194 results on '"SEQ"'
Search Results
102. Identification of antisense long noncoding RNAs that function as SINEUPs in human cells
- Author
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Stefano Gustincich, Sakari Kauppinen, Aleks Schein, Piero Carninci, and Silvia Zucchelli
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0301 basic medicine ,Untranslated region ,Protein subunit ,translation ,Biology ,Article ,03 medical and health sciences ,Exon ,Myosin-Light-Chain Phosphatase ,seq ,Settore BIO/13 - Biologia Applicata ,Gene expression ,Humans ,gene-expression, transcription, translation, landscape, disease, genome, galaxy, atlas, seq ,atlas ,RNA, Antisense ,RNA, Messenger ,genome ,Cells, Cultured ,Repetitive Sequences, Nucleic Acid ,Genetics ,Messenger RNA ,disease ,Multidisciplinary ,Gene Expression Profiling ,RNA ,Brain ,Computational Biology ,Translation (biology) ,landscape ,gene-expression ,Cell biology ,Gene expression profiling ,030104 developmental biology ,Protein Biosynthesis ,RNA, Long Noncoding ,galaxy ,transcription - Abstract
Mammalian genomes encode numerous natural antisense long noncoding RNAs (lncRNAs) that regulate gene expression. Recently, an antisense lncRNA to mouse Ubiquitin carboxyl-terminal hydrolase L1 (Uchl1) was reported to increase UCHL1 protein synthesis, representing a new functional class of lncRNAs, designated as SINEUPs, for SINE element-containing translation UP-regulators. Here, we show that an antisense lncRNA to the human protein phosphatase 1 regulatory subunit 12A (PPP1R12A), named as R12A-AS1, which overlaps with the 5′ UTR and first coding exon of the PPP1R12A mRNA, functions as a SINEUP, increasing PPP1R12A protein translation in human cells. The SINEUP activity depends on the aforementioned sense-antisense interaction and a free right Alu monomer repeat element at the 3′ end of R12A-AS1. In addition, we identify another human antisense lncRNA with SINEUP activity. Our results demonstrate for the first time that human natural antisense lncRNAs can up-regulate protein translation, suggesting that endogenous SINEUPs may be widespread and present in many mammalian species.
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- 2016
103. Reversible methylation of m
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Bastian Linder, Alexandre Blanjoie, Steven S. Gross, Xiaobing Luo, Deepak P. Patil, Anya V. Grozhik, Jan Mauer, Samie R. Jaffrey, Jean-Jacques Vasseur, Megerditch Kiledjian, Françoise Debart, Olivier Elemento, Qiuying Chen, Brian F. Pickering, Xinfu Jiao, Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), New Mexico Highlands University, and Weill Medical College of Cornell University [New York]
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0301 basic medicine ,Male ,Adenosine ,RNA Stability ,PROTEIN ,Epigenesis, Genetic ,Substrate Specificity ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,ARGONAUTE ,In Situ Hybridization ,Multidisciplinary ,Cap binding complex ,Guanosine ,MRNA modification ,CLIP ,Methylation ,SEQ ,030220 oncology & carcinogenesis ,Transcription Initiation Site ,Half-Life ,RNA Caps ,Five-prime cap ,DATABASE ,Longevity ,Alpha-Ketoglutarate-Dependent Dioxygenase FTO ,Biology ,Article ,03 medical and health sciences ,METHYLOME ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Endoribonucleases ,N-6-METHYLADENOSINE ,Animals ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,RNA, Messenger ,CELL ,Molecular Biology ,Messenger RNA ,RNA ,ALKBH5 ,Molecular biology ,MicroRNAs ,030104 developmental biology ,HEK293 Cells ,DEMETHYLASE ,chemistry ,MRNA methylation ,N6-Methyladenosine ,Transcriptome - Abstract
International audience; Internal bases in mRNA can be subjected to modifications that influence the fate of mRNA in cells. One of the most prevalent modified bases is found at the 5' end of mRNA, at the first encoded nucleotide adjacent to the 7-methylguanosine cap. Here we show that this nucleotide, N-6,2'-O-dimethyladenosine (m(6)A(m)), is a reversible modification that influences cellular mRNA fate. Using a transcriptome-wide map of m(6)A(m) we find that m(6)A(m)-initiated transcripts are markedly more stable than mRNAs that begin with other nucleotides. We show that the enhanced stability of m(6)A(m)-initiated transcripts is due to resistance to the mRNA-decapping enzyme DCP2. Moreover, we find that m(6)A(m) is selectively demethylated by fat mass and obesity-associated protein (FTO). FTO preferentially demethylates m(6)A(m) rather than N-6-methyladenosine (m(6)A), and reduces the stability of m(6)A(m) mRNAs. Together, these findings show that the methylation status of m(6)A(m) in the 5' cap is a dynamic and reversible epitranscriptomic modification that determines mRNA stability.
- Published
- 2016
104. Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
- Author
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Liselotte Vesterlund, Juha Kere, Jingwen Wang, Hong Jiao, Juha Kere / Principal Investigator, Medicum, and Department of Medical and Clinical Genetics
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0301 basic medicine ,TOPHAT ,Molecular biology ,Gene Expression ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,Polymerase Chain Reaction ,Transcriptome ,Database and Informatics Methods ,Sequencing techniques ,EMBRYOGENESIS ,Ensembl ,lcsh:Science ,Zebrafish ,Genetics ,Multidisciplinary ,Massive parallel sequencing ,biology ,Fishes ,Gene Expression Regulation, Developmental ,RNA sequencing ,Animal Models ,Genomics ,Genomic Databases ,Molecular Sequence Annotation ,SEQ ,Osteichthyes ,Vertebrates ,Transcriptome Analysis ,Research Article ,animal structures ,Danio ,Research and Analysis Methods ,03 medical and health sciences ,Model Organisms ,Extraction techniques ,Animals ,Gene ,lcsh:R ,Organisms ,Biology and Life Sciences ,Computational Biology ,Reverse Transcriptase-Polymerase Chain Reaction ,biology.organism_classification ,Genome Analysis ,GENE ,Genome Annotation ,RNA extraction ,030104 developmental biology ,Molecular biology techniques ,Biological Databases ,lcsh:Q ,3111 Biomedicine ,Zebrafish Information Network genome database - Abstract
Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.
- Published
- 2016
105. DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
- Author
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Jo Vandesompele, Franki Speleman, Maté Ongenaert, Anneleen Decock, and Wim Van Criekinge
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0301 basic medicine ,Statistics and Probability ,Data Descriptor ,Library and Information Sciences ,Biology ,BIOCONDUCTOR PACKAGE ,Education ,Paediatric cancer ,03 medical and health sciences ,Neuroblastoma ,neuroblastoma ,Biomarkers, Tumor ,Medicine and Health Sciences ,Humans ,Methylated DNA immunoprecipitation ,Copy-number variation ,Epigenetics ,Gene ,GENE-EXPRESSION ,Genetics ,DNA methylation ,epigenetics ,REARRANGEMENTS ,Biology and Life Sciences ,CLUSTER ,DNA, Neoplasm ,DNA Fingerprinting ,Computer Science Applications ,Methyl-CpG-binding domain ,READ ALIGNMENT ,INSIGHTS ,030104 developmental biology ,SEQ ,DNA profiling ,CpG site ,DIFFERENTIAL EXPRESSION ANALYSIS ,Next-generation sequencing ,CpG Islands ,methyl-CpG-binding domain (MBD) sequencing ,Statistics, Probability and Uncertainty ,Information Systems - Abstract
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.
