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Integrative pathway enrichment analysis of multivariate omics data
Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu, Diala Abd-Rabbo, Miles W. Mee, Paul C. Boutros, Federico Abascal, Samirkumar B. Amin, Rameen Beroukhim, Johanna Bertl, Søren Brunak, Peter J. Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Ken Chen, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach, J. Lynn Fink, Nuno A. Fonseca, Joan Frigola, Carlo Gambacorti‐Passerini, Dale W. Garsed, Mark Gerstein, Gad Getz, Abel González-Pérez, Qianyun Guo, Marta Gut, David Haan, Mark Hamilton, Nicholas J. Haradhvala, Arif Harmanci, Mohamed Helmy, Carl Herrmann, Julian M. Hess, Ermin Hodzic, Chen Hong, Henrik Hornshøj, Keren Isaev, José M. G. Izarzugaza, Rory Johnson, Todd A. Johnson, Randi Istrup Juul, Ekta Khurana, Jaegil Kim, Jong K. Kim, Young-Wook Kim, Jan O. Korbel, Sushant Kumar, Andrés Lanzós, Shantao Li, Kjong-Van Lehmann, Xiaotong Li, Ziao Lin, Eric Minwei Liu, Shaoke Lou, Kathleen Marchal, Alexander Martinez‐Fundichely, Yosef E. Maruvka, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Hidewaki Nakagawa, Morten Muhlig Nielsen, Keunchil Park, Kiejung Park, Jakob Skou Pedersen, Oriol Pich, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Esther Rheinbay, Mark A. Rubin, Carlota Rubio-Pérez, Radhakrishnan Sabarinathan, S. Cenk Şahinalp, Gordon Saksena, Leonidas Salichos, Steven E. Schumacher, Ofer Shapira, Ciyue Shen, Raunak Shrestha, Shimin Shuai, Lina Sieverling, Lincoln Stein, Joshua M. Stuart, David Tamborero, Tatsuhiko Tsunoda, Husen M. Umer, Liis Uusküla-Reimand, Alfonso Valencia, Lieven P. C. Verbeke, Jonathan Warrell, Sebastian M. Waszak, Guanming Wu, Jun Yu, Jing Zhang, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Christian von Mering, Jüri Reimand, Lauri A. Aaltonen, Adam Abeshouse, Hiroyuki Aburatani, David J. Adams, Nishant Agrawal, Keun Soo Ahn, Sung‐Min Ahn, Hiroshi Aikata, Rehan Akbani, Kadir C. Akdemir, Hikmat Al‐Ahmadie, Sultan T. Al‐Sedairy, Fátima Al‐Shahrour, Malik Alawi, Monique Albert, Kenneth Aldape, Ludmil B. Alexandrov, Adrian Ally, Kathryn Alsop, Eva G. Álvarez, Fernanda Amary, Brice Aminou, Ole Ammerpohl, Matthew J. Anderson, Yeng Ang, Davide Antonello, Pavana Anur, Samuel Aparício, Elizabeth L. Appelbaum, Yasuhito Arai, Axel Aretz, Koji Arihiro, Shun‐ichi Ariizumi, Joshua Armenia, Laurent Arnould, L. Sylvia, Yassen Assenov, Gurnit Atwal, Sietse Aukema, J. Todd Auman, Miriam R. R. Aure, Philip Awadalla, Marta Aymerich, Adrian Baez‐Ortega, Matthew H. Bailey, Peter J. Bailey, Miruna Balasundaram, Saianand Balu, Pratiti Bandopadhayay, Rosamonde E. Banks, Stefano Barbi, Andrew P. Barbour, Jill S. Barnholtz‐Sloan, Hugh Barr, Elisabet Barrera, John Bartlett, Javier Bartolomé, Claudio Bassi, Oliver F. Bathe, Daniel Baumhoer, Prashant Bavi, Stephen B. Baylin, Wojciech Bażant, Duncan Beardsmore, Tim