Additional file 2: 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)

Publication date

October 2018

DOI

10.6084/m9.figshare.7269794.v1

Abstract

Figure S1. Box-plots of panel #1 (miR-34b/c, miR-193b) and panel #2 (APC, GSTP1, and RARβ2) promoter methylation levels in morphologically normal prostatic tissue (MNPT) and prostate cancer patients submitted to prostate biopsy (PCa) (cohort #1). (Mann-Whitney U test, ****P < 0.0001). (TIFF 1344 kb

Extracted data

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Additional file 2: 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)

Open link

Publication date

October 2018

DOI

10.6084/m9.figshare.7269794.v1

Abstract

Extracted data

João Ramalho-Carvalho (213300)
Inês Graça (388023)
Antonio Gomez (3445997)
Jorge Oliveira (33493)
Rui Henrique (33490)
Manel Esteller (74345)
Carmen Jerónimo (33496)

February 2017

DNA methylation changes in microRNAs´ promoters in prostate cancer (PCa), determined by Infinium Hum...

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 3: 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

Figure S2. Box-plots of panel #1 (miR-34b/c, miR-193b) and panel #2 (APC, RARβ2) promoter methylatio...

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 2: Figure S1. of MiR-193b promoter methylation accurately detects prostate cancer in urine sediments and miR-34b/c or miR-129-2 promoter methylation define subsets of clinically aggressive tumors

Jorge Torres-Ferreira (3764845)
João Ramalho-Carvalho (213300)
Antonio Gomez (3445997)
Francisco Menezes (3764839)
Rui Freitas (3764833)
Jorge Oliveira (33493)
Luís Antunes (701921)
Maria Bento (3472109)
Manel Esteller (74345)
Rui Henrique (33490)
Carmen Jerónimo (33496)

January 2017

Distribution of miR’s promoter methylation levels in prostatic, vesical and renal tissues. MNPT - mo...

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 2: 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 OâReilly (6005870)
Sarah Kelly (573743)
Colin Cooper (239930)
Daniel Brewer (21016)
Antoinette Perry (6005825)
Jeremy Clark (120973)
Neil Fleshner (361896)
Bharati Bapat (112041)

November 2018

Figure S1. Diagnostic and prognostic ability of ProCUrE and age-adjusted PSA in the training cohort....

Additional file 2: of CD38 is methylated in prostate cancer and regulates extracellular NAD+

Jack Mottahedeh (5119268)
Michael Haffner (5779562)
Tristan Grogan (628047)
Takao Hashimoto (662481)
Preston Crowell (5779565)
Himisha Beltran (5779568)
Andrea Sboner (180596)
Rohan Bareja (5779571)
David Esopi (4347547)
William Isaacs (4458526)
Srinivasan Yegnasubramanian (27577)
Matthew Rettig (146731)
David Elashoff (195366)
Elizabeth Platz (3624092)
Angelo De Marzo (200674)
Michael Teitell (5779574)
Andrew Goldstein (5779577)

September 2018

In silico analysis of TCGA data correlating DNA methylation and mRNA expression of commonly methylat...

Additional file 2: of Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/CtIP is almost exclusively methylated in bladder cancer

Jolein Mijnes (3155121)
JĂźrgen Veeck (3777349)
Nadine Gaisa (4831452)
Eduard Burghardt (4831449)
Tim de Ruijter (4831455)
Sonja Gostek (4831458)
Edgar Dahl (42758)
David Pfister (2570215)
Sebastian Schmid (775115)
Ruth KnĂźchel (3777352)
Michael Rose (321021)

February 2018

Detailed frequency of DNAm of BRCA1, MGMT, and ERCC1 across cancer entities and corresponding normal...

Additional file 1: Table S1. of Downregulation of miR-130b~301b cluster is mediated by aberrant promoter methylation and impairs cellular senescence in prostate cancer

João Ramalho-Carvalho (213300)
Inês Graça (388023)
Antonio Gomez (3445997)
Jorge Oliveira (33493)
Rui Henrique (33490)
Manel Esteller (74345)
Carmen Jerónimo (33496)

February 2017

Clinical and pathological data of the patients included in the study. Table S2. Primers used in the ...

Additional file 2: Figure S2. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

Rafael Fort (4624405)
Cecilia Mathó (4819026)
Murilo Geraldo (3406595)
María Ottati (4819032)
Alex Yamashita (4819041)
Kelly Saito (4819038)
Katia Leite (4819035)
Manuel Méndez (4819044)
Noemí Maedo (4819047)
Laura Méndez (4819050)
Beatriz Garat (408302)
Edna Kimura (3406598)
José Sotelo-Silveira (3457943)
María Duhagon (4819029)

February 2018

Hierarchical cluster of 50 paired normal and tumor tissue of PrCa patients from TCGA-PRAD dataset. A...