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- 2016
106. Globin mRNA reduction for whole-blood transcriptome sequencing
- Author
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Eeva-Mari Jouhilahti, Cilla Söderhäll, Hannes Lohi, Liselotte Vesterlund, Mario Plaas, Kaarel Krjutškov, Ülle Jaakma, Shintaro Katayama, Andres Salumets, Elisabet Einarsdottir, Juha Kere, Mariann Koel, Anne Mari Roost, 'European Union (EU)' and 'Horizon 2020', Research Programme for Molecular Neurology, Research Programs Unit, Hannes Tapani Lohi / Principal Investigator, and Juha Kere / Principal Investigator
- Subjects
Male ,0301 basic medicine ,Buffy coat ,Article ,Transcriptome ,03 medical and health sciences ,Complementary DNA ,Gene expression ,Humans ,RNA, Messenger ,Globin ,Zebrafish ,Blood Cells ,Multidisciplinary ,STABILITY ,biology ,Oligonucleotide ,High-Throughput Nucleotide Sequencing ,RNA ,RNA sequencing ,biology.organism_classification ,Molecular biology ,Globins ,SEQ ,030104 developmental biology ,Female ,3111 Biomedicine - Abstract
The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat and so far incompletely studied cow, dog and zebrafish.
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- 2016
- Full Text
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107. Globin mRNA reduction for whole-blood transcriptome sequencing
- Author
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University of Helsinki, Research Program of Molecular Neurology, University of Helsinki, Research Programs Unit, Krjutskov, Kaarel, Koel, Mariann, Roost, Anne Mari, Katayama, Shintaro, Einarsdottir, Elisabet, Jouhilahti, Eeva-Mari, Soderhall, Cilla, Jaakma, Ulle, Plaas, Mario, Vesterlund, Liselotte, Lohi, Hannes, Salumets, Andres, Kere, Juha, University of Helsinki, Research Program of Molecular Neurology, University of Helsinki, Research Programs Unit, Krjutskov, Kaarel, Koel, Mariann, Roost, Anne Mari, Katayama, Shintaro, Einarsdottir, Elisabet, Jouhilahti, Eeva-Mari, Soderhall, Cilla, Jaakma, Ulle, Plaas, Mario, Vesterlund, Liselotte, Lohi, Hannes, Salumets, Andres, and Kere, Juha
- Abstract
The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat, and so far incompletely studied cow, dog and zebrafish.
- Published
- 2016
108. Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing
- Author
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University of Helsinki, Juha Kere / Principal Investigator, Wang, Jingwen, Vesterlund, Liselotte, Kere, Juha, Jiao, Hong, University of Helsinki, Juha Kere / Principal Investigator, Wang, Jingwen, Vesterlund, Liselotte, Kere, Juha, and Jiao, Hong
- Abstract
Zebrafish (Danio rerio) has emerged as a model organism to investigate vertebrate development and human genetic diseases. However, the zebrafish genome annotation is still ongoing and incomplete, and there are still new gene transcripts to be found. With the introduction of massive parallel sequencing, whole transcriptome studies became possible. In the present study, we aimed to discover novel transcribed regions (NTRs) using developmental transcriptome data from RNA sequencing. In order to achieve this, we developed an in-house bioinformatics pipeline for NTR discovery. Using the pipeline, we detected 152 putative NTRs that at the time of discovery were not annotated in Ensembl and NCBI gene database. Four randomly selected NTRs were successfully validated using RT-PCR, and expression profiles of 10 randomly selected NTRs were evaluated using qRT-PCR. The identification of these 152 NTRs provide new information for zebrafish genome annotation as well as new candidates for studies of zebrafish gene function.
- Published
- 2016
109. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer
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Zehua Wang, Bo Yang, Min Zhang, Weiwei Guo, Zhiyuan Wu, Yue Wang, Lin Jia, Song Li, Wen Xie, Da Yang, 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 (Julia) 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, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Inode Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, 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, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael 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 De Rose, Felice Giuliante, Marc 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, Tomas Zelinka, Joseph 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 Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. 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, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, 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 R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer 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 Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey 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 Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel 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 Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James 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 Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima 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 Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze, SAIC-F-Frederick, Inc, Leidos Biomedical Research, Inc., Wang Z., Yang B., Zhang M., Guo W., Wu Z., Wang Y., Jia L., Li S., Caesar-Johnson S.J., Demchok J.A., Felau I., Kasapi M., Ferguson M.L., Hutter C.M., Sofia H.J., Tarnuzzer R., Yang L., Zenklusen J.C., Zhang J.J., Chudamani S., Liu J., Lolla L., Naresh R., Pihl T., Sun Q., Wan Y., Wu Y., Cho J., DeFreitas T., Frazer S., Gehlenborg N., Getz G., Heiman D.I., Kim J., Lawrence M.S., Lin P., Meier S., Noble M.S., Saksena G., Voet D., Zhang H., Bernard B., Chambwe N., Dhankani V., Knijnenburg T., Kramer R., Leinonen K., Liu Y., Miller M., Reynolds S., Shmulevich I., Thorsson V., Zhang W., Akbani R., Broom B.M., Hegde A.M., Ju Z., Kanchi R.S., Korkut A., Li J., Liang H., Ling S., Liu W., Lu Y., Mills G.B., Ng K.