Beck, Sam Behjati, Andreas Behren, Beifang Niu, Cindy Bell, Sergi Beltrán, Christopher C. Benz, Andrew Berchuck, Anke K. Bergmann, Erik N. Bergstrom, Benjamin P. Berman, Daniel M. Berney, Mario Berríos, Samantha Bersani, Miguel Betancourt, Vinayak Bhandari, Shriram G. Bhosle, Andrew V. Biankin, Matthias Bieg, Darell D. Bigner, Hans Binder, Ewan Birney, Michael Birrer, Nidhan K. Biswas, Bodil Bjerkehagen, Tom Bodenheimer, Lori Boice, Giada Bonizzato, Johann S. de Bono, Arnoud Boot, Åke Borg, Arndt Borkhardt, Ivan Borozan, Christoph W. Borst, Marcus Bosenberg, Mattia Bosio, Jacqueline Boultwood, Guillaume Bourque, G. Steven Bova, David Bowen, Reanne Bowlby, David D.L. Bowtell, Sandrine Boyault, Rich Boyce, Jeffrey M. Boyd, Alvis Brāzma, Paul Brennan, Daniel S. Brewer, Arie B. Brinkman, Robert G. Bristow, Russell R. Broaddus, Jane E. Brock, Malcolm V. Brock, Annegien Broeks, Angela N. Brooks, Denise Brooks, Benedikt Brors, Timothy J. C. Bruxner, Alicia L. Bruzos, Alex Buchanan, Ivo Buchhalter, Christiane Buchholz, Susan Bullman, Hazel Burke, Birgit Burkhardt, Kathleen H. Burns, John Busanovich, Carlos D. Bustamante, Adam P. Butler, Atul J. Butte, Niall J. Byrne, Anne‐Lise Børresen‐Dale, Andy Cafferkey, Declan Cahill, Claudia Calabrese, Carlos Caldas, Fabien Calvo, Niedzica Camacho, Elı́as Campo, Cinzia Cantù, Shaolong Cao, Thomas E. Carey, Rebecca Carlsen, Ivana Cataldo, Mario Cazzola, Jonathan Cebon, Robert Cerfolio, Dianne Chadwick, Drc Chalmers, Kin Chan, Michelle Chan‐Seng‐Yue, Vishal S. Chandan, David K. Chang, Stephen J. Chanock, Aurélien Chateigner, Nilanjan Chatterjee, Kazuaki Chayama, Hsiao-Wei Chen, Jieming Chen, Yiwen Chen, Zhaohong Chen, Andrew D. Cherniack, Jeremy Chien, Yoke-Eng Chiew, Suet‐Feung Chin, Juok Cho, Sunghoon Cho, Wan Choi, Christine Chomienne, Zechen Chong, Su Pin Choo, Angela Chou, Angelika N. Christ, Elizabeth L. Christie, Eric Chuah, Carrie Cibulskis, Kristian Cibulskis, Sara Cingarlini, Peter Clapham, Alexander Claviez, Sean P. Cleary, Nicole Cloonan, Marek Cmero, Colin C. Collins, Ashton A. Connor, Susanna L. Cooke, Colin S. Cooper, Leslie Cope, Vincenzo Corbo, Matthew G. Cordes, Stephen Cordner, Isidro Cortés‐Ciriano, Kyle R. Covington, Prue A. Cowin, Brian Craft, David Craft, Chad J. Creighton, Yupeng Cun, Erin Curley, Ioana Cutcutache, Karolina Czajka, Bogdan Czerniak, Rebecca A. Dagg, Ludmila Danilova, Maria Vittoria Davì, Natalie R. Davidson, Helen Davies, Ian J. Davis, Brandi N. Davis‐Dusenbery, Kevin J. Dawson, Francisco M. De La Vega, Ricardo De Paoli‐Iseppi, Timothy Defreitas, Angelo Paolo Dei Tos, Olivier Delaneau, John A. Demchok, Jonas Demeulemeester, German Demidov, Deniz Demircioğlu, Nening M. Dennis, Robert E. Denroche, Stefan C. Dentro, Nikita Desai, Vikram Deshpande, Amit G. Deshwar, Christine Desmedt, Noreen Dhalla, Neesha C. Dhani, Rajiv Dhir, Anthony DiBiase, Li Ding, Huy Q. Dinh, Luc Dirix, HarshaVardhan