FANTOM5 CAGE profiles of human and mouse samples

Jay W. Shin | Thomas J. Ha | Kelly J. Morris | Louise N. Winteringham | Kelly J. Hitchens | J. Kere | Christophe Simon | M. Fagiolini | R. Passier | C. Mummery | T. Gingeras | J. Kawai | Piero Carninci | Y. Hayashizaki | Y. Okazaki | Harukazu Suzuki | D. Hume | T. Lassmann | A. Sajantila | M. Herlyn | H. Clevers | A. Forrest | G. Faulkner | T. Kasukawa | C. Wells | M. Furuno | S. Gustincich | V. Orlando | C. Schneider | R. Verardo | S. Fukuda | M. Kanamori-Katayama | T. Arakawa | M. Itoh | H. Kawaji | T. Kawashima | N. Ninomiya | M. Tagami | J. Severin | G. Schulze-Tanzil | C. Daub | A. Pombo | R. Axton | Christian Schmidl | E. Arner | J. Baillie | Y. Ishizu | N. Kondo | A. Lennartsson | P. Heutink | M. Rehli | C. Davis | A. Mackay-Sim | P. Arner | D. Ovchinnikov | S. Zucchelli | M. Okada-Hatakeyama | M. Detmar | H. Enomoto | D. Goldowitz | Mitsuyoshi Murata | A. Kubosaki | A. Edge | M. Fisher | J. Briggs | E. Wolvetang | Masayuki Yamamoto | P. Rizzu | Y. Yamaguchi | M. Babina | M. van de Wetering | M. Lizio | J. Harshbarger | H. Shimoji | S. Şahin | I. Abugessaisa | Fumi Hori | Sachi Ishikawa-Kato | Shohei Noma | A. Hasegawa | S. Kojima | Yukio Nakamura | L. Khachigian | T. Geijtenbeek | A. Blumenthal | S. Koyasu | Hiromasa Morikawa | A. Knox | D. Sugiyama | S. Ogishima | Hiroshi Tanaka | Shuhei Noguchi | Hiromi Nishiyori-Sueki | N. Mejhert | T. Sengstag | H. Koseki | F. Brombacher | A. Saxena | A. Beckhouse | B. Bodega | A. Ehrlund | M. Endoh | A. Eslami | L. Fairbairn | C. Ferrai | L. Forrester | R. Guler | Mitsuko Hara | T. Ikawa | C. Kai | H. Kawamoto | S. Klinken | Sarah Klein | Y. Mizuno | M. Morimoto | Y. Nakachi | M. Patrikakis | Xian-Yang Qin | Sugata Roy | Hiroki Sato | Suzana Savvi | Anita Schwegmann | A. Tomoiu | Chiyo Yanagi-Mizuochi | M. Yoneda | Peter G Zhang | M. Kojima | Sayaka Nagao-Sato | K. Summers | A. Bonetti | H. Tatsukawa | S. Sakaguchi | K. Ekwall | T. Nozaki | K. Nakazato | R. Manabe | H. Ohno | M. Edinger | Y. Hasegawa | Masanori Suzuki | A. Kaiho | H. Motohashi | Guojun Sheng | F. Nakahara | Hironori Satoh | Jun Takai | A. Carlisle | S. Guhl | Weonju Lee | M. Ohshima | H. Toyoda | T. Kitamura | T. C. Barnett | A. Kondo | J. Kempfle | T. Kenna | K. Moro | N. Ohkura | T. Sugiyama | M. Hamaguchi | T. Dohi | Y. Kawamura | D. Vijayan | Rie Fujita | Toshiyuki Nakamura | L. M. van den Berg | A. Saka | S. Pradhan-Bhatt | Mizuho Sakai | N. Takahashi | M. Farach-Carson | K. Kaida | Eri Saijyo | Naoko Suzuki | Shoko Watanabe | Shigehiro Yoshida | J. Furusawa | Y. Yonekura | Kaoru Kaida | M. Okada‐Hatakeyama | Ri-ichiroh Manabe | T. Barnett

[1]  Finn Drabløs,et al.  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals , 2016, Nucleic Acids Res..

[2]  Piero Carninci,et al.  FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki , 2016, Database J. Biol. Databases Curation.

[3]  Brian T. Lee,et al.  The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Res..

[4]  Piero Carninci,et al.  Paradigm shifts in genomics through the FANTOM projects , 2015, Mammalian Genome.

[5]  Pietro Liò,et al.  The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..

[6]  Thomas J. Ha,et al.  Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.

[7]  Derek W Wright,et al.  Gateways to the FANTOM5 promoter level mammalian expression atlas , 2015, Genome Biology.

[8]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[9]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[10]  Yoshihide Hayashizaki,et al.  Interactive visualization and analysis of large-scale sequencing datasets using ZENBU , 2014, Nature Biotechnology.

[11]  Ting Wang,et al.  Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser , 2013, Bioinform..

[12]  Carsten O. Daub,et al.  MOIRAI: a compact workflow system for CAGE analysis , 2014, BMC Bioinformatics.

[13]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[14]  Do Won Kim,et al.  Vitamin D increases expression of cathelicidin in cultured sebocytes , 2012, Archives of Dermatological Research.

[15]  Piero Carninci,et al.  Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer , 2012, PloS one.

[16]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[17]  Piero Carninci,et al.  Unamplified Cap Analysis of Gene Expression on a Single-molecule Sequencer , 2022 .

[18]  Daniel Rios,et al.  Ensembl 2011 , 2010, Nucleic Acids Res..

[19]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[20]  Ariel S. Schwartz,et al.  An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man , 2010, Cell.

[21]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[22]  Xinqiao Jia,et al.  Perlecan domain IV peptide stimulates salivary gland cell assembly in vitro. , 2009, Tissue engineering. Part A.

[23]  J. Kawai,et al.  Tiny RNAs associated with transcription start sites in animals , 2009, Nature Genetics.

[24]  J. Kawai,et al.  The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.

[25]  Martin S. Taylor,et al.  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line , 2009, Nature Genetics.

[26]  Y. Yamaguchi,et al.  In vitro characterization of the cytokine profile of the epithelial cell rests of Malassez. , 2008, Journal of periodontology.

[27]  Paul T. Spellman,et al.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.

[28]  J. Harrow,et al.  GENCODE: producing a reference annotation for ENCODE , 2006, Genome Biology.

[29]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[30]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[31]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[32]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[33]  S. Hirakawa,et al.  Hepatocyte growth factor promotes lymphatic vessel formation and function , 2005, The EMBO journal.

[34]  D. Reidel,et al.  The Transcriptional Landscape of the Mammalian Genome The FANTOM Consortium* and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)* , 2005 .

[35]  T. Nomura,et al.  Control of Regulatory T Cell Development by the Transcription Factor Foxp3 , 2002 .

[36]  S. Brody,et al.  Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population. , 2002, American journal of physiology. Lung cellular and molecular physiology.

[37]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[38]  C. Bult,et al.  Functional annotation of a full-length mouse cDNA collection , 2001, Nature.