-S., Rao A., Ryan M., Wang J., Weinstein J.N., Zhang J., Abeshouse A., Armenia J., Chakravarty D., Chatila W.K., Bruijn I., Gao J., Gross B.E., Heins Z.J., Kundra R., La K., Ladanyi M., Luna A., Nissan M.G., Ochoa A., Phillips S.M., Reznik E., Sanchez-Vega F., Sander C., Schultz N., Sheridan R., Sumer S.O., Sun Y., Taylor B.S., Anur P., Peto M., Spellman P., Benz C., Stuart J.M., Wong C.K., Yau C., Hayes D.N., Parker J.S., Wilkerson M.D., Ally A., Balasundaram M., Bowlby R., Brooks D., Carlsen R., Chuah E., Dhalla N., Holt R., Jones S.J.M., Kasaian K., Lee D., Ma Y., Marra M.A., Mayo M., Moore R.A., Mungall A.J., Mungall K., Robertson A.G., Sadeghi S., Schein J.E., Sipahimalani P., Tam A., Thiessen N., Tse K., Wong T., Berger A.C., Beroukhim R., Cherniack A.D., Cibulskis C., Gabriel S.B., Gao G.F., Ha G., Meyerson M., Schumacher S.E., Shih J., Kucherlapati M.H., Kucherlapati R.S., Baylin S., Cope L., Danilova L., Bootwalla M.S., Lai P.H., Maglinte D.T., Van Den Berg D.J., Weisenberger D.J., Auman J.T., Balu S., Bodenheimer T., Fan C., Hoadley K.A., Hoyle A.P., Jefferys S.R., Jones C.D., Meng S., Mieczkowski P.A., Mose L.E., Perou A.H., Perou C.M., Roach J., Shi Y., Simons J.V., Skelly T., Soloway M.G., Tan D., Veluvolu U., Fan H., Hinoue T., Laird P.W., Shen H., Zhou W., Bellair M., Chang K., Covington K., Creighton C.J., Dinh H., Doddapaneni H., Donehower L.A., Drummond J., Gibbs R.A., Glenn R., Hale W., Han Y., Hu J., Korchina V., Lee S., Lewis L., Li W., Liu X., Morgan M., Morton D., Muzny D., Santibanez J., Sheth M., Shinbrot E., Wang L., Wang M., Wheeler D.A., Xi L., Zhao F., Hess J., Appelbaum E.L., Bailey M., Cordes M.G., Ding L., Fronick C.C., Fulton L.A., Fulton R.S., Kandoth C., Mardis E.R., McLellan M.D., Miller C.A., Schmidt H.K., Wilson R.K., Crain D., Curley E., Gardner J., Lau K., Mallery D., Morris S., Paulauskis J., Penny R., Shelton C., Shelton T., Sherman M., Thompson E., Yena P., Bowen J., Gastier-Foster J.M., Gerken M., Leraas K.M., Lichtenberg T.M., Ramirez N.C., Wise L., Zmuda E., Corcoran N., Costello T., Hovens C., Carvalho A.L., de Carvalho A.C., Fregnani J.H., Longatto-Filho A., Reis R.M., Scapulatempo-Neto C., Silveira H.C.S., Vidal D.O., Burnette A., Eschbacher J., Hermes B., Noss A., Singh R., Anderson M.L., Castro P.D., Ittmann M., Huntsman D., Kohl B., Le X., Thorp R., Andry C., Duffy E.R., Lyadov V., Paklina O., Setdikova G., Shabunin A., Tavobilov M., McPherson C., Warnick R., Berkowitz R., Cramer D., Feltmate C., Horowitz N., Kibel A., Muto M., Raut C.P., Malykh A., Barnholtz-Sloan J.S., Barrett W., Devine K., Fulop J., Ostrom Q.T., Shimmel K., Wolinsky Y., Sloan A.E., De Rose A., Giuliante F., Goodman M., Karlan B.Y., Hagedorn C.H., Eckman J., Harr J., Myers J., Tucker K., Zach L.A., Deyarmin B., Hu H., Kvecher L., Larson C., Mural R.J., Somiari S., Vicha A., Zelinka T., Bennett J., Iacocca M., Rabeno B., Swanson P., Latour M., Lacombe L., Tetu B., Bergeron A., McGraw M., Staugaitis S.M., Chabot J., Hibshoosh H., Sepulveda A., Su T., Wang T., Potapova O., Voronina O., Desjardins L., Mariani O., Roman-Roman S., Sastre X., Stern M.-H., Cheng F., Signoretti S., Berchuck A., Bigner D., Lipp E., Marks J., McCall S., McLendon R., Secord A., Sharp A., Behera M., Brat D.J., Chen A., Delman K., Force S., Khuri F., Magliocca K., Maithel S., Olson J.J., Owonikoko T., Pickens A., Ramalingam S., Shin D.M., Sica G., Van Meir E.G., Eijckenboom W., Gillis A., Korpershoek E., Looijenga L., Oosterhuis W., Stoop H., van Kessel K.E., Zwarthoff E.C., Calatozzolo C., Cuppini L., Cuzzubbo S., DiMeco F., Finocchiaro G., Mattei L., Perin A., Pollo B., Chen C., Houck J., Lohavanichbutr P., Hartmann A., Stoehr C., Stoehr R., Taubert H., Wach S., Wullich B., Kycler W., Murawa D., Wiznerowicz M., Chung K., Edenfield W.J., Martin J., Baudin E., Bubley G., Bueno R., De Rienzo A., Richards W.G., Kalkanis S., Mikkelsen T., Noushmehr H., Scarpace L., Girard N., Aymerich M., Campo E., Gine E., Guillermo A.L., Van Bang N., Hanh P.T., Phu B.D., Tang Y., Colman H., Evason K., Dottino P.R., Martignetti J.A., Gabra H., Juhl H., Akeredolu T., Stepa S., Hoon D., Ahn K., Kang K.J., Beuschlein F., Breggia A., Birrer M., Bell D., Borad M., Bryce A.H., Castle E., Chandan V., Cheville J., Copland J.A., Farnell M., Flotte T., Giama N., Ho T., Kendrick M., Kocher J.-P., Kopp K., Moser C., Nagorney D., O'Brien D., O'Neill B.P., Patel T., Petersen G., Que F., Rivera M., Roberts L., Smallridge R., Smyrk T., Stanton M., Thompson R.H., Torbenson M., Yang J.D., Zhang L., Brimo F., Ajani J.A., Gonzalez A.M.A., Behrens C., Bondaruk J., Broaddus R., Czerniak B., Esmaeli B., Fujimoto J., Gershenwald J., Guo C., Lazar A.J., Logothetis C., Meric-Bernstam F., Moran C., Ramondetta L., Rice D., Sood A., Tamboli P., Thompson T., Troncoso P., Tsao A., Wistuba I., Carter C., Haydu L., Hersey P., Jakrot V., Kakavand H., Kefford R., Lee K., Long G., Mann G., Quinn M., Saw R., Scolyer R., Shannon K., Spillane A., Stretch J., Synott M., Thompson J., Wilmott J., Al-Ahmadie H., Chan T.A., Ghossein R., Gopalan A., Levine D.A., Reuter V., Singer S., Singh B., Tien N.V., Broudy T., Mirsaidi C., Nair P., Drwiega P., Miller J., Smith J., Zaren H., Park J.-W., Hung N.P., Kebebew E., Linehan W.M., Metwalli A.R., Pacak K., Pinto P.A., Schiffman M., Schmidt L.S., Vocke C.D., Wentzensen N., Worrell R., Yang H., Moncrieff M., Goparaju C., Melamed J., Pass H., Botnariuc N., Caraman I., Cernat M., Chemencedji I., Clipca A., Doruc S., Gorincioi G., Mura S., Pirtac M., Stancul I., Tcaciuc D., Albert M., Alexopoulou I., Arnaout A., Bartlett J., Engel J., Gilbert S., Parfitt J., Sekhon H., Thomas G., Rassl D.M., Rintoul R.C., Bifulco C., Tamakawa R., Urba W., Hayward N., Timmers H., Antenucci A., Facciolo F., Grazi G., Marino M., Merola R., de Krijger R., Gimenez-Roqueplo A.-P., Piche A., Chevalier S., McKercher G., Birsoy K., Barnett G., Brewer C., Farver C., Naska T., Pennell N.A., Raymond D., Schilero C., Smolenski K., Williams F., Morrison C., Borgia J.A., Liptay M.J., Pool M., Seder C.W., Junker K., Omberg L., Dinkin M., Manikhas G., Alvaro D., Bragazzi M.C., Cardinale V., Carpino G., Gaudio E., Chesla D., Cottingham S., Dubina M., Moiseenko F., Dhanasekaran R., Becker K.-F., Janssen K.-P., Slotta-Huspenina J., Abdel-Rahman M.H., Aziz D., Bell S., Cebulla C.M., Davis A., Duell R., Elder J.B., Hilty J., Kumar B., Lang J., Lehman N.L., Mandt R., Nguyen P., Pilarski R., Rai K., Schoenfield L., Senecal K., Wakely P., Hansen P., Lechan R., Powers J., Tischler A., Grizzle W.E., Sexton K.C., Kastl A., Henderson J., Porten S., Waldmann J., Fassnacht M., Asa S.L., Schadendorf D., Couce M., Graefen M., Huland H., Sauter G., Schlomm T., Simon R., Tennstedt P., Olabode O., Nelson M., Bathe O., Carroll P.R., Chan J.M., Disaia P., Glenn P., Kelley R.K., Landen C.N., Phillips J., Prados M., Simko J., Smith-McCune K., VandenBerg S., Roggin K., Fehrenbach A., Kendler A., Sifri S., Steele R., Jimeno A., Carey F., Forgie I., Mannelli M., Carney M., Hernandez B., Campos B., Herold-Mende C., Jungk C., Unterberg A., von Deimling A., Bossler A., Galbraith J., Jacobus L., Knudson M., Knutson T., Ma D., Milhem M., Sigmund R., Godwin A.K., Madan R., Rosenthal H.G., Adebamowo C., Adebamowo S.N., Boussioutas A., Beer D., Giordano T., Mes-Masson A.-M., Saad F., Bocklage T., Landrum L., Mannel R., Moore K., Moxley K., Postier R., Walker J., Zuna R., Feldman M., Valdivieso F., Dhir R., Luketich J., Pinero E.M.M., Quintero-Aguilo M., Carlotti C.G., Dos Santos J.S., Kemp R., Sankarankuty A., Tirapelli D., Catto J., Agnew K., Swisher E., Creaney J., Robinson B., Shelley C.S., Godwin E.M., Kendall S., Shipman C., Bradford C., Carey T., Haddad A., Moyer J., Peterson L., Prince M., Rozek L., Wolf G., Bowman R., Fong K.M., Yang I., Korst R., Rathmell W.K., Fantacone-Campbell J.L., Hooke J.A., Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Xie W., and Yang D.