Doddapaneni, Nilgun Donmez, Michelle T. Dow, Ronny Drapkin, Oliver Drechsel, Ruben M. Drews, Serge Serge, Tim Dudderidge, Ana Dueso-Barroso, Andrew Dunford, Michael Dunn, Lewis Jonathan Dursi, Fraser R. Duthie, Ken Dutton‐Regester, Jenna Eagles, Douglas F. Easton, Stuart Edmonds, Paul A. Edwards, Sandra E. Edwards, Rosalind A. Eeles, Anna Ehinger, Roland Eils, Adel K. El‐Naggar, Matthew Eldridge, Kyle Ellrott, Serap Erkek, Geòrgia Escaramís, Shadrielle M. G. Espiritu, Xavier Estivill, Dariush Etemadmoghadam, Jórunn E. Eyfjörd, Bishoy M. Faltas, Daiming Fan, Yu Fan, William C. Faquin, Claudiu Farcas, Matteo Fassan, Aquila Fatima, Francesco Favero, Nodirjon Fayzullaev, Ina Felau, Sián Fereday, Martin L. Ferguson, Vincent Ferretti, Matthew A. Field, Gaetano Finocchiaro, Cyril Fisher, Matthew W. Fittall, Anna Fitzgerald, Rebecca C. Fitzgerald, Adrienne M. Flanagan, Neil Fleshner, Paul Flicek, John A. Foekens, Kwun M. Fong, Christopher S. Foster, Michael Fraser, Scott Frazer, Milana Frenkel‐Morgenstern, William A. Friedman, Catrina C. Fronick, Akihiro Fujimoto, Masashi Fujita, Masashi Fukayama, Lucinda A. Fulton, Robert S. Fulton, Mayuko Furuta, P. Andrew Futreal, Anja Füllgrabe, Stacey Gabriel, Steven Gallinger, Jianjiong Gao, Shengjie Gao, Levi A. Garraway, Øystein Garred, Erik Garrison, Nils Gehlenborg, Josep L. L. Gelpi, Joshy George, Daniela S. Gerhard, Clarissa Gerhäuser, Moritz Gerstung, Mohammed Ghori, Ronald Ghossein, Nasra H. Giama, Richard A. Gibbs, Bob Gibson, Anthony J. Gill, Pelvender Gill, Dilip D. Giri, Dominik Głodzik, Vincent J. Gnanapragasam, Maria Elisabeth Goebler, Mary J. Goldman, Carmen Gómez, Santiago Gonzalez, Dmitry A. Gordenin, James Gossage, Kunihito Gotoh, Ramaswamy Govindan, Dorthe Grabau, Janet S. Graham, Robert C. Grant, Anthony R. Green, Eric Green, Liliana Greger, Nicola Grehan, Sonia Grimaldi, Sean M. Grimmond, Robert L. Grossman, Adam Grundhoff, Gunes Gundem, Manaswi Gupta, Shailja Gupta, Jonathan Göke, Gavin Ha, Andrea Haake, Siegfried Haas, Kerstin Haase, James E. Haber, Faraz Hach, Syed Haider, Natsuko Hama, Freddie C. Hamdy, Anne Hamilton, Leng Han, George B. Hanna, Martin Hansmann, Olivier Harismendy, Ivon Harliwong, Arif O. Harmanci, Eoghan Harrington, Takanori Hasegawa, David Haussler, Steve Hawkins, Shinya Hayami, Shuto Hayashi, D. Neil Hayes, Stephen J. Hayes, Nicholas K. Hayward, Steven Hazell, Xiaotong Yao, Allison P. Heath, Simon Heath, David W. Hedley, Apurva M. Hegde, David I. Heiman, Michael C. Heinold, Zachary Heins, Lawrence E. Heisler, Eva Hellstrom-Lindberg, Seong Gu Heo, Austin J. Hepperla, José María Heredia‐Genestar, Peter Hersey, Hólmfríður Hilmarsdóttir, Jonathan Hinton, Satoshi Hirano, Nobuyoshi Hiraoka, Katherine A. Hoadley, Jessica I. Hoell, Steve Hoffmann, Oliver Hofmann, Andrea Holbrook, Aliaksei Z. Holik, Michael A. Hollingsworth, Oliver Holmes, Robert A. Holt, Chen Hong, Eun Pyo