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 2: Figure S1. of Downregulation of miR-130b~301b cluster is mediated by aberrant promoter methylation and impairs cellular senescence in prostate cancer

João Ramalho-Carvalho (213300)
Inês Graça (388023)
Antonio Gomez (3445997)
Jorge Oliveira (33493)
Rui Henrique (33490)
Manel Esteller (74345)
Carmen Jerónimo (33496)

February 2017

DNA methylation changes in microRNAs´ promoters in prostate cancer (PCa), determined by Infinium Hum...

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 3: 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

Figure S2. Box-plots of panel #1 (miR-34b/c, miR-193b) and panel #2 (APC, RARβ2) promoter methylatio...

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...

Jorge Torres-Ferreira (3764845)
João Ramalho-Carvalho (213300)
Antonio Gomez (3445997)
Francisco Menezes (3764839)
Rui Freitas (3764833)
Jorge Oliveira (33493)
Luís Antunes (701921)
Maria Bento (3472109)
Manel Esteller (74345)
Rui Henrique (33490)
Carmen Jerónimo (33496)

January 2017

Distribution of miR’s promoter methylation levels in prostatic, vesical and renal tissues. MNPT - mo...

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 2: 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 OâReilly (6005870)
Sarah Kelly (573743)
Colin Cooper (239930)
Daniel Brewer (21016)
Antoinette Perry (6005825)
Jeremy Clark (120973)
Neil Fleshner (361896)
Bharati Bapat (112041)

November 2018

Figure S1. Diagnostic and prognostic ability of ProCUrE and age-adjusted PSA in the training cohort....

Additional file 2: of CD38 is methylated in prostate cancer and regulates extracellular NAD+

Jack Mottahedeh (5119268)
Michael Haffner (5779562)
Tristan Grogan (628047)
Takao Hashimoto (662481)
Preston Crowell (5779565)
Himisha Beltran (5779568)
Andrea Sboner (180596)
Rohan Bareja (5779571)
David Esopi (4347547)
William Isaacs (4458526)
Srinivasan Yegnasubramanian (27577)
Matthew Rettig (146731)
David Elashoff (195366)
Elizabeth Platz (3624092)
Angelo De Marzo (200674)
Michael Teitell (5779574)
Andrew Goldstein (5779577)

September 2018

In silico analysis of TCGA data correlating DNA methylation and mRNA expression of commonly methylat...

Additional file 2: of Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/CtIP is almost exclusively methylated in bladder cancer

Jolein Mijnes (3155121)
JĂźrgen Veeck (3777349)
Nadine Gaisa (4831452)
Eduard Burghardt (4831449)
Tim de Ruijter (4831455)
Sonja Gostek (4831458)
Edgar Dahl (42758)
David Pfister (2570215)
Sebastian Schmid (775115)
Ruth KnĂźchel (3777352)
Michael Rose (321021)

February 2018

Detailed frequency of DNAm of BRCA1, MGMT, and ERCC1 across cancer entities and corresponding normal...

Additional file 1: Table S1. of Downregulation of miR-130b~301b cluster is mediated by aberrant promoter methylation and impairs cellular senescence in prostate cancer

João Ramalho-Carvalho (213300)
Inês Graça (388023)
Antonio Gomez (3445997)
Jorge Oliveira (33493)
Rui Henrique (33490)
Manel Esteller (74345)
Carmen Jerónimo (33496)

February 2017

Clinical and pathological data of the patients included in the study. Table S2. Primers used in the ...

Additional file 2: Figure S2. of Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth

Rafael Fort (4624405)
Cecilia Mathó (4819026)
Murilo Geraldo (3406595)
María Ottati (4819032)
Alex Yamashita (4819041)
Kelly Saito (4819038)
Katia Leite (4819035)
Manuel Méndez (4819044)
Noemí Maedo (4819047)
Laura Méndez (4819050)
Beatriz Garat (408302)
Edna Kimura (3406598)
José Sotelo-Silveira (3457943)
María Duhagon (4819029)

February 2018

Hierarchical cluster of 50 paired normal and tumor tissue of PrCa patients from TCGA-PRAD dataset. A...

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 2: Figure S1. of Downregulation of miR-130b~301b cluster is mediated by aberrant promoter methylation and impairs cellular senescence in prostate cancer

João Ramalho-Carvalho (213300)
Inês Graça (388023)
Antonio Gomez (3445997)
Jorge Oliveira (33493)
Rui Henrique (33490)
Manel Esteller (74345)
Carmen Jerónimo (33496)

February 2017

DNA methylation changes in microRNAs´ promoters in prostate cancer (PCa), determined by Infinium Hum...

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

Abstract

Extracted data

Additional file 2: of Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients

Abstract

Extracted data

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