alexandra Tuzova (6005819)
Eve O’Reilly (6005822)
Sarah Kelly (573743)
Colin Cooper (239930)
Daniel Brewer (21016)
Antoinette Perry (6005825)
Jeremy Clark (120973)
Neil Fleshner (361896)
Bharati Bapat (112041)

November 2018

Table S1. Correlations. Spearman’s rank correlations for the PMR values of each biomarker, ProCUrE, ...

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...

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

Cheng Y
Monteiro C
Matos M
You J
Fraga A
Pereira C
Catalán V
Rodríguez A
Gómez-Ambrosi J
Frühbeck G
Ribeiro R
Hu P

January 2018

Background: Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cance...

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 9: 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 S7. Pathway enrichment analysis of promoter hypermethylated genes. Pathway enrichment analysis...

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 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 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 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 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 8: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Donia Macartney-Coxson (326420)
Miles Benton (321392)
Ray Blick (3999590)
Richard Stubbs (688395)
Ronald Hagan (290342)
Michael Langston (3446957)

May 2017

Enrichment results for genes mapping to DMRs observed in both the before and after weight loss analy...

Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposit : a pilot study

Cheng, Yan
Monteiro, Cátia
Matos, Andreia
You, Jiaying
Fraga, Avelino
Pereira, Carina
Catalán, Victoria
Rodríguez, Amaia
Gómez-Ambrosi, Javier
Frühbeck, Gema
Ribeiro, Ricardo
Hu, Pingzhao

January 2018

Additional file 1: of A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer

Fang Zhao (11980)
Ekaterina Olkhov-Mitsel (1975102)
Shivani Kamdar (3423416)
Renu Jeyapala (6005801)
Julia Garcia (6005807)
Rachel Hurst (227017)
Marcelino Hanna (6005813)
Robert Mills (6005816)
Alexandra Tuzova (6005819)
Eve O’Reilly (6005822)
Sarah Kelly (573743)
Colin Cooper (239930)
Daniel Brewer (21016)
Antoinette Perry (6005825)
Jeremy Clark (120973)
Neil Fleshner (361896)
Bharati Bapat (112041)

November 2018

Table S1. Correlations. Spearman’s rank correlations for the PMR values of each biomarker, ProCUrE, ...

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...

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

Cheng Y
Monteiro C
Matos M
You J
Fraga A
Pereira C
Catalán V
Rodríguez A
Gómez-Ambrosi J
Frühbeck G
Ribeiro R
Hu P

January 2018

Background: Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cance...

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 9: 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 S7. Pathway enrichment analysis of promoter hypermethylated genes. Pathway enrichment analysis...

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 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 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 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 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 8: of Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals

Donia Macartney-Coxson (326420)
Miles Benton (321392)
Ray Blick (3999590)
Richard Stubbs (688395)
Ronald Hagan (290342)
Michael Langston (3446957)

May 2017

Enrichment results for genes mapping to DMRs observed in both the before and after weight loss analy...

Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposit : a pilot study

Cheng, Yan
Monteiro, Cátia
Matos, Andreia
You, Jiaying
Fraga, Avelino
Pereira, Carina
Catalán, Victoria
Rodríguez, Amaia
Gómez-Ambrosi, Javier
Frühbeck, Gema
Ribeiro, Ricardo
Hu, Pingzhao

January 2018

Additional file 1: of A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer

Fang Zhao (11980)
Ekaterina Olkhov-Mitsel (1975102)
Shivani Kamdar (3423416)
Renu Jeyapala (6005801)
Julia Garcia (6005807)
Rachel Hurst (227017)
Marcelino Hanna (6005813)
Robert Mills (6005816)
Alexandra Tuzova (6005819)
Eve O’Reilly (6005822)
Sarah Kelly (573743)
Colin Cooper (239930)
Daniel Brewer (21016)
Antoinette Perry (6005825)
Jeremy Clark (120973)
Neil Fleshner (361896)
Bharati Bapat (112041)

November 2018

Table S1. Correlations. Spearman’s rank correlations for the PMR values of each biomarker, ProCUrE, ...

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...

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

Cheng Y
Monteiro C
Matos M
You J
Fraga A
Pereira C
Catalán V
Rodríguez A
Gómez-Ambrosi J
Frühbeck G
Ribeiro R
Hu P

January 2018

Background: Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cance...

Additional file 10: 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 10: 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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