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0301 basic medicine ,breast cancer ,CIMP ,ENSG00000224271 ,EPIC1 ,LOC284930 ,long noncoding RNA ,MYC ,P21 ,TCGA pan-cancer ,Cancer Research ,PROTEIN ,Cancer Genome Atlas Research Network ,medicine.disease_cause ,ANALYSES REVEAL ,Epigenesis, Genetic ,Mice ,LS2_1 ,LS4_6 ,610 Medicine & health ,Promoter Regions, Genetic ,GENE-EXPRESSION ,Regulation of gene expression ,FENÓTIPOS ,Cell Cycle ,METHYLATION ,Cell cycle ,Prognosis ,Long non-coding RNA ,Up-Regulation ,TRANSCRIPTIONAL NETWORK ,GENOME ,Gene Expression Regulation, Neoplastic ,SEQ ,CpG site ,Oncology ,DNA methylation ,Female ,RNA, Long Noncoding ,Life Sciences & Biomedicine ,Breast Neoplasm ,Human ,Prognosi ,Breast Neoplasms ,Biology ,BINDING-SITES ,Article ,NO ,Proto-Oncogene Proteins c-myc ,03 medical and health sciences ,Cell Line, Tumor ,medicine ,C-MYC ,Animals ,Humans ,1112 Oncology and Carcinogenesis ,Epigenetics ,Oncology & Carcinogenesis ,Science & Technology ,Binding Sites ,Animal ,Binding Site ,Cancer ,Cell Biology ,DNA Methylation ,medicine.disease ,030104 developmental biology ,Cancer research ,CpG Islands ,CpG Island ,Carcinogenesis ,1109 Neurosciences ,Neoplasm Transplantation - Abstract
We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1,006 lncRNA genes in cancer, including EPIC1 (epigenetically-induced lncRNA1). Overexpression of EPIC1 is associated with poor prognosis in luminal B breast cancer patients and enhances tumor growth in vitro and in vivo. Mechanistically, EPIC1 promotes cell-cycle progression by interacting with MYC through EPIC1's 129–283 nt region. EPIC1 knockdown reduces the occupancy of MYC to its target genes (e.g., CDKN1A, CCNA2, CDC20, and CDC45). MYC depletion abolishes EPIC1's regulation of MYC target and luminal breast cancer tumorigenesis in vitro and in vivo. Wang et al. characterize the epigenetic landscape of lncRNAs genes across a large number of human tumors and cancer cell lines and observe recurrent hypomethylation of lncRNA genes, including EPIC1. EPIC1 RNA promotes cell-cycle progression by interacting with MYC and enhancing its binding to target genes.
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- 2018
110. Selective strictness and parametricity in structural operational semantics, inequationally
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Patricia Johann and Janis Voigtländer
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Parametric polymorphism ,General Computer Science ,Identity extension ,0102 computer and information sciences ,02 engineering and technology ,computer.software_genre ,01 natural sciences ,Operational semantics ,Functional programming languages ,Theoretical Computer Science ,Clean ,seq ,0202 electrical engineering, electronic engineering, information engineering ,Observational equivalence ,Equivalence (formal languages) ,Logical relations ,computer.programming_language ,Mathematics ,Extensionality principles ,Lambda calculus ,Short cut fusion ,Functional programming ,Programming language ,Theorems for free ,020207 software engineering ,Mixing strict and nonstrict semantics ,16. Peace & justice ,Informatik ,Program transformations ,TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES ,010201 computation theory & mathematics ,Haskell ,TheoryofComputation_LOGICSANDMEANINGSOFPROGRAMS ,Types ,Fixpoint recursion ,Computer Science::Programming Languages ,Parametricity ,computer ,Algorithm ,Computer Science(all) - Abstract
Parametric polymorphism constrains the behavior of pure functional programs in a way that allows the derivation of interesting theorems about them solely from their types, i.e., virtually for free. The formal background of such 'free theorems' is well developed for extensions of the Girard-Reynolds polymorphic lambda calculus by algebraic datatypes and general recursion, provided the resulting calculus is endowed with either a purely strict or a purely nonstrict semantics. But modern functional languages like Clean and Haskell, while using nonstrict evaluation by default, also provide means to enforce strict evaluation of subcomputations at will. The resulting selective strictness gives the advanced programmer explicit control over evaluation order, but is not without semantic consequences: it breaks standard parametricity results. This paper develops an operational semantics for a core calculus supporting all the language features emphasized above. Its main achievement is the characterization of observational approximation with respect to this operational semantics via a carefully constructed logical relation. This establishes the formal basis for new parametricity results, as illustrated by several example applications, including the first complete correctness proof for short cut fusion in the presence of selective strictness. The focus on observational approximation, rather than equivalence, allows a finer-grained analysis of computational behavior in the presence of selective strictness than would be possible with observational equivalence alone. © 2007 Elsevier Ltd. All rights reserved.
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- 2007
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111. Gene expression profiling of pre-eclamptic placentae by RNA sequencing
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Anjuska Kyllönen, Juha Kere, Hannele Laivuori, Alejandra Cervera, Tea Kaartokallio, Krista Laivuori, Medicum, Clinicum, Department of Medical and Clinical Genetics, Pregnancy and Genes, Research Programs Unit, Genome-Scale Biology (GSB) Research Program, Sampsa Hautaniemi / Principal Investigator, Pekka Heino / Principal Investigator, Juha Kere / Principal Investigator, Research Programme for Molecular Neurology, Institute for Molecular Medicine Finland, Department of Obstetrics and Gynecology, and HUS Gynecology and Obstetrics
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Adult ,Microarray ,Placenta ,Population ,Biology ,Polymerase Chain Reaction ,Article ,Transcriptome ,Pre-Eclampsia ,MICROARRAY ,Pregnancy ,PCR DATA ,3123 Gynaecology and paediatrics ,GROWTH RESTRICTION ,Gene expression ,PREGNANCIES ,Humans ,RNA, Messenger ,education ,Gene ,POPULATION ,RISK ,Genetics ,education.field_of_study ,Multidisciplinary ,Base Sequence ,Sequence Analysis, RNA ,Microarray analysis techniques ,Gene Expression Profiling ,Microarray Analysis ,Corrigenda ,3. Good health ,Gene expression profiling ,SEQ ,ARTERIES ,CELLS ,ONSET PREECLAMPSIA ,Female ,3111 Biomedicine ,Biomarkers ,Pregnancy disorder - Abstract
Pre-eclampsia is a common and complex pregnancy disorder that often involves impaired placental development. In order to identify altered gene expression in pre-eclamptic placenta, we sequenced placental transcriptomes of nine pre-eclamptic and nine healthy pregnant women in pools of three. The differential gene expression was tested both by including all the pools in the analysis and by excluding some of the pools based on phenotypic characteristics. From these analyses, we identified altogether 53 differently expressed genes, a subset of which was validated by qPCR in 20 cases and 19 controls. Furthermore, we conducted pathway and functional analyses which revealed disturbed vascular function and immunological balance in pre-eclamptic placenta. Some of the genes identified in our study have been reported by numerous microarray studies (BHLHE40, FSTL3, HK2, HTRA4, LEP, PVRL4, SASH1, SIGLEC6), but many have been implicated in only few studies or have not previously been linked to pre-eclampsia (ARMS2, BTNL9, CCSAP, DIO2, FER1L4, HPSE, LOC100129345, LYN, MYO7B, NCMAP, NDRG1, NRIP1, PLIN2, SBSPON, SERPINB9, SH3BP5, TET3, TPBG, ZNF175). Several of the molecules produced by these genes may have a role in the pathogenesis of pre-eclampsia and some could qualify as biomarkers for prediction or detection of this pregnancy complication.
