Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Tathiane M. Malta,Artem Sokolov,Andrew J. Gentles,Tomasz Burzykowski,Laila M. Poisson,John N. Weinstein,Bozena Kaminska,Joerg Huelsken,Larsson Omberg,Olivier Gevaert,Antonio Colaprico,Patrycja Czerwińska,Sylwia Mazurek,Lopa Mishra,Holger Heyn,Alexander Krasnitz,Andrew K. Godwin,Alexander J. Lazar,Joshua M. Stuart,Katherine A Hoadley,Peter W. Laird,Houtan Noushmehr,Maciej Wiznerowicz +22 more
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TLDR
Novel stemness indices for assessing the degree of oncogenic dedifferentiation are provided and it is found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors.About:
This article is published in Cell.The article was published on 2018-04-05 and is currently open access. It has received 1099 citations till now. The article focuses on the topics: Cancer stem cell & Induced pluripotent stem cell.read more
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Hallmarks of Cancer: New Dimensions
TL;DR: The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles as mentioned in this paper , which are used to understand mechanisms of cancer development and malignant progression, and apply that knowledge to cancer medicine.
Journal ArticleDOI
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
Katherine A Hoadley,Christina Yau,Christina Yau,Toshinori Hinoue,Denise M. Wolf,Alexander J. Lazar,Esther Drill,Ronglai Shen,Alison M. Taylor,Alison M. Taylor,Andrew D. Cherniack,Andrew D. Cherniack,Vesteinn Thorsson,Rehan Akbani,Reanne Bowlby,Christopher K. Wong,Maciej Wiznerowicz,Maciej Wiznerowicz,Francisco Sanchez-Vega,A. Gordon Robertson,Barbara G. Schneider,Michael S. Lawrence,Michael S. Lawrence,Houtan Noushmehr,Houtan Noushmehr,Tathiane M. Malta,Tathiane M. Malta,Samantha J. Caesar-Johnson,John A. Demchok,Ina Felau,Melpomeni Kasapi,Martin L. Ferguson,Carolyn M. Hutter,Heidi J. Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Jiashan Zhang,Sudha Chudamani,Jia Liu,Laxmi Lolla,Rashi Naresh,Todd Pihl,Qiang Sun,Yunhu Wan,Ye Wu,Juok Cho,Timothy Defreitas,Scott Frazer,Nils Gehlenborg,Gad Getz,David I. Heiman,Jaegil Kim,Pei Lin,Sam Meier,Michael S. Noble,Gordon Saksena,Doug Voet,Hailei Zhang,Brady Bernard,Nyasha Chambwe,Varsha Dhankani,Theo A. Knijnenburg,Roger Kramer,Kalle Leinonen,Yuexin Liu,Michael W. Miller,Sheila Reynolds,Ilya Shmulevich,Wei Zhang,Bradley M. Broom,Apurva M. Hegde,Zhenlin Ju,Rupa S. Kanchi,Anil Korkut,Jun Li,Han Liang,Shiyun Ling,Wen-Bin Liu,Yiling Lu,Gordon B. Mills,Kwok Shing Ng,Arvind Rao,Michael T. Ryan,Jing Wang,John N. Weinstein,Jiexin Zhang,Adam Abeshouse,Joshua Armenia,Debyani Chakravarty,Walid K. Chatila,Ino de Bruijn,Jianjiong Gao,Benjamin Gross,Zachary J. Heins,Ritika Kundra,Konnor La,Marc Ladanyi,Augustin Luna,Moriah G. Nissan,Angelica Ochoa,Sarah Phillips,Ed Reznik,Chris Sander,Nikolaus Schultz,Robert L. Sheridan,S. Onur Sumer,Yichao Sun,Barry S. Taylor,Jioajiao Wang,Hongxin Zhang,Pavana Anur,Myron Peto,Paul T. Spellman,Christopher C. Benz,Joshua M. Stuart,D. Neil Hayes,Joel S. Parker,Matthew D. Wilkerson,Adrian