Hong, Jongwhi H. Hong, Gerrit K. Hooijer, Fumie Hosoda, Yong Hou, Volker Hovestadt, William Howat, Alan P. Hoyle, Ralph H. Hruban, Taobo Hu, Xing Hua, Kuan-lin Huang, Mei Huang, Mi Ni Huang, Vincent Huang, Yi Huang, Wolfgang Huber, Thomas J. Hudson, Michael Hummel, Jillian A. Hung, David G. Huntsman, Ted R. Hupp, Jason T. Huse, Matthew R. Huska, Barbara Hutter, Carolyn M. Hutter, Daniel Hübschmann, Christine A. Iacobuzio–Donahue, Charles D. Imbusch, Marcin Imieliński, Seiya Imoto, William B. Isaacs, Shumpei Ishikawa, Murat Iskar, S. M. Ashiqul Islam, Michael Ittmann, Sinisa Ivkovic, Jocelyne Jacquemier, Valerie Jakrot, Nigel B. Jamieson, Gun Ho Jang, Se Jin Jang, Joy C. Jayaseelan, Reyka G. Jayasinghe, Karine Jegalian, Jennifer L. Jennings, Seung-Hyup Jeon, Lara Jerman, Yuan Ji, Wei Jiao, Peter A. Johansson, Amber L. Johns, Jeremy Johns, Clemency Jolly, Yann Joly, Jón G. Jónasson, Corbin D. Jones, David Jones, Nic Jones, Steven J.M. Jones, Jos Jonkers, Young Seok Ju, Hartmut Juhl, Jongsun Jung, Natalie Jäger, Rolf Kabbe, Vera B. Kaiser, Hojabr Kakavand, Sangeetha Kalimuthu, Christof von Kalle, Koo Jeong Kang, Katalin Karászi, Beth Y. Karlan, Rosa Karlić, Dennis Karsch, Katayoon Kasaian, Karin S. Kassahn, Hitoshi Katai, Mamoru Kato, Hiroto Katoh, Yoshiiku Kawakami, Jonathan D. Kay, Stephen H. Kazakoff, Marat D. Kazanov, Maria Keays, Electron Kebebew, Richard Kefford, James G. Kench, Catherine J. Kennedy, Jules N. A. Kerssemakers, David Khoo, Vincent Khoo, Narong Khuntikeo, Helena Kilpinen, Hark Kyun Kim, Hyung‐Lae Kim, Hyung-Yong Kim, Hyunghwan Kim, Tari A. King, Wolfgang Hiddemann, Kortine Kleinheinz, Leszek J. Klimczak, Stian Knappskog, Michael Kneba, Bartha Maria Knoppers, Youngil Koh, Daisuke Komura, Mitsuhiro Komura, Gu Kong, Marcel Kool, Viktoriya Korchina, Andrey Korshunov, Michael Koscher, Roelof Koster, Zsofia Kote‐Jarai, Antonios Koures, Milena Kovačević, Bárbara Kremeyer, Helene Kretzmer, Markus Kreuz, Savitri Krishnamurthy, Dieter Kube, Kiran Kumar, Pardeep Kumar, Yogesh Kumar, Ritika Kundra, Kirsten Kübler, Ralf Küppers, Jesper Lagergren, Phillip H. Lai, Peter W. Laird, Sunil R. Lakhani, Christopher M. Lalansingh, Emilie Lalonde, Fabien C. Lamaze, Adam Lambert, Eric Lander, Pablo Landgraf, Luca Landoni, Anita Langerød, Denis Larsimont, Erik G. Larsson, Mark Lathrop, Loretta M. S. Lau, Chris Lawerenz, Rita T. Lawlor, Alexander J. Lazar, Ana Mijalkovic Lazic, Xuan Le, Darlene Lee, Eunjung Alice Lee, Hee Jin Lee, Jake June-Koo Lee, Jeong‐Yeon Lee, Ju‐Hee Lee, Ming Ta Michael Lee, Henry Lee-Six, Hans Lehrach, Dido Lenze, Conrad Leonard, Daniel Leongamornlert, Ignaty Leshchiner, Louis Létourneau, Ivica Letunić, Douglas A. Levine, Lora Lewis, Tim Ley, Chang Li, Constance H. Li, Haiyan Irene Li, Jun Li, Lin Li, Siliang Li, Xiaobo Li, Xinyue Li, Yilong Li, Han Liang, Sheng‐Ben Liang, Peter Lichter, Pei Lin, W. Marston Linehan, Ole Christian