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- 2015
112. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
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Andrea Sass, Dieter Deforce, Jörg Vogel, Konrad U. Förstner, Tom Coenye, Heleen Van Acker, and Filip Van Nieuwerburgh
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TRANSLATION INITIATION ,Burkholderia cenocepacia ,Genome ,Start codon ,Transcription start site ,Transcription (biology) ,Genetics ,Humans ,CEPACIA COMPLEX ,PATHOGEN ,ddc:610 ,Genomic islands ,Gene ,Antisense RNA ,biology ,IDENTIFICATION ,PERSISTENCE ,Small RNAs ,Biofilm ,Biology and Life Sciences ,Drug Resistance, Microbial ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,GLOBAL GENE-EXPRESSION ,Anti-Bacterial Agents ,SEQ ,Biofilms ,dRNA-Seq ,BACTERIA ,DNA microarray ,Transcription Initiation Site ,RESISTANCE ,Genome, Bacterial ,Reference genome ,Biotechnology ,Research Article - Abstract
Background Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1993-3) contains supplementary material, which is available to authorized users.
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- 2015
113. Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
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Marijke R. van der Sijde, Jingyuan Fu, Kristin M. Abbott, K. Joeri van der Velde, Cisca Wijmenga, Juha Karjalainen, Mark de Haan, Patrick Deelen, Richard J. Sinke, Lude Franke, Marc Jan Bonder, Morris A. Swertz, Daria V. Zhernakova, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Center for Liver, Digestive and Metabolic Diseases (CLDM), and Stem Cell Aging Leukemia and Lymphoma (SALL)
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False discovery rate ,European Nucleotide Archive ,genetic processes ,Population ,Genome-wide association study ,Computational biology ,ALLELE-SPECIFIC EXPRESSION ,SUSCEPTIBILITY ,Biology ,DISEASE ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,Exponential growth ,Gene expression ,Genotype ,IMPUTATION ,Genetics ,Genetics(clinical) ,natural sciences ,GENOME-WIDE ASSOCIATION ,TRANSCRIPTOME ,education ,Gene ,Molecular Biology ,Exome ,POPULATION ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Research ,Genetic variants ,RNA ,CANCER ,SEQ ,REGULATORY VARIATION ,Expression quantitative trait loci ,Molecular Medicine ,Identification (biology) ,030217 neurology & neurosurgery ,Imputation (genetics) - Abstract
Background RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves. Methods We downloaded the raw reads for all available human RNA-seq datasets. Using these reads we performed gene expression quantification. All samples were jointly normalized and subjected to a strict quality control. We also derived genotypes using the RNA-seq reads and used imputation to infer non-coding variants. This allowed us to perform eQTL mapping and ASE analyses jointly on all samples that passed quality control. Our results were validated using samples for which DNA-seq genotypes were available. Results 4,978 public human RNA-seq runs, representing many different tissues and cell-types, passed quality control. Even though these data originated from many different laboratories, samples reflecting the same cell type clustered together, suggesting that technical biases due to different sequencing protocols are limited. In a joint analysis on the 1,262 samples with high quality genotypes, we identified cis-eQTLs effects for 8,034 unique genes (at a false discovery rate ≤0.05). eQTL mapping on individual tissues revealed that a limited number of samples already suffice to identify tissue-specific eQTLs for known disease-associated genetic variants. Additionally, we observed strong ASE effects for 34 rare pathogenic variants, corroborating previously observed effects on the corresponding protein levels. Conclusions By deriving and imputing genotypes from RNA-seq data, it is possible to identify both eQTLs and ASE effects. Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0152-4) contains supplementary material, which is available to authorized users.
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- 2015
114. Characterization and comparative analysis of the milk transcriptome in two dairy sheep breeds using RNA sequencing
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Christophe Klopp, Juan José Arranz, Beatriz Gutiérrez-Gil, Gwenola Tosser-Klopp, Aroa Suárez-Vega, Christèle Robert-Granié, Universidad de León [León], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
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0301 basic medicine ,Data Descriptor ,[SDV]Life Sciences [q-bio] ,cow ,lactation ,Biology ,Breeding ,Transcriptome ,cheese ,03 medical and health sciences ,stress ,angiogenesis ,Mammary Glands, Animal ,seq ,Lactation ,Casein ,Gene expression ,Animal physiology ,medicine ,Animals ,[INFO]Computer Science [cs] ,somatic-cell count ,rat mammary-gland ,gene-expression ,beta-casein ,[MATH]Mathematics [math] ,Sheep milk ,Gene ,2. Zero hunger ,Genetics ,Comparative Genomic Hybridization ,Multidisciplinary ,Sheep ,Sequence Analysis, RNA ,Domestic sheep reproduction ,RNA sequencing ,Breed ,030104 developmental biology ,medicine.anatomical_structure ,Milk ,RNA ,Female - Abstract
This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected 573 differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.
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- 2015
115. Gene expression profiling of pre-eclamptic placentae by RNA sequencing
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University of Helsinki, Medicum, University of Helsinki, Research Programs Unit, University of Helsinki, Department of Medical Genetics, University of Helsinki, Institute for Molecular Medicine Finland (FIMM), Kaartokallio, Tea, Cervera, Alejandra, Kyllonen, Anjuska, Laivuori, Krista, Kere, Juha, Laivuori, Hannele, FINNPEC Core Invest Grp, University of Helsinki, Medicum, University of Helsinki, Research Programs Unit, University of Helsinki, Department of Medical Genetics, University of Helsinki, Institute for Molecular Medicine Finland (FIMM), Kaartokallio, Tea, Cervera, Alejandra, Kyllonen, Anjuska, Laivuori, Krista, Kere, Juha, Laivuori, Hannele, and FINNPEC Core Invest Grp
- Abstract
Pre-eclampsia is a common and complex pregnancy disorder that often involves impaired placental development. In order to identify altered gene expression in pre-eclamptic placenta, we sequenced placental transcriptomes of nine pre-eclamptic and nine healthy pregnant women in pools of three. The differential gene expression was tested both by including all the pools in the analysis and by excluding some of the pools based on phenotypic characteristics. From these analyses, we identified altogether 53 differently expressed genes, a subset of which was validated by qPCR in 20 cases and 19 controls. Furthermore, we conducted pathway and functional analyses which revealed disturbed vascular function and immunological balance in pre-eclamptic placenta. Some of the genes identified in our study have been reported by numerous microarray studies (BHLHE40, FSTL3, HK2, HTRA4, LEP, PVRL4, SASH1, SIGLEC6), but many have been implicated in only few studies or have not previously been linked to pre-eclampsia (ARMS2, BTNL9, CCSAP, DIO2, FER1L4, HPSE, LOC100129345, LYN, MYO7B, NCMAP, NDRG1, NRIP1, PLIN2, SBSPON, SERPINB9, SH3BP5, TET3, TPBG, ZNF175). Several of the molecules produced by these genes may have a role in the pathogenesis of pre-eclampsia, and some could qualify as biomarkers for prediction or detection of this pregnancy complication.