Ally,Miruna Balasundaram,Denise Brooks,Rebecca Carlsen,Eric Chuah,Noreen Dhalla,Robert A. Holt,Steven J.M. Jones,Katayoon Kasaian,Darlene Lee,Yussanne Ma,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,Karen Mungall,Sara Sadeghi,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Kane Tse,Tina Wong,Ashton C. Berger,Rameen Beroukhim,Carrie Cibulskis,Stacey Gabriel,Galen F. Gao,Gavin Ha,Matthew Meyerson,Steven E. Schumacher,Juliann Shih,Melanie H. Kucherlapati,Raju Kucherlapati,Stephen B. Baylin,Leslie Cope,Ludmila Danilova,Moiz S. Bootwalla,Phillip H. Lai,Dennis T. Maglinte,David Van Den Berg,Daniel J. Weisenberger,J. Todd Auman,Saianand Balu,Tom Bodenheimer,Cheng Fan,Alan P. Hoyle,Stuart R. Jefferys,Corbin D. Jones,Shaowu Meng,Piotr A. Mieczkowski,Lisle E. Mose,Amy H. Perou,Charles M. Perou,Jeffrey Roach,Yan Shi,Janae V. Simons,Tara Skelly,Matthew G. Soloway,Donghui Tan,Umadevi Veluvolu,Huihui Fan,Peter W. Laird,Hui Shen,Wanding Zhou,Michelle Bellair,Kyle Chang,Kyle R. Covington,Chad J. Creighton,Huyen Dinh,Harshavardhan Doddapaneni,Lawrence A. Donehower,Jennifer Drummond,Richard A. 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Hovens,André Lopes Carvalho,Ana Carolina de Carvalho,José Humberto Tavares Guerreiro Fregnani,Adhemar Longatto-Filho,Rui Manuel Reis,Cristovam Scapulatempo-Neto,Henrique César Santejo Silveira,Daniel Onofre Vidal,Andrew Burnette,Jennifer M. Eschbacher,Beth Hermes,Ardene Noss,Rosy Singh,Matthew L. Anderson,Patricia Castro,Michael Ittmann,David G. Huntsman,Bernard Kohl,Xuan Le,Richard Thorp,Chris Andry,Elizabeth R. Duffy,Vladimir Lyadov,Oxana Paklina,Galiya Setdikova,Alexey Shabunin,Mikhail Tavobilov,Christopher M. McPherson,Ronald E. Warnick,Ross S. Berkowitz,Daniel W. Cramer,Colleen M. Feltmate,Neil S. Horowitz,Adam S. Kibel,Michael G. Muto,Chandrajit P. Raut,Andrei Malykh,Jill S. Barnholtz-Sloan,Wendi Barrett,Karen Devine,Jordonna Fulop,Quinn T. Ostrom,Kristen Shimmel,Yingli Wolinsky,Andrew E. Sloan,Agostino Maria De Rose,Felice Giuliante,Marc T. Goodman,Beth Y. Karlan,Curt H. Hagedorn,John Eckman,Jodi Harr,Jerome Myers,Kelinda Tucker,Leigh Anne Zach,Brenda Deyarmin,Hai Hu,Leonid Kvecher,Caroline Larson,Richard J. Mural,Stella Somiari,Ales Vicha,Tomáš Zelinka,Joseph J. Bennett,Mary Iacocca,Brenda Rabeno,Patricia Swanson,Mathieu Latour,Louis Lacombe,Bernard Têtu,Alain Bergeron,Mary McGraw,Susan M. Staugaitis,John Chabot,Hanina Hibshoosh,Antonia R. Sepulveda,Tao Su,Timothy C. Wang,Olga Potapova,Olga Voronina,Laurence Desjardins,Odette Mariani,Sergio Roman-Roman,Xavier Sastre,Marc-Henri Stern,Feixiong Cheng,Sabina Signoretti,Andrew Berchuck,Darell D. Bigner,Eric S. Lipp,Jeffrey R. Marks,Shannon J. McCall,Roger E. McLendon,Angeles Alvarez Secord,Alexis Sharp,Madhusmita Behera,Daniel J. Brat,Amy Y. Chen,Keith A. Delman,Seth D. Force,Fadlo R. Khuri,Kelly R. Magliocca,Shishir K. Maithel,Jeffrey J. Olson,Taofeek K. Owonikoko,Alan Pickens,Suresh S. Ramalingam,Dong M. Shin,Gabriel Sica,Erwin G. Van Meir,Hongzheng Zhang,Wil Eijckenboom,Ad J. M. Gillis,Esther Korpershoek,Leendert H. J. Looijenga,Wolter Oosterhuis,Hans Stoop,Kim E.M. van Kessel,Ellen C. Zwarthoff,Chiara Calatozzolo,Lucia Cuppini,Stefania Cuzzubbo,Francesco DiMeco,Gaetano Finocchiaro,Luca Mattei,Alessandro Perin,Bianca Pollo,Chu Chen,John Houck,Pawadee Lohavanichbutr,Arndt Hartmann,Christine Stoehr,Robert Stoehr,Helge Taubert,Sven Wach,Bernd Wullich,Witold Kycler,Dawid Murawa,Ki Chung,W. Jeffrey Edenfield,Julie S. Martin,Eric Baudin,Glenn J. Bubley,Raphael Bueno,Assunta De Rienzo,William G. Richards,Steven N. Kalkanis,Tom Mikkelsen,Lisa Scarpace,Nicolas Girard,Marta Aymerich,Elias Campo,Eva Giné,Armando López Guillermo,Nguyen Van Bang,Phan Thi Hanh,Bui Duc Phu,Yufang Tang,Howard Colman,Kimberley Evason,Peter Dottino,John A. Martignetti,Hani Gabra,Hartmut Juhl,Teniola Akeredolu,Serghei Stepa,Dave S.B. Hoon,Keunsoo Ahn,Koo Jeong Kang,Felix Beuschlein,Anne Breggia,Michael J. Birrer,Debra A. Bell,Mitesh J. Borad,Alan H. Bryce,Erik P. Castle,Vishal S. Chandan,John C. Cheville,John A. Copland,Michael B. Farnell,Thomas J. Flotte,Nasra H. Giama,Thai H. Ho,Michael L. Kendrick,Jean Pierre A. Kocher,Karla Kopp,Catherine D. Moser,David M. Nagorney,Daniel R. O'Brien,Brian P. O'Neill,Tushar Patel,Gloria M. Petersen,Florencia G. Que,Michael Rivera,Lewis R. Roberts,Robert C. Smallridge,Thomas C. Smyrk,Melissa L. Stanton,R. Houston Thompson,Michael Torbenson,Ju Dong Yang,Lizhi Zhang,Fadi Brimo,Jaffer A. Ajani,Ana Maria Angulo Gonzalez,Carmen Behrens,olanta Bondaruk,Russell Broaddus,Bogdan Czerniak,Bita Esmaeli,Junya Fujimoto,Jeffrey E. Gershenwald,Charles C. Guo,Christopher J. Logothetis,Funda Meric-Bernstam,Cesar A. Moran,Lois M. Ramondetta,David C. Rice,Anil K. Sood,Pheroze Tamboli,Timothy C. Thompson,Patricia Troncoso,Anne Tsao,Ignacio I. Wistuba,Candace Carter,Lauren E. Haydu,Peter Hersey,Valerie Jakrot,Hojabr Kakavand,Richard F. Kefford,Kenneth K. Lee,Georgina V. Long,Graham J. Mann,Michael A. Quinn,Robyn P. M. Saw,Richard A. Scolyer,Kerwin F. Shannon,Andrew J. Spillane,Jonathan R. Stretch,Maria Synott,John F. Thompson,James S. Wilmott,Hikmat Al-Ahmadie,Timothy A. Chan,Ronald Ghossein,Anuradha Gopalan,Douglas A. Levine,Victor E. Reuter,Samuel Singer,Bhuvanesh Singh,Nguyen Viet Tien,Thomas Broudy,Cyrus Mirsaidi,Praveen Nair,Paul Drwiega,Judy Miller,Jennifer S. Smith,Howard Zaren,Joong-Won Park,Nguyen Phi Hung,Electron Kebebew,W. Marston Linehan,Adam R. Metwalli,Karel Pacak,Peter A. Pinto,Mark Schiffman,Laura S. Schmidt,Cathy D. Vocke,Nicolas Wentzensen,Robert Worrell,Hannah P. Yang,Marc Moncrieff,Chandra Goparaju,Jonathan Melamed,Harvey I. Pass,Natalia Botnariuc,Irina Caraman,Mircea Cernat,Inga Chemencedji,Adrian Clipca,Serghei Doruc,Ghenadie Gorincioi,Sergiu Mura,Maria Pirtac,Irina Stancul,Diana Tcaciuc,Monique Albert,Iakovina Alexopoulou,Angel Arnaout,John Bartlett,Jay Engel,Sebastien Gilbert,Jeremy Parfitt,Harman Sekhon,George Thomas,Doris M. Rassl,Robert C. Rintoul,Carlo Bifulco,Raina Tamakawa,Walter J. Urba,Nicholas K. Hayward,Henri J L M Timmers,Anna Antenucci,Francesco Facciolo,Gian Luca Grazi,Mirella Marino,Roberta Merola,Ronald R. de Krijger,Anne Paule Gimenez-Roqueplo,Alain Piché,Simone Chevalier,Ginette McKercher,Kıvanç Birsoy,Gene H. Barnett,Cathy Brewer,Carol Farver,Theresa Naska,Nathan A. Pennell,Daniel P. Raymond,Cathy Schilero,Kathy Smolenski,Felicia Williams,Carl Morrison,Jeffrey A. Borgia,Michael J. Liptay,Mark Pool,Christopher W. Seder,Kerstin Junker,Larsson Omberg,Mikhail Dinkin,George Manikhas,Domenico Alvaro,Maria Consiglia Bragazzi,Vincenzo Cardinale,Guido Carpino,Eugenio Gaudio,David Chesla,Sandra Cottingham,Michael Dubina,Fedor Moiseenko,Renumathy Dhanasekaran,Karl-Friedrich Becker,Klaus-Peter Janssen,Julia Slotta-Huspenina,Mohamed H. Abdel-Rahman,Dina Aziz,Sue E. Bell,Colleen M. Cebulla,Amy Davis,Rebecca Duell,J. Bradley Elder,Joe Hilty,Bahavna Kumar,James C. Lang,Norman L. Lehman,Randy Mandt,Phuong Nguyen,Robert Pilarski,Karan Rai,Lynn Schoenfield,Kelly Senecal,Paul Wakely,Paul Hansen,Ronald Lechan,James Powers,Arthur S. Tischler,William E. Grizzle,Katherine C. Sexton,Alison Kastl,Joel M. Henderson,Sima P. Porten,Jens Waldmann,Martin Fassnacht,Sylvia L. Asa,Dirk Schadendorf,Marta Couce,Markus Graefen,Hartwig Huland,Guido Sauter,Thorsten Schlomm,Ronald Simon,Pierre Tennstedt,Oluwole Olabode,Mark Nelson,Oliver F. Bathe,Peter R. Carroll,June M. Chan,Philip J. DiSaia,Pat Glenn,Robin Kate Kelley,Charles N. Landen,Joanna J. Phillips,Michael D. Prados,Jeffry P. Simko,Karen Smith-McCune,Scott R. VandenBerg,Kevin K. Roggin,Ashley Fehrenbach,Ady Kendler,Suzanne Sifri,Ruth Steele,Antonio Jimeno,Francis Carey,Ian Forgie,Massimo Mannelli,Michael E. Carney,Brenda Y. Hernandez,Benito Campos,Christel Herold-Mende,Christin Jungk,Andreas Unterberg,Andreas von Deimling,Aaron D. Bossler,Joseph Galbraith,Laura Jacobus,Michael Knudson,Tina Knutson,Deqin Ma,Mohammed M. Milhem,Rita Sigmund,Andrew K. Godwin,Rashna Madan,Howard G. Rosenthal,Clement Adebamowo,Sally N. Adebamowo,Alex Boussioutas,David G. Beer,Thomas J. Giordano,Anne Marie Mes-Masson,Fred Saad,Thèrése Bocklage,Lisa M. Landrum,Robert S. Mannel,Kathleen N. Moore,Katherine M. Moxley,Russel Postier,Joan L. Walker,Rosemary E. Zuna,Michael Feldman,Federico Valdivieso,Rajiv Dhir,James D. Luketich,Edna M. Mora Pinero,Mario Quintero-Aguilo,Carlos Gilberto Carlotti,Jose Sebastião Dos Santos,Rafael Kemp,Ajith Sankarankuty,Daniela Pretti da Cunha Tirapelli,James W.F. Catto,Kathy Agnew,Elizabeth M. Swisher,Jenette Creaney,Bruce W. S. Robinson,Carl Simon Shelley,Eryn M. Godwin,Sara Kendall,Cassaundra Shipman,Carol R. Bradford,Thomas E. Carey,Andrea Haddad,Jeffey Moyer,Lisa A. Peterson,Mark E. Prince,Laura S. Rozek,Gregory T. Wolf,Rayleen V. Bowman,Kwun M. Fong,Ian A. Yang,Robert Korst,W. Kimryn Rathmell,J. Leigh Fantacone-Campbell,Jeffrey A. Hooke,Albert J. Kovatich,Craig D. Shriver,John F. DiPersio,Bettina F. Drake,Ramaswamy Govindan,Sharon Heath,Timothy J. Ley,Brian A. Van Tine,Peter Westervelt,Mark A. Rubin,Jung Il Lee,Natália D. Aredes,Armaz Mariamidze,Christopher C. Benz +738 more
TL;DR: Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, Pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which may inform strategies for future therapeutic development.
Journal ArticleDOI
Hallmarks of Cancer: New Dimensions.
TL;DR: The prospect is raised that phenotypic plasticity and disrupted differentiation is a discrete hallmark capability, and that nonmutational epigenetic reprogramming and polymorphic microbiomes both constitute distinctive enabling characteristics that facilitate the acquisition of hallmark capabilities.
Posted ContentDOI
The UCSC Xena platform for public and private cancer genomics data visualization and interpretation
Mary Goldman,Brian Craft,Mim Hastie,Kristupas Repečka,Fran McDade,Akhil Kamath,Ayan Banerjee,Yunhai Luo,Dave Rogers,Angela N. Brooks,Jingchun Zhu,David Haussler +11 more
TL;DR: UCSC Xena as mentioned in this paper is a web-based visualization tool for both public and private omics data, supported through Xena Browser and multiple turn-key Xena Hubs, allowing researchers to view their own data securely, using private Xena hubs, simultaneously visualizing large public cancer genomics datasets, including TCGA and the GDC.
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Hallmarks of cancer: the next generation.
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TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Wouter Meuleman,Jason Ernst,Misha Bilenky,Angela Yen,Angela Yen,Alireza Heravi-Moussavi,Pouya Kheradpour,Pouya Kheradpour,Zhizhuo Zhang,Zhizhuo Zhang,Jianrong Wang,Jianrong Wang,Michael J. Ziller,Viren Amin,John W. Whitaker,Matthew D. Schultz,Lucas D. Ward,Lucas D. Ward,Abhishek Sarkar,Abhishek Sarkar,Gerald Quon,Gerald Quon,Richard Sandstrom,Matthew L. Eaton,Matthew L. Eaton,Yi-Chieh Wu,Yi-Chieh Wu,Andreas R. Pfenning,Andreas R. Pfenning,Xinchen Wang,Xinchen Wang,Melina Claussnitzer,Melina Claussnitzer,Yaping Liu,Yaping Liu,Cristian Coarfa,R. Alan Harris,Noam Shoresh,Charles B. Epstein,Elizabeta Gjoneska,Elizabeta Gjoneska,Danny Leung,Wei Xie,R. David Hawkins,Ryan Lister,Chibo Hong,Philippe Gascard,Andrew J. Mungall,Richard A. Moore,Eric Chuah,Angela Tam,Theresa K. Canfield,R. Scott Hansen,Rajinder Kaul,Peter J. Sabo,Mukul S. Bansal,Mukul S. Bansal,Mukul S. Bansal,Annaick Carles,Jesse R. Dixon,Kai How Farh,Soheil Feizi,Soheil Feizi,Rosa Karlic,Ah Ram Kim,Ah Ram Kim,Ashwinikumar Kulkarni,Daofeng Li,Rebecca F. Lowdon,Ginell Elliott,Tim R. Mercer,Shane Neph,Vitor Onuchic,Paz Polak,Paz Polak,Nisha Rajagopal,Pradipta R. Ray,Richard C Sallari,Richard C Sallari,Kyle Siebenthall,Nicholas A Sinnott-Armstrong,Nicholas A Sinnott-Armstrong,Michael Stevens,Robert E. Thurman,Jie Wu,Bo Zhang,Xin Zhou,Arthur E. Beaudet,Laurie A. Boyer,Philip L. De Jager,Philip L. De Jager,Peggy J. Farnham,Susan J. Fisher,David Haussler,Steven J.M. Jones,Steven J.M. Jones,Wei Li,Marco A. Marra,Michael T. McManus,Shamil R. Sunyaev,Shamil R. Sunyaev,James A. Thomson,Thea D. Tlsty,Li-Huei Tsai,Li-Huei Tsai,Wei Wang,Robert A. Waterland,Michael Q. Zhang,Lisa Helbling Chadwick,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Joseph F. Costello,Joseph R. Ecker,Martin Hirst,Alexander Meissner,Aleksandar Milosavljevic,Bing Ren,John A. Stamatoyannopoulos,Ting Wang,Manolis Kellis,Manolis Kellis +123 more
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.