Lingjærde, Dongbing Liu, Fei-Fei Fei Liu, Fenglin Liu, Jia Liu, Xingmin Liu, Julie Livingstone, Dimitri Livitz, Naomi Livni, Markus Loeffler, Georgina V. Long, Armando López‐Guillermo, David N. Louis, Laurence Lovat, Yiling Lu, Yong‐Jie Lu, Youyong Lu, Claudio Luchini, Ilinca M. Lungu, Xuemei Luo, Hayley J. Luxton, Andy G. Lynch, Lisa Lype, Cristina López, Carlos López-Otı́n, Z. Eric, Yussanne Ma, Gaëtan MacGrogan, Shona MacRae, Geoff Macintyre, Kazuhiro Maejima, Andrea Mafficini, Dennis T. Maglinte, Arindam Maitra, Partha P. Majumder, Luca Malcovati, Salem Malikić, Giuseppe Malleo, Graham J. Mann, Luisa Mantovani‐Löffler, Giovanni Marchegiani, Elaine R. Mardis, Adam A. Margolin, Maximillian G. Marin, Florian Markowetz, Julia Markowski, Jeffrey S. Marks, Tomàs Marquès‐Bonet, Marco A. Marra, Luke Marsden, John W.M. Martens, Sancha Martin, José I. Martín‐Subero, R. Jay Mashl, Charlie E. Massie, Thomas J. Matthew, Lucy Matthews, Erik Mayer, Simon Mayes, Michael Mayo, Faridah Mbabaali, Karen McCune, Ultan McDermott, Michael D. McLellan, John D. McPherson, John R. McPherson, Treasa A. McPherson, Samuel R. Meier, Alice Meng, Shaowu Meng, Andrew Menzies, Neil D. Merrett, Sue Merson, Matthew Meyerson, Piotr A. Mieczkowski, George L. Mihaiescu, Sanja Mijalković, Tom Mikkelsen, Michele Stanislaw Milella, Linda Mileshkin, Christopher A. Miller, David K. Miller, Jessica K. Miller, Gordon B. Mills, Ana Milovanovic, Sarah Minner, Marco Miotto, Gisela Mir Arnau, Thomas J. Mitchell, Satoru Miyano, Naoki Miyoshi, Shinichi Mizuno, Fruzsina Molnár-Gábor, Malcolm J. Moore, Richard A. Moore, Sandro Morganella, Quaid Morris, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, Elizabeth A. Musgrove, Ville Mustonen, David G. Mutch, Francesc Muyas, Donna M. Muzny, Alfonso Muñoz, Jerome K. Myers, Ola Myklebost, Peter Möller, Genta Nagae, Adnan Nagrial, Hardeep K. Nahal-Bose, Hitoshi Nakagama, Hiromi Nakamura, Tõru Nakamura, Kaoru Nakano, Tannistha Nandi, Jyoti Nangalia, Mia Nastic, Arcadi Navarro, Fábio C. P. Navarro, David E. Neal, Gerd Nettekoven, Felicity Newell, Steven Newhouse, Yulia Newton, Alvin Wei Tian Ng, Chi‐Fai Ng, Jonathan Nicholson, David Nicol, Yongzhan Nie, G. Petur Nielsen, Serena Nik‐Zainal, Michael S. Noble, Kátia Nones, Paul A. Northcott, Faiyaz Notta, Brian D. O’Connor, Peter O’Donnell, Maria O’Donovan, Sarah O’Meara, Brian Patrick O’Neill, J. Robert O’Neill, David Ocaña, Angelica Ochoa, Layla Oesper, Christopher Ogden, Hideki Ohdan, Kazuhiro Ohi, Lucila Ohno‐Machado, Karin A. Oien, Akinyemi I. Ojesina, Hidenori Ojima, Takuji Okusaka, Larsson Omberg, Choon Kiat Ong, Stephan Ossowski, German Ott, B. F. Francis Ouellette, Christine P’ng, Salvatore Paiella, Chawalit Pairojkul, Marina Pajic, Qiang Pan‐Hammarström, Elli Papaemmanuil, Irene Papatheodorou, Nagarajan Paramasivam, Ji Wan Park, Joong‐Won Park, Peter J. Park, Joel S. Parker, Simon L. Parsons, Harvey