- Published
- 2015
116. Sequencing degraded RNA addressed by 3' tag counting
- Author
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Joakim Lundeberg, Benjamín Sigurgeirsson, and Olof Emanuelsson
- Subjects
Microarrays ,RNA Stability ,lcsh:Medicine ,Biochemistry ,Transcriptome ,Degradation ,Gene expression ,Biologiska vetenskaper ,Genome Sequencing ,lcsh:Science ,Genetics ,Multidisciplinary ,Number ,food and beverages ,Genomics ,Biological Sciences ,Genomic Databases ,Bioassays and Physiological Analysis ,SEQ ,RNA extraction ,Transcriptome Analysis ,Sequence Analysis ,Transcription ,Research Article ,Biotechnology ,Integrity ,DNA transcription ,Sequence Databases ,Biological Data Management ,Biology ,Research and Analysis Methods ,Cell Line, Tumor ,Quantification ,Humans ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,Sequence Assembly Tools ,Biology and life sciences ,cDNA library ,Sequence Analysis, RNA ,lcsh:R ,RNA ,Computational Biology ,Ribosomal RNA ,Genome Analysis ,Gene expression profiling ,Small Molecules ,lcsh:Q ,Genome Expression Analysis - Abstract
RNA sequencing has become widely used in gene expression profiling experiments. Prior to any RNA sequencing experiment the quality of the RNA must be measured to assess whether or not it can be used for further downstream analysis. The RNA integrity number (RIN) is a scale used to measure the quality of RNA that runs from 1 (completely degraded) to 10 (intact). Ideally, samples with high RIN (>8) are used in RNA sequencing experiments. RNA, however, is a fragile molecule which is susceptible to degradation and obtaining high quality RNA is often hard, or even impossible when extracting RNA from certain clinical tissues. Thus, occasionally, working with low quality RNA is the only option the researcher has. Here we investigate the effects of RIN on RNA sequencing and suggest a computational method to handle data from samples with low quality RNA which also enables reanalysis of published datasets. Using RNA from a human cell line we generated and sequenced samples with varying RINs and illustrate what effect the RIN has on the basic procedure of RNA sequencing; both quality aspects and differential expression. We show that the RIN has systematic effects on gene coverage, false positives in differential expression and the quantification of duplicate reads. We introduce 3' tag counting (3TC) as a computational approach to reliably estimate differential expression for samples with low RIN. We show that using the 3TC method in differential expression analysis significantly reduces false positives when comparing samples with different RIN, while retaining reasonable sensitivity. QC 20140423
- Published
- 2014
117. Sequencing Degraded RNA Addressed by 3' Tag Counting
- Author
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Sigurgeirsson, Benjamin, Emanuelsson, Olof, Lundeberg, Joakim, Sigurgeirsson, Benjamin, Emanuelsson, Olof, and Lundeberg, Joakim
- Abstract
RNA sequencing has become widely used in gene expression profiling experiments. Prior to any RNA sequencing experiment the quality of the RNA must be measured to assess whether or not it can be used for further downstream analysis. The RNA integrity number (RIN) is a scale used to measure the quality of RNA that runs from 1 (completely degraded) to 10 (intact). Ideally, samples with high RIN (>8) are used in RNA sequencing experiments. RNA, however, is a fragile molecule which is susceptible to degradation and obtaining high quality RNA is often hard, or even impossible when extracting RNA from certain clinical tissues. Thus, occasionally, working with low quality RNA is the only option the researcher has. Here we investigate the effects of RIN on RNA sequencing and suggest a computational method to handle data from samples with low quality RNA which also enables reanalysis of published datasets. Using RNA from a human cell line we generated and sequenced samples with varying RINs and illustrate what effect the RIN has on the basic procedure of RNA sequencing; both quality aspects and differential expression. We show that the RIN has systematic effects on gene coverage, false positives in differential expression and the quantification of duplicate reads. We introduce 3' tag counting (3TC) as a computational approach to reliably estimate differential expression for samples with low RIN. We show that using the 3TC method in differential expression analysis significantly reduces false positives when comparing samples with different RIN, while retaining reasonable sensitivity., QC 20140423
- Published
- 2014
- Full Text
- View/download PDF
118. Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer
- Author
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Xing Dai, Xiaohui Xie, Jacob Biesinger, Brian S. Roberts, William Arthur, Kazuhide Watanabe, Michele A. Cleary, Michael L. Salmans, and Bogi Andersen
- Subjects
Microarrays ,lcsh:Medicine ,Kaplan-Meier Estimate ,dna ,0302 clinical medicine ,Cell Signaling ,Molecular Cell Biology ,Basic Cancer Research ,Medicine and Health Sciences ,Genome Sequencing ,lcsh:Science ,Wnt Signaling Pathway ,Tissue homeostasis ,beta Catenin ,WNT Signaling Cascade ,Oligonucleotide Array Sequence Analysis ,Genetics ,Regulation of gene expression ,Feedback, Physiological ,0303 health sciences ,Multidisciplinary ,Stem Cells ,Systems Biology ,LGR5 ,Wnt signaling pathway ,Life Sciences ,Genomics ,Chromatin ,Signaling Cascades ,3. Good health ,Gene Expression Regulation, Neoplastic ,Intestines ,Bioassays and Physiological Analysis ,Oncology ,030220 oncology & carcinogenesis ,Colonic Neoplasms ,Information Technology ,Transcriptome Analysis ,chromatin occupancy ,Research Article ,Signal Transduction ,signaling pathway ,Chromatin Immunoprecipitation ,Computer and Information Sciences ,Cell Survival ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,seq ,Cell Line, Tumor ,Gastrointestinal Tumors ,Humans ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,030304 developmental biology ,Microarray analysis techniques ,Gene Expression Profiling ,lcsh:R ,colorectal-cancer ,Reproducibility of Results ,Biology and Life Sciences ,Computational Biology ,Cancers and Neoplasms ,beta-catenin ,Cell Biology ,Gene signature ,Genome Analysis ,Gene expression profiling ,wnt ,Gene Ontology ,activation ,lcsh:Q ,protein ,repression ,Genome Expression Analysis ,Chromatin immunoprecipitation ,Software - Abstract
Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer Kazuhide Watanabe 1 , Jacob Biesinger 2,3 , Michael L. Salmans 1 , Brian S. Roberts 4 , William T. Arthur 4 , Michele Cleary 4 , Bogi Andersen 1 , Xiaohui Xie 2,3 , Xing Dai 1,2 * 1 Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America, 2 Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America, 3 Department of Computer Science, University of California Irvine, Irvine, California, United States of America, 4 Rosetta Inpharmatics, LLC, Merck & Co Inc., Seattle, Washington, United States of America Abstract Background: Deregulation of canonical Wnt/CTNNB1 (beta-catenin) pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are highly frequent in colon cancer and cause aberrant stabilization of CTNNB1, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of CTNNB1 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of CTNNB1 in colon cancer cells. Results: We observed 3629 CTNNB1 binding peaks across the genome and a significant correlation between CTNNB1 binding and knockdown-induced gene expression change. Our integrative analysis led to the discovery of a direct Wnt target signature composed of 162 genes. Gene ontology analysis of this signature revealed a significant enrichment of Wnt pathway genes, suggesting multiple feedback regulations of the pathway. We provide evidence that this gene signature partially overlaps with the Lgr5 + intestinal stem cell signature, and is significantly enriched in normal intestinal stem cells as well as in clinical colorectal cancer samples. Interestingly, while the expression of the CTNNB1 target gene set does not correlate with survival, elevated expression of negative feedback regulators within the signature predicts better prognosis. Conclusion: Our data provide a genome-wide view of chromatin occupancy and gene regulation of Wnt/CTNNB1 signaling in colon cancer cells. Citation: Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, et al. (2014) Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer. PLoS ONE 9(3): e92317. doi:10.1371/journal.pone.0092317 Editor: Ted S. Acott, Casey Eye Institute, United States of America Received October 30, 2013; Accepted February 20, 2014; Published March 20, 2014 Copyright: s 2014 Watanabe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funding from Susan G. Komen grant KG110897 (XD), a U.S. Department of Defense BCRP Postdoctoral Fellowship (K.W. W81XWH-10-1-0383), and National Institutes of Health grant R01HG006870 (to XX). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Brian S. Roberts and William T. Arthur are former employees of Rosetta Inpharmatics, LLC, Merck & Co Inc. Michele Cleary is currently an employee of Merck & Co., Inc. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. * E-mail: xdai@uci.edu leads to abnormal proliferation of mutated cells through activation of target genes such as MYC and CCND1 [7]. However, given the divergent cellular roles of Wnt/CTNNB1 signaling, other target genes may also contribute to the pathogenesis of CRCs. Thus, identification and characterization of CTNNB1 target genes genome-wide have been an important pursuit in CRC studies. Transcriptional profiling was used to identify Wnt/ CTNNB1 target genes in colon cancer cells [8]. However, analysis of gene expression alone is limited due to inability to distinguish between primary and secondary effects of Wnt pathway activation. More recently, chromatin immunoprecipitation (ChIP) followed by large-scale DNA analysis such as DNA-chip (ChIP-chip) or high-throughput sequencing (ChIP-seq) [9,10] was used to identify the genomic loci to which CTNNB1 or TCF factors directly bind [11–14]. However, ChIP-based studies of various transcription factors suggest that not all binding events identified correlate with Background Wnt/CTNNB1 signaling is a conserved pathway that plays fundamental roles in embryonic development, tissue homeostasis and maintenance of stem cells. In normal intestine, this pathway is essential for the development and maintenance of intestinal stem cells [1,2]. Activation of canonical Wnt signaling involves stabilization of cytoplasmic CTNNB1, which is otherwise degrad- ed by the proteasome through a degradation complex composed of tumor suppressor protein APC, serine/threonine kinase GSK-3, and Axin. Stabilized CTNNB1 translocates into the nucleus where it binds to TCF/LEF transcription factors and activates target gene expression [2]. A key initiation event of colorectal cancers (CRCs) is CTNNB1 stabilization through loss of the APC gene or activating mutations in the CTNNB1 gene [3]. This genetic event occurs primarily in the intestinal stem cell population [4–6] and PLOS ONE | www.plosone.org March 2014 | Volume 9 | Issue 3 | e92317
- Published
- 2013
119. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
- Author
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Milkha M. Leimena, Erwin G. Zoetendal, Michiel Kleerebezem, Mark Davids, Jos Boekhorst, Hauke Smidt, Bartholomeus van den Bogert, Eddy J. Smid, Peter J. Schaap, and Javier Ramiro-Garcia
- Subjects
Single-end reads ,Levensmiddelenmicrobiologie ,Microbiologie ,Databases, Genetic ,Intestine, Small ,Paired-end reads ,Systems and Synthetic Biology ,bacteria ,Phylogeny ,Genetics ,Systeem en Synthetische Biologie ,Phylogenetic tree ,Human small intestine microbiota ,Illumina sequencing ,ribosomal-rna ,Middle Aged ,Reference Standards ,identities ,communities ,Metabolic pathways ,quality ,KEGG ,Bioinformatic pipeline ,Female ,DNA microarray ,Metabolic Networks and Pathways ,Research Article ,Biotechnology ,Metatranscriptome ,Energy and redox metabolism [NCMLS 4] ,Computational biology ,Biology ,Microbiology ,DNA sequencing ,diversity ,seq ,COG ,transcriptomes ,Humans ,RNA, Messenger ,Host-Microbe Interactomics ,Illumina dye sequencing ,Aged ,VLAG ,metagenomics ,Sequence Analysis, RNA ,Gene Expression Profiling ,Computational Biology ,Ribosomal RNA ,gene-expression ,Metagenomics ,WIAS ,Food Microbiology ,Metagenome ,Pyrosequencing - Abstract
Background Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy. Results The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems. Conclusions A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.
- Published
- 2013
120. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals
- Author
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Kofler, R, Orozco-terWengel, P, De Maio, Nicola, Pandey, RV, Nolte, V, Futschik, A, Kosiol, C, Schlötterer, C, Kayser, M, and Kayser, M
- Subjects
0106 biological sciences ,Evolutionary Genetics ,Source code ,SAMPLES ,Pooling ,lcsh:Medicine ,Population genetics ,01 natural sciences ,Sliding window protocol ,Statistics ,Natural Selection ,lcsh:Science ,MUTATION ,media_common ,computer.programming_language ,Genetics ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Software Engineering ,Gene Pool ,Genomics ,Genome Scans ,ALIGNMENT ,SEQ ,Data Interpretation, Statistical ,Sequence Analysis ,Algorithms ,Research Article ,media_common.quotation_subject ,Population ,Biology ,010603 evolutionary biology ,DNA sequencing ,Plot (graphics) ,03 medical and health sciences ,Genome Analysis Tools ,DNA POLYMORPHISM ,Humans ,education ,030304 developmental biology ,Internet ,Evolutionary Biology ,Base Sequence ,Models, Genetic ,Software Tools ,lcsh:R ,Genetic Drift ,Computational Biology ,Sequence Analysis, DNA ,EVOLUTION ,RECOMBINATION RATES ,Genetics, Population ,DROSOPHILA-MELANOGASTER ,Computer Science ,Genetic Polymorphism ,lcsh:Q ,Perl ,computer ,Population Genetics - Abstract
Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θWatterson, θπ, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.
- Published
- 2010
121. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
- Author
-
Leimena, M.M., Ramiro-Garcia, J., Davids, M., van den Bogert, B., Smidt, H., Smid, E.J., te Boekhorst, J., Zoetendal, E.G., Schaap, P.J., Kleerebezem, M., Leimena, M.M., Ramiro-Garcia, J., Davids, M., van den Bogert, B., Smidt, H., Smid, E.J., te Boekhorst, J., Zoetendal, E.G., Schaap, P.J., and Kleerebezem, M.
- Abstract
Background: Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy. Results: The metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems. Conclusions: A reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.
