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Destination: titlink1 Children: Item: Title: Introduction Destination: flink1 Item: Title: Results Destination: flink2 Children: Item: Title: Pan-Cancer landscape of DNA methylation and associated functional changes Destination: slink1 Item: Title: cis-Acting aberrant DNA methylation as a possible driver event Destination: slink2 Item: Title: Hypomethylated RTKs are newly identified driver events Destination: slink3 Item: Title: Hypermethylation of STAT5A is associated with pervasive changes in STAT5A regulon activity Destination: slink4 Item: Title: Hypermethylated STAT5A is associated with immune cell depletion in squamous tumors Destination: slink5 Item: Title: Aberrant methylation associated with therapeutic vulnerabilities Destination: slink6 Item: Title: Discussion Destination: flink3 Item: Title: Supplemental information Destination: falink4 Item: Title: Consortia Destination: flink5 Item: Title: Acknowledgments Destination: acklink1 Item: Title: Author contributions Destination: acklink2 Item: Title: Declaration of interests Destination: acklink3 Item: Title: Inclusion and diversity Destination: acklink4 Item: Title: Declaration of generative AI and AI-assisted technologies in the writing process Destination: acklink5 Item: Title: References Destination: blink1 Item: Title: STAR★Methods Destination: flink6 Children: Item: Title: Key resources table Destination: slink7 Item: Title: Resource availability Destination: slink8 Children: Item: Title: Lead contact Destination: tlink1 Item: Title: Materials availability Destination: tlink2 Item: Title: Data and code availability Destination: tlink3 Item: Title: Experimental model and study participant details Destination: slink9 Children: Item: Title: Human participants Destination: tlink4 Item: Title: Clinical data annotation Destination: tlink5 Item: Title: Methods details Destination: slink10 Children: Item: Title: CPTAC datasets description Destination: tlink6 Item: Title: DNA methylation data preprocessing Destination: tlink7 Item: Title: Batch correction of DNA methylation value Destination: tlink8 Item: Title: Multi-omic data correlation analysis Destination: tlink9 Item: Title: Defining aberrant DNA methylation using RESET Destination: tlink10 Item: Title: Validation in TCGA cohorts Destination: tlink11 Item: Title: DEG analysis using scRNA-seq dataset Destination: tlink12 Item: Title: Defining cancer-associated genes Destination: tlink13 Item: Title: TFBS enrichment analysis Destination: tlink14 Item: Title: Profiling genetic alterations at driver genes Destination: tlink15 Item: Title: Histone acetylation analysis Destination: tlink16 Item: Title: Frequency of gene hyper- or hypomethylation Destination: tlink17 Item: Title: Regulon association analysis Destination: tlink18 Item: Title: Cell type enrichment deconvolution Destination: tlink19 Item: Title: Immunohistochemistry analysis Destination: tlink20 Item: Title: Methylation-driven subtyping Destination: tlink21 Item: Title: Pathway over-representation analysis Destination: tlink22 Item: Title: Identification of significantly mutated genes Destination: tlink23 Item: Title: RNA expression-based subtypes Destination: tlink24 Item: Title: Druggable genes with aberrant methylation Destination: tlink25 Item: Title: Quantification and statistical analysis Destination: slink11 Children: Item: Title: Statistical analysis Destination: tlink26 Item: Title: Additional resources Destination: slink12 Info: Title: Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin Author: Wen-Wei Liang Subject: Cancer Cell, 41 (2023) 1567-1592. doi:10.1016/j.ccell.2023.07.013 Creator: Elsevier Producer: Acrobat Distiller 8.1.0 (Windows) CreationDate: Mon Sep 04 04:08:23 CEST 2023 ModDate: Mon Sep 04 