I. Pass, Danielle Pasternack, Alessandro Pastore, Ann‐Marie Patch, Iris Pauporté, Antonio Pea, John V. Pearson, Chandra Sekhar Pedamallu, Paolo Pederzoli, Martin Peifer, Nathan A. Pennell, Charles M. Perou, Marc D. Perry, Gloria M. Petersen, Myron Peto, Nicholas Petrelli, Robert Petryszak, Stefan M. Pfister, Mark Phillips, Hilda A. Pickett, Todd Pihl, Nischalan Pillay, Sarah Pinder, Mark Pinese, Andreia V. Pinho, Esa Pitkänen, Xavier Pivot, Elena Piñeiro-Yáñez, Laura Planko, Christoph Plass, Paz Polak, Irinel Popescu, Olga Potapova, Aparna Prasad, Shaun R. Preston, Manuel Prinz, Antonia L. Pritchard, Stephenie D. Prokopec, Elena Provenzano, Xosé S. Puente, Montserrat Puiggròs, Gulietta M. Pupo, Colin A. Purdie, Michael C. Quinn, Raquel Rabionet, Janet S. Rader, Bernhard Radlwimmer, Petar Radovic, Benjamin Raeder, Keiran Raine, Manasa Ramakrishna, Kamna Ramakrishnan, Suresh Ramalingam, W. Kimryn Rathmell, Tobias Rausch, Guido Reifenberger, Jorge S. Reis‐Filho, Victor E. Reuter, Sheila M. Reynolds, Yasser Riazalhosseini, Andrea L. Richardson, Julia Richter, Matthew D. Ringel, Markus Ringnér, Yasushi Rino, Karsten Rippe, Jeffrey Roach, Lewis R. Roberts, Nicola D. Roberts, Steven A. Roberts, A. Gordon Robertson, Alan J. Robertson, Javier Bartolomé Rodriguez, Bernardo Rodríguez–Martín, F. 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Segrè, Iris Selander, Colin A. Semple, Yasin Şenbabaoğlu, Subhajit Sengupta, Elisabetta Sereni, Stefano Serra, Dennis C. Sgroi, Nimish Shah, Sagedeh Shahabi, Catherine A. Shang, Ping Shang, Troy Shelton, Hui Shen, Rebecca Shepherd, Ruian Shi, Yan Shi, Yu-Jia Shiah, Tatsuhiro Shibata, Juliann Shih, Eigo Shimizu, Kiyo Shimizu, Seung Jun Shin, Yuichi Shiraishi, Tal Shmaya, Ilya Shmulevich, Solomon I. Shorser, Charles Short, Suyash Shringarpure, Craig D. Shriver, Reiner Siebert, Anieta M. Sieuwerts, Sabina Signoretti, Katarzyna Sikora, Michele Simbolo, Ronald Simon, Janae V. Simons, Jared T. Simpson, Peter T. Simpson, Samuel Singer, Payal Sipahimalani, Tara Skelly, Marcel Smid, Jaclyn Smith, Karen Smith‐McCune, Nicholas D. Socci, Heidi J. Sofia, Matthew G. Soloway, Lei Song, Anil K. Sood, Sharmila Sothi, Christos Sotiriou, Cameron M. Soulette, Paul N. Span, Paul T. Spellman, Nicola Sperandio, Andrew J. Spillane, Oliver Spiro, Jonathan Spring, Johan Staaf, Peter F. Stadler, Peter Staib, Stefan G. Stark, Lucy Stebbings, Ólafur Andri Stefánsson, Oliver Stegle, Alasdair Stenhouse, Chip Stewart, Stephan Stilgenbauer, Miranda D. Stobbe, Michael R. Stratton, Jonathan R. Stretch, Adam J. Struck, Henk G. Stunnenberg, Hong Su, Xiaoping Su, Ren Sun, Stéphanie Sungalee, Hana Sušak, Akihiro Suzuki, Fred C.G.J. Sweep, Monika Szczepanowski, Holger Sültmann, Takashi Yugawa, Angela Tam, Benita Kiat Tee Tan, Donghui Tan, Patrick Tan, Hiroko Tanaka, Hirokazu Taniguchi, Tomas Tanskanen, Maxime Tarabichi, Roy Tarnuzzer, Patrick Tarpey, Morgan L. Taschuk, Kenji