- Published
- 2013
122. Profondità dell’elaborazione e alleanza terapeutica: un’indagine empirica
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Gentile, Daniela and Tanzilli, Annalisa
- Subjects
SEQ ,processo terapeutico ,Alleanza terapeutica ,profondità dell'elaborazione ,PQS ,WAI-O - Published
- 2008
123. Tools for a sustainable built environment: guidelines for subtropical design
- Author
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Tsenkova, S, Kennedy, Rosemary, Katoshevski, Rachel, Tsenkova, S, Kennedy, Rosemary, and Katoshevski, Rachel
- Abstract
South East Queensland (SEQ) is Australia's fastest-growing region, attracting an average of 55,000 new residents each year. The historic South East Queensland Regional Plan 2005-2006 (OUM,2005), and subsequent Draft South East Queensland Regional Plan 2009-2031 (DIP, 2008) aim to manage growth sustainably through a policy of compact urbanisation and consolidation. This requires a shift to a level of density not previously experienced in the generally low-density environment of Queensland. A critical characteristic of the regional vision is that 'development is sustainable, well designed, and the subtropical character of the region is recognised and reinforced'. The explict inclusion of the subtropical aspect with sustainability in the regional identity and appropriate design for climate play in the achievement of ecologically sustainable development.----- This chapter discusses the development of subtropical design principles and guidelines to support sustainable outcomes for SEQ. The chapter begins with a description of the region, and a discussion of subtropical character and identity. The guidelines themselves have been through a process of development including peer review of the initial draft, and testing and validation of the second draft. A sample of one of the principles is included with excerpts from feedback from planners elicited via a detailed questionnaire.
- Published
- 2009
124. Bitcoin's Biggest Name Forgot a Rule for Selling Shovels.
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Culpan, Tim
- Subjects
BITCOIN ,DIGITAL currency ,CRYPTOCURRENCIES ,ECONOMICS - Published
- 2018
125. Samsung's Winning Big From a Boom in the Boring Stuff: Gadfly.
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Culpan, Tim
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SMARTPHONE design & construction - Published
- 2018
126. LG Display's Loss Points to a Structural Change in Tech: Gadfly.
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Culpan, Tim
- Subjects
WORKING capital - Published
- 2018
127. Sing It From the Mountains, iPhone Supercycle Is Dead: Gadfly.
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Webb, Alex
- Subjects
IPHONE (Smartphone) - Published
- 2018
128. Trump Takes Broadcom From Photo-Op to Full Stop on Deal: Gadfly.
- Author
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Sutherland, Brooke
- Subjects
- TRUMP, Donald, 1946-, BROADCOM Inc.
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- 2018
129. Blocking the Qualcomm Deal Was the Right Thing to Do: Editorial.
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MERGERS & acquisitions ,GOVERNMENT policy - Published
- 2018
130. Forget About Bitcoin. Cash Is TSMC's Real Future: Gadfly.
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Culpan, Tim
- Subjects
BITCOIN ,BELLHOPS - Published
- 2018
131. Apple Largess Could Cut Both Ways for Its Suppliers: Gadfly.
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Culpan, Tim
- Subjects
CAPITAL investments - Published
- 2018
132. China Has Reasons to Be Gleeful at Intel's FUD Factor: Gadfly.
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Culpan, Tim
- Published
- 2018
133. The Machines Are Coming. To Boost Your Tech Portfolio: Gadfly.
- Author
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Culpan, Tim
- Subjects
TECHNOLOGY - Published
- 2017
134. Elliott Finally Puts a Price on NXP. Your Move, Qualcomm: Gadfly.
- Author
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Sutherland, Brooke
- Subjects
- ELLIOTT Management Corp., NXP Semiconductors NV, QUALCOMM Inc.
- Published
- 2017
135. Hey Now Toshiba, Don't Dream It's Over for the Chip Unit: Gadfly.
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Banjo, Shelly
- Subjects
INTEGRATED circuits ,COMPUTER storage devices - Published
- 2017
136. Analyse, Validation et Simulation d'un Nouvel Algorithme de Consensus
- Author
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Gula, Pascal, Real time and interoperability (TRIO), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
seq ,consensus ,distributed algorithmic ,[INFO.INFO-OH]Computer Science [cs]/Other [cs.OH] ,real-time ,temps réel ,algorithmique distribuée - Abstract
Stage de DEA. Rapport de stage.; Ce rapport se concentre sur l'étude d'une solution algorithmique liée au problème du consensus, à savoir sa complexité, ses propriétés temporelles et sa validation en environnement simulé. En effet, lors d'un précédent projet du nom d'ATR (Accord Temps Réel ), la société AXLOG Ingénierie, en collaboration avec des laboratoires de recherche, s'est penchée sur la validation d'un algorithme de diffusion atomique. Les résultats de cette dernière étant forts encourageants, AXLOG décida de poursuivre son effort sur un autre problème d'algorithmique distribuée, le consensus, en collaboration avec M. Gérard Le Lann de l'INRIA. Il s'agira pour nous de proposer les solutions " les meilleures " à des problèmes ayant des contraintes différentes (en coûts, performance, sûreté de fonctionnement). Ainsi pour une première implantation qui aura pour cible des satellites, nous étudierons une solution essentiellement " hardware " afin de garantir de meilleures performances. || This report focuses on the latest consensus algorithm, its complexity, its temporal properties, and its validation under an simulated environment. Indeed, in a former project named ATR, AXLOG Ingénierie, associated with some research laboratories, deals w
- Published
- 2001
137. Chang Exit Has Market Waiting for The Godfather Part II: Gadfly.
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Culpan, Tim
- Subjects
- CHANG, Morris, 1931-, TAIWAN Semiconductor Manufacturing Co. Ltd., MEDIATEK Inc.
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- 2017
138. Chip Battle Over, Toshiba Must Now Put Legal War to Bed: Gadfly.
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Culpan, Tim
- Subjects
BIDDING strategies - Published
- 2017
139. Death of a China Chip Deal Isn't MoneyGram's Top Risk: Gadfly.
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Culpan, Tim
- Subjects
SEMICONDUCTOR industry - Published
- 2017
140. Foxconn to Western Digital -- How D'Ya Like Them Apples?: Gadfly.
- Author
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Culpan, Tim
- Subjects
SEMICONDUCTOR manufacturing - Published
- 2017
141. Patience Proves Most Powerful Weapon in Toshiba Siege: Gadfly.
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Culpan, Tim
- Subjects
WEAPONS - Published
- 2017
142. Don't Fret About iPhones; an Indian Startup Hurt Foxconn: Gadfly.
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Culpan, Tim
- Subjects
IPHONE (Smartphone) - Published
- 2017
143. Neat Trick, Samsung. Now Show Me How You Did That Again: Gadfly.
- Author
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Culpan, Tim
- Subjects
CORPORATE profits ,STOCKS (Finance) - Published
- 2017
144. 20/20 Hindsight -- The M&A Slam Dunk That Took Years: Gadfly.
- Author
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Tan, Gillian
- Subjects
LASER industry ,MERGERS & acquisitions - Published
- 2017
145. Accept It, Toshiba. Western Digital Isn't Going Anywhere: Gadfly.
- Author
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Gopalan, Nisha
- Subjects
JOINT ventures - Published
- 2017
146. Some Neighborhood Rivalry Left Taiwan Investors on Top: Gadfly.
- Author
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Culpan, Tim
- Subjects
CHINA-Taiwan relations ,COMMERCE - Published
- 2017
147. Struggling Chipmakers Need You to Talk to Things: Gadfly.
- Author
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Culpan, Tim
- Subjects
CORPORATE profits - Published
- 2017
148. That Sugar High From Samsung Holds Risk of a Comedown: Gadfly.
- Author
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Culpan, Tim
- Subjects
STOCKS (Finance) - Published
- 2017
149. Toshiba's Slide Into Obscurity Should Worry Shareholders: Gadfly.
- Author
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Gopalan, Nisha
- Subjects
STOCKHOLDERS ,STOCKS (Finance) ,SOCIETIES - Published
- 2017
150. Strong Dollar Claims First Victim. No, Not the Greenback: Gadfly.
- Author
-
Culpan, Tim
- Subjects
BUSINESS conditions ,SALES - Published
- 2017
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