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Literature DB >> 16352711

A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells.

Asim S Siddiqui¹, Jaswinder Khattra, Allen D Delaney, Yongjun Zhao, Caroline Astell, Jennifer Asano, Ryan Babakaiff, Sarah Barber, Jaclyn Beland, Slavita Bohacec, Mabel Brown-John, Steve Chand, David Charest, Anita M Charters, Rebecca Cullum, Noreen Dhalla, Ruth Featherstone, Daniela S Gerhard, Brad Hoffman, Robert A Holt, Juan Hou, Byron Y-L Kuo, Lisa L C Lee, Stephanie Lee, Derek Leung, Kevin Ma, Corey Matsuo, Michael Mayo, Helen McDonald, Anna-liisa Prabhu, Pawan Pandoh, Gregory J Riggins, Teresa Ruiz de Algara, James L Rupert, Duane Smailus, Jeff Stott, Miranda Tsai, Richard Varhol, Pavle Vrljicak, David Wong, Mona K Wu, Yuan-Yun Xie, George Yang, Ida Zhang, Martin Hirst, Steven J M Jones, Cheryl D Helgason, Elizabeth M Simpson, Pamela A Hoodless, Marco A Marra.

Abstract

We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.

Entities: Disease Species

Mesh：

Substances：
RNA, Untranslated

Year: 2005 PMID： 16352711 PMCID： PMC1311911 DOI： 10.1073/pnas.0509455102

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

36 in total

1. The human genome browser at UCSC.

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Journal: Genome Res Date: 2002-06 Impact factor: 9.043

2. Initial sequencing and comparative analysis of the mouse genome.

Authors: Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal: Nature Date: 2002-12-05 Impact factor: 49.962

Review 3. Alternative pre-mRNA splicing and proteome expansion in metazoans.

Authors: Tom Maniatis; Bosiljka Tasic
Journal: Nature Date: 2002-07-11 Impact factor: 49.962

4. NCBI Reference Sequence project: update and current status.

Authors: Kim D Pruitt; Tatiana Tatusova; Donna R Maglott
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

Authors: Piero Carninci; Kazunori Waki; Toshiyuki Shiraki; Hideaki Konno; Kazuhiro Shibata; Masayoshi Itoh; Katsunori Aizawa; Takahiro Arakawa; Yoshiyuki Ishii; Daisuke Sasaki; Hidemasa Bono; Shinji Kondo; Yuichi Sugahara; Rintaro Saito; Naoki Osato; Shiro Fukuda; Kenjiro Sato; Akira Watahiki; Tomoko Hirozane-Kishikawa; Mari Nakamura; Yuko Shibata; Ayako Yasunishi; Noriko Kikuchi; Atsushi Yoshiki; Moriaki Kusakabe; Stefano Gustincich; Kirk Beisel; William Pavan; Vassilis Aidinis; Akira Nakagawara; William A Held; Hiroo Iwata; Tomohiro Kono; Hiromitsu Nakauchi; Paul Lyons; Christine Wells; David A Hume; Michela Fagiolini; Takao K Hensch; Michelle Brinkmeier; Sally Camper; Junji Hirota; Peter Mombaerts; Masami Muramatsu; Yasushi Okazaki; Jun Kawai; Yoshihide Hayashizaki
Journal: Genome Res Date: 2003-06 Impact factor: 9.043

6. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.

Authors: Mihaela Zavolan; Shinji Kondo; Christian Schonbach; Jun Adachi; David A Hume; Yoshihide Hayashizaki; Terry Gaasterland
Journal: Genome Res Date: 2003-06 Impact factor: 9.043

7. Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized.

Authors: Hidenori Kiyosawa; Nathan Mise; Shigeru Iwase; Yoshihide Hayashizaki; Kuniya Abe
Journal: Genome Res Date: 2005-03-21 Impact factor: 9.043

8. Large-scale analysis of the human and mouse transcriptomes.

Authors: Andrew I Su; Michael P Cooke; Keith A Ching; Yaron Hakak; John R Walker; Tim Wiltshire; Anthony P Orth; Raquel G Vega; Lisa M Sapinoso; Aziz Moqrich; Ardem Patapoutian; Garret M Hampton; Peter G Schultz; John B Hogenesch
Journal: Proc Natl Acad Sci U S A Date: 2002-03-19 Impact factor: 11.205

9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Authors: Robert L Strausberg; Elise A Feingold; Lynette H Grouse; Jeffery G Derge; Richard D Klausner; Francis S Collins; Lukas Wagner; Carolyn M Shenmen; Gregory D Schuler; Stephen F Altschul; Barry Zeeberg; Kenneth H Buetow; Carl F Schaefer; Narayan K Bhat; Ralph F Hopkins; Heather Jordan; Troy Moore; Steve I Max; Jun Wang; Florence Hsieh; Luda Diatchenko; Kate Marusina; Andrew A Farmer; Gerald M Rubin; Ling Hong; Mark Stapleton; M Bento Soares; Maria F Bonaldo; Tom L Casavant; Todd E Scheetz; Michael J Brownstein; Ted B Usdin; Shiraki Toshiyuki; Piero Carninci; Christa Prange; Sam S Raha; Naomi A Loquellano; Garrick J Peters; Rick D Abramson; Sara J Mullahy; Stephanie A Bosak; Paul J McEwan; Kevin J McKernan; Joel A Malek; Preethi H Gunaratne; Stephen Richards; Kim C Worley; Sarah Hale; Angela M Garcia; Laura J Gay; Stephen W Hulyk; Debbie K Villalon; Donna M Muzny; Erica J Sodergren; Xiuhua Lu; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madan; Alice C Young; Yuriy Shevchenko; Gerard G Bouffard; Robert W Blakesley; Jeffrey W Touchman; Eric D Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard M Myers; Yaron S N Butterfield; Martin I Krzywinski; Ursula Skalska; Duane E Smailus; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Marco A Marra
Journal: Proc Natl Acad Sci U S A Date: 2002-12-11 Impact factor: 11.205

10. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

Authors: Hidemasa Bono; Ken Yagi; Takeya Kasukawa; Itoshi Nikaido; Naoko Tominaga; Rika Miki; Yosuke Mizuno; Yasuhiro Tomaru; Hitoshi Goto; Hiroyuki Nitanda; Daisuke Shimizu; Hirochika Makino; Tomoyuki Morita; Junshin Fujiyama; Takehito Sakai; Takashi Shimoji; David A Hume; Yoshihide Hayashizaki; Yasushi Okazaki
Journal: Genome Res Date: 2003-06 Impact factor: 9.043

60 in total

1. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.

Authors: Brad G Hoffman; Gordon Robertson; Bogard Zavaglia; Mike