Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer
<p>5hmC levels are enriched in gene bodies and are independently associated with gene expression in mCRPC. <b>A,</b> Location of hypomethylated regions defined by whole-genome bisulfite sequencing and location of 5hmC enrichment (peaks called by MACS2). Regions were mapped to Genco...
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2025
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| _version_ | 1849927639666524160 |
|---|---|
| author | Martin Sjöström (14845882) |
| author2 | Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Martin Sjöström (14845882) Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| author_role | author |
| dc.creator.none.fl_str_mv | Martin Sjöström (14845882) Shuang G. Zhao (12227671) Samuel Levy (14960811) Meng Zhang (14960814) Yuhong Ning (279537) Raunak Shrestha (14949693) Arian Lundberg (14960817) Cameron Herberts (14960820) Adam Foye (14960823) Rahul Aggarwal (14960826) Junjie T. Hua (14960829) Haolong Li (1532230) Anna Bergamaschi (14960832) Corinne Maurice-Dror (14960835) Ashutosh Maheshwari (14960838) Sujun Chen (3553841) Sarah W.S. Ng (14960841) Wenbin Ye (14960844) Jessica Petricca (14960847) Michael Fraser (522709) Lisa Chesner (14960850) Marc D. Perry (14960853) Thaidy Moreno-Rodriguez (14960856) William S. Chen (14960859) Joshi J. Alumkal (14950518) Jonathan Chou (14957015) Alicia K. Morgans (5600567) Tomasz M. Beer (14960862) George V. Thomas (13187926) Martin Gleave (146446) Paul Lloyd (14960865) Tierney Phillips (4664332) Erin McCarthy (14960868) Michael C. Haffner (14960871) Amina Zoubeidi (14960874) Matti Annala (219688) Robert E. Reiter (14960877) Matthew B. Rettig (14960880) Owen N. Witte (14960883) Lawrence Fong (14960886) Rohit Bose (14960889) Franklin W. Huang (10726678) Jianhua Luo (14960892) Anders Bjartell (199682) Joshua M. Lang (12227674) Nupam P. Mahajan (14960895) Primo N. Lara (13009812) Christopher P. Evans (14960898) Phuoc T. Tran (14960901) Edwin M. Posadas (14960904) Chuan He (178952) Xiao-Long Cui (2020402) Jiaoti Huang (88989) Wilbert Zwart (14960907) Luke A. Gilbert (5513207) Christopher A. Maher (14960910) Paul C. Boutros (14954698) Kim N. Chi (14960913) Alan Ashworth (14957030) Eric J. Small (14960916) Housheng H. He (14960919) Alexander W. Wyatt (14960922) David A. Quigley (14957012) Felix Y. Feng (14845891) |
| dc.date.none.fl_str_mv | 2025-11-24T22:43:46Z |
| dc.identifier.none.fl_str_mv | 10.1158/0008-5472.30699421 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Figure_1_from_The_5-Hydroxymethylcytosine_Landscape_of_Prostate_Cancer/30699421 |
| dc.rights.none.fl_str_mv | CC BY info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |
| dc.title.none.fl_str_mv | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>5hmC levels are enriched in gene bodies and are independently associated with gene expression in mCRPC. <b>A,</b> Location of hypomethylated regions defined by whole-genome bisulfite sequencing and location of 5hmC enrichment (peaks called by MACS2). Regions were mapped to Gencode v.28 transcripts per sample and the frequencies averaged across 93 mCRPC samples. <b>B,</b> 5hmC enrichment in and around gene bodies for different gene expression levels. Protein coding genes were assigned to expression quintile per sample and log<sub>2</sub> 5hmC enrichment over input control (similar to low-pass WGS without 5hmC enrichment) was calculated using the NGSplot tool (<a href="#bib32" target="_blank">32</a>). 5hmC enrichment was then averaged across 93 mCRPC samples. <b>C,</b> Correlation between promoter methylation (average CpG methylation by whole-genome bisulfite sequencing), gene copy number, and 5hmC gene body counts, and gene expression, respectively, for protein coding genes across the 93 mCRPC samples. Genes with missing data or with no RNA-seq counts were excluded. Dashed lines, median correlation per data type. <b>D,</b> Gene expression was modeled for each gene by promoter methylation (PM), copy number (CN), SNVs, SVs, and 5hmC gene body counts (5hmC). Gene expression and 5hmC gene body counts were scaled (transformed to Z-score) to give comparable coefficients. Gray boxes, adjusted R-square of the model without 5hmC; blue boxes, adjusted R-square of the model including 5hmC. Analysis was done for 93 mCRPC samples. Boxplot shows median with hinges at 25th and 75th percentiles and whiskers at largest/smallest value within 1.5 × interquartile range. <b>E,</b> The adjusted 5hmC coefficients for individual genes modeled as in <b>D</b>. Genes in the Hallmark androgen response pathway are labeled black. <i>P</i> value was calculated by two-sided Wilcoxon rank-sum test for difference in scaled 5hmC coefficients between genes in the androgen response pathway including <i>AR</i> (<i>N</i> = 98) and all other protein coding genes (<i>N</i> = 18,434). Boxplots show distribution of AR response genes vs. other protein coding genes.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_ee41ab6efca5ba3a27928545136c555d |
