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)

Publication date

April 2018

DOI

10.6084/m9.figshare.6153230.v1

Abstract

Table S6. GO molecular function analysis of promoter hypermethylated genes. GO molecular function analysis for 404 promoter hypermethylated genes. (XLSX 13 kb

Extracted data

Topics

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Data Protection

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)

Open link

Publication date

April 2018

DOI

10.6084/m9.figshare.6153230.v1

Abstract

Table S6. GO molecular function analysis of promoter hypermethylated genes. GO molecular function analysis for 404 promoter hypermethylated genes. (XLSX 13 kb

Extracted data

Topics

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...

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 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

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 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 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 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 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 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 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 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: 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 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 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-...

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...

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 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

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 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 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 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 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 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 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 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: 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 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 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-...

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...

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 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

Abstract

Extracted data

Topics

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

Abstract

Extracted data

Topics

Related items

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