04:09:30 CEST 2023 ID: 0x3ef256ca3bd8f00636f356276e9101f4, 0xb9c1545b7a141a4395f51c8b6004b12e Filters: FilterPipeline: FlateDecode 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1 FontDescriptor: FontName: PIAHIA+AdvOTd877c31c+03 Flags: Symbolic FontBBox: 24, -10, 407, 460 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: PKICMK+Helvetica-Bold FontSubset: true FirstChar: 65 LastChar: 108 FontDescriptor: FontName: PKICMK+Helvetica-Bold Flags: Nonsymbolic, ForceBold FontBBox: -170, -228, 1003, 962 FontFile3: true Encoding: WinAnsiEncoding XMP: application/pdf doi:10.1016/j.ccell.2023.07.013 Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin Wen-Wei Liang Rita Jui-Hsien Lu Reyka G. Jayasinghe Steven M. Foltz Eduard Porta-Pardo Yifat Geffen Michael C. Wendl Rossana Lazcano Iga Kolodziejczak Yizhe Song Akshay Govindan Elizabeth G. Demicco Xiang Li Yize Li Sunantha Sethuraman Samuel H. Payne David Fenyö Henry Rodriguez Maciej Wiznerowicz Hui Shen D.R. Mani Karin D. Rodland Alexander J. Lazar Ana I. Robles Li Ding Clinical Proteomic Tumor Analysis Consortium François Aguet Yo Akiyama Eunkyung An Shankara Anand Meenakshi Anurag Ozgun Babur Jasmin Bavarva Chet Birger Michael Birrer Anna Calinawan Lewis C. Cantley Song Cao Steve Carr Michele Ceccarelli Daniel Chan Arul Chinnaiyan Hanbyul Cho Shrabanti Chowdhury Marcin Cieslik Karl Clauser Antonio Colaprico Daniel Cui Zhou Felipe da Veiga Leprevost Corbin Day Mohan Dhanasekaran Marcin Domagalski Yongchao Dou Brian Druker Nathan Edwards Matthew Ellis Myvizhi Esai Selvan Alicia Francis Gad Getz Michael A. Gillette Tania Gonzalez Robles Sara Gosline Zeynep Gümüş David Heiman Tara Hiltke Runyu Hong Galen Hostetter Yingwei Hu Chen Huang Emily Huntsman Antonio Iavarone Eric Jaehnig Scott Jewel Jiayi Ji Wen Jiang Jared Lee Johnson Lizabeth Katsnelson Karen Ketchum Karsten Krug Chandan Kumar-Sinha Jonathan Lei Yuxing Liao Caleb Lindgren Tao Liu Wenke Liu Weiping Ma Fernanda Martins Rodrigues Wilson McKerrow Mehdi Mesri Alexey I. Nesvizhskii Chelsea Newton Robert Oldroyd Gilbert Omenn Amanda Paulovich Francesca Petralia Pietro Pugliese Boris Reva Kelly Ruggles Dmitry Rykunov Shankha Satpathy Sara Savage Eric Schadt Michael Schnaubelt Tobias Schraink Zhiao Shi Dick Smith Xiaoyu Song Vasileios Stathias Erik Storrs Jimin Tan Nadezhda Terekhanova Ratna Thangudu Mathangi Thiagarajan Nicole Tignor Joshua Wang Liang-Bo Wang Pei Wang Ying (Cindy) Wang Bo Wen Yige Wu Lijun Yao Tomer M. Yaron Xinpei Yi Bing Zhang Hui Zhang Qing Zhang Xu Zhang Zhen Zhang Daniel W. Chan Saravana M. Dhanasekaran Stephan Schürer Richard D. Smith Matthew A. Wyczalkowski Cancer Cell, 41 (2023) 1567-1592. doi:10.1016/j.ccell.2023.07.013 The Author(s) journal Cancer Cell © 2023 The Author(s). Published by Elsevier Inc. 1535-6108 41 9 11 September 2023 2023-09-11 1567-1585.e7 1567 1585.e7 10.1016/j.ccell.2023.07.013 https://doi.org/10.1016/j.ccell.2023.07.013 2010-04-23 true 10.1016/j.ccell.2023.07.013 elsevier.com sciencedirect.com VoR 10.1016/j.ccell.2023.07.013 noindex true 2010-04-23 true sciencedirect.com elsevier.com Elsevier 2023-09-04T07:08:23+05:30 2023-09-04T07:09:30+05:30 2023-09-04T07:09:30+05:30 True Acrobat Distiller 8.1.0 (Windows) uuid:a33811cc-bca9-4db6-a4d8-0d4f020ee231 uuid:36308afc-fa80-442b-b39f-f0de418bb33d http://creativecommons.org/licenses/by-nc-nd/4.0/ Pages: Page: Label: 1567 Sequence: 1 Annotations: Annotation: Subtype: Link Rect: 354, 496, 430, 506 Annotation: Subtype: Link Rect: 104, 48, 268, 56 Annotation: Subtype: Link Rect: 53, 56, 69, 72 Page: Label: 1568 Sequence: 2 Annotations: Annotation: Subtype: Link Rect: 118, 584, 124, 593 Destination: 1 Annotation: Subtype: Link Rect: 124, 584, 129, 593 Destination: 1 Annotation: Subtype: Link Rect: 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