| identifier_str_mv | 10.1158/0008-5472.30699421 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30699421 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY |
| spelling | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate CancerMartin Sjöström (14845882)Shuang G. Zhao (12227671)Samuel Levy (14960811)Meng Zhang (14960814)Yuhong Ning (279537)Raunak Shrestha (14949693)Arian Lundberg (14960817)Cameron Herberts (14960820)Adam Foye (14960823)Rahul Aggarwal (14960826)Junjie T. Hua (14960829)Haolong Li (1532230)Anna Bergamaschi (14960832)Corinne Maurice-Dror (14960835)Ashutosh Maheshwari (14960838)Sujun Chen (3553841)Sarah W.S. Ng (14960841)Wenbin Ye (14960844)Jessica Petricca (14960847)Michael Fraser (522709)Lisa Chesner (14960850)Marc D. Perry (14960853)Thaidy Moreno-Rodriguez (14960856)William S. Chen (14960859)Joshi J. Alumkal (14950518)Jonathan Chou (14957015)Alicia K. Morgans (5600567)Tomasz M. Beer (14960862)George V. Thomas (13187926)Martin Gleave (146446)Paul Lloyd (14960865)Tierney Phillips (4664332)Erin McCarthy (14960868)Michael C. Haffner (14960871)Amina Zoubeidi (14960874)Matti Annala (219688)Robert E. Reiter (14960877)Matthew B. Rettig (14960880)Owen N. Witte (14960883)Lawrence Fong (14960886)Rohit Bose (14960889)Franklin W. Huang (10726678)Jianhua Luo (14960892)Anders Bjartell (199682)Joshua M. Lang (12227674)Nupam P. Mahajan (14960895)Primo N. Lara (13009812)Christopher P. Evans (14960898)Phuoc T. Tran (14960901)Edwin M. Posadas (14960904)Chuan He (178952)Xiao-Long Cui (2020402)Jiaoti Huang (88989)Wilbert Zwart (14960907)Luke A. Gilbert (5513207)Christopher A. Maher (14960910)Paul C. Boutros (14954698)Kim N. Chi (14960913)Alan Ashworth (14957030)Eric J. Small (14960916)Housheng H. He (14960919)Alexander W. Wyatt (14960922)David A. Quigley (14957012)Felix Y. Feng (14845891)CancerCancer Risk FactorsMolecular and Cellular BiologyMethods and TechnologyEpigeneticsEpigenomicsGenitourinary CancersProstate cancerLiquid Biopsy<p>5hmC levels are enriched in gene bodies and are independently associated with gene expression in mCRPC. <b>A,</b> Location of hypomethylated regions defined by whole-genome bisulfite sequencing and location of 5hmC enrichment (peaks called by MACS2). Regions were mapped to Gencode v.28 transcripts per sample and the frequencies averaged across 93 mCRPC samples. <b>B,</b> 5hmC enrichment in and around gene bodies for different gene expression levels. Protein coding genes were assigned to expression quintile per sample and log<sub>2</sub> 5hmC enrichment over input control (similar to low-pass WGS without 5hmC enrichment) was calculated using the NGSplot tool (<a href="#bib32" target="_blank">32</a>). 5hmC enrichment was then averaged across 93 mCRPC samples. <b>C,</b> Correlation between promoter methylation (average CpG methylation by whole-genome bisulfite sequencing), gene copy number, and 5hmC gene body counts, and gene expression, respectively, for protein coding genes across the 93 mCRPC samples. Genes with missing data or with no RNA-seq counts were excluded. Dashed lines, median correlation per data type. <b>D,</b> Gene expression was modeled for each gene by promoter methylation (PM), copy number (CN), SNVs, SVs, and 5hmC gene body counts (5hmC). Gene expression and 5hmC gene body counts were scaled (transformed to Z-score) to give comparable coefficients. Gray boxes, adjusted R-square of the model without 5hmC; blue boxes, adjusted R-square of the model including 5hmC. Analysis was done for 93 mCRPC samples. Boxplot shows median with hinges at 25th and 75th percentiles and whiskers at largest/smallest value within 1.5 × interquartile range. <b>E,</b> The adjusted 5hmC coefficients for individual genes modeled as in <b>D</b>. Genes in the Hallmark androgen response pathway are labeled black. <i>P</i> value was calculated by two-sided Wilcoxon rank-sum test for difference in scaled 5hmC coefficients between genes in the androgen response pathway including <i>AR</i> (<i>N</i> = 98) and all other protein coding genes (<i>N</i> = 18,434). Boxplots show distribution of AR response genes vs. other protein coding genes.</p>2025-11-24T22:43:46ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1158/0008-5472.30699421https://figshare.com/articles/figure/Figure_1_from_The_5-Hydroxymethylcytosine_Landscape_of_Prostate_Cancer/30699421CC BYinfo:eu-repo/semantics/openAccessoai:figshare.com:article/306994212025-11-24T22:43:46Z |
| spellingShingle | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer Martin Sjöström (14845882) Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |
| status_str | publishedVersion |
| title | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_full | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_fullStr | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_full_unstemmed | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_short | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| title_sort | Figure 1 from The 5-Hydroxymethylcytosine Landscape of Prostate Cancer |
| topic | Cancer Cancer Risk Factors Molecular and Cellular Biology Methods and Technology Epigenetics Epigenomics Genitourinary Cancers Prostate cancer Liquid Biopsy |