Tatsuno, Simon Tavaré, Darrin F. Taylor, Amaro Taylor‐Weiner, Jon W. Teague, Bin Tean Teh, Varsha Tembe, Javier Temes, Kevin Thai, Sarah P. Thayer, Nina Thiessen, Gilles Thomas, Sarah Thomas, Alan Thompson, Alastair M. Thompson, John F. Thompson, R. Houston Thompson, Heather Thorne, Leigh B. Thorne, Adrian Thorogood, Nebojša Tijanić, Lee E. Timms, Roberto Tirabosco, Marta Tojo, Stefania Tommasi, Christopher W. Toon, Umut H. Toprak, David Torrents, Giampaolo Tortora, Jörg Tost, Yasushi Totoki, David Townend, Nadia Traficante, Isabelle Treilleux, Jean-Rémi Trotta, Lorenz Trümper, Ming‐Sound Tsao, José M. C. Tubío, Olga Tucker, Richard Turkington, Daniel J. Turner, Andrew Tutt, Masaki Ueno, Naoto T. Ueno, Christopher B. Umbricht, Tim Underwood, Lara Urban, Tomoko Urushidate, Tetsuo Ushiku, David Van Den Berg, Steven Van Laere, Peter Van Loo, Erwin G. Van Meir, Gert G. Van den Eynden, Theodorus van der Kwast, Naveen Vasudev, Ravikiran Vedururu, Umadevi Veluvolu, Shankar Vembu, Peter Vermeulen, Clare Verrill, Alain Viari, David Vicente, Caterina Vicentini, K. VijayRaghavan, Juris Vīksna, Ricardo E. Vilain, Izar Villasante, Anne Vincent‐Salomon, Tapio Visakorpi, Douglas Voet, Paresh Vyas, Ignacio Vázquez-Garćıa, Nick M. Waddell, Nicola Waddell, Rabea Wagener, Jeremiah A. Wala, Jian Wang, Linghua Wang, Qi Wang, Wenyi Wang, Yumeng Wang, Zhining Wang, Paul Waring, Hans-Jörg Warnatz, Anne Y. Warren, David C. Wedge, Dieter Weichenhan, Paul Weinberger, John N. Weinstein, Daniel J. Weisenberger, Ian Welch, Michael C. Wendl, Johannes Werner, Justin P. Whalley, Hayley C. Whitaker, Dennis A. Wigle, Matthew D. Wilkerson, Ashley Williams, James S. Wilmott, Gavin W. Wilson, Julie M. Wilson, Richard K. Wilson, Boris Winterhoff, Jeffrey A. Wintersinger, Maciej Wiznerowicz, Stephan Wolf, Bernice H. Wong, Tina Wong, Winghing Wong, Youngchoon Woo, Scott Wood, Bradly G. Wouters, A. Jordan Wright, Derek Wright, Mark H. Wright, Chin‐Lee Wu, Dai‐Ying Wu, Jianmin Wu, Kui Wu, Yang Wu, Zhenggang Wu, Xi Liu, Tian Xia, Qian Xiang, Xiao Xiao, Rui Xing, Heng Xiong, Qinying Xu, Yanxun Xu, Hong Xue, Shinichi Yachida, Sergei Yakneen, Takafumi N. Yamaguchi, Masakazu Yamamoto, Shogo Yamamoto, Hiroki Yamaue, Fan Yang, Huanming Yang, Jean Yang, Liming Yang, Lixing Yang, Shanlin Yang, Tsun-Po Yang, Yang Yang, Marie‐Laure Yaspo, Lucy Yates, Christina Yau, Chen Ye, Kai Ye, Venkata Yellapantula, Christopher J. Yoon, Sung-Soo Yoon, Fouad Yousif, Kaixian Yu, Willie Yu, Yingyan Yu, Ke Yuan, Yuan Yuan, Denis Yuen, Christina K. Yung, Olga Zaikova, Jorge Zamora, Marc Zapatka, Jean C. Zenklusen, Thorsten Zenz, Nikolajs Zeps, Cheng‐Zhong Zhang, Fan Zhang, Hailei Zhang, Hongwei Zhang, Hongxin Zhang, Jiashan Zhang, Junjun Zhang, Xiuqing Zhang, Yan Zhang, Zemin Zhang, Liangtao Zheng, Xiuqing Zheng, Wanding Zhou, Yong Zhou, Bin Zhu, Hongtu Zhu, Jingchun Zhu, Shida Zhu, Xueqing Zou, Anna DeFazio, Nicholas van As, Carolien H. M. van Deurzen, Marc J. van de Vijver, L. van’t Veer
Notice bibliographique
RevueNature Communications · 2020
Typearticle
Langueen
DomaineBiochemistry, Genetics and Molecular Biology
ThématiqueHippo pathway signaling and YAP/TAZ
Établissements canadiensUniversity of British ColumbiaProstate Cancer CanadaUniversité de MontréalHospital for Sick ChildrenGenome CanadaLunenfeld-Tanenbaum Research InstituteMount Sinai HospitalPrincess Margaret Cancer CentreUniversity of CalgaryCanada Research ChairsVector InstituteCanada's Michael Smith Genome Sciences CentreUniversity of OttawaMcGill UniversitySimon Fraser UniversityMcGill University and Génome Québec Innovation CentreToronto General HospitalUniversity Health NetworkBC Cancer AgencySickKids FoundationUniversity of TorontoInstitute of Cancer ResearchOntario Institute for Cancer Research
Organismes subventionnairesNational Institute of Environmental Health SciencesNatural Sciences and Engineering Research Council of CanadaNational Institute of General Medical SciencesCancer Research SocietyTerry Fox Research InstituteUniversity of TorontoNational Cancer InstituteCancer Research UKFrancis Crick InstituteCanada First Research Excellence FundGovernment of OntarioCanadian Institutes of Health Research
Mots-clésComputational biologyBiologyTranscriptomeGenomeGeneSystems biologyGenomicsGeneticsGene expression
Résumé
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
score de la tête « metaresearch » (Codex)0,002
score de la tête « metaresearch » (Gemma)0,004
Version: metacan-v3-hybrid-931329e0061cStatut de validation: machine_predicted_unvalidated
Catégories candidatesaucune
Catégories consensuellesaucune
DomaineSignal candidat: aucune · Signal consensuel: aucune
Devis d'étudeSignal candidat: Simulation ou modélisation · Signal consensuel: aucune
GenreSignal candidat: Empirique · Signal consensuel: aucune
Score de désaccord entre enseignants0,007
Score d'incertitude au seuil0,013
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,004 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,003 |
| Bibliométrie | 0,007 | 0,005 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,002 | 0,001 |
| Science ouverte | 0,001 | 0,002 |
| Intégrité de la recherche | 0,000 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,004 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
Tête enseignante Opus0,045
Tête enseignante GPT0,333
Écart entre enseignants0,287 · la distance entre les deux têtes enseignantes sur ce seul travail
Statut de validation
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Les modèles n’ont appliqué aucune catégorie : rien dans la taxonomie ne correspondait à ce travail.
Devis d'étudeSimulation ou modélisation
Domainenon disponible
GenreEmpirique
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».
En bref
Citations236
Publié2020
Routes d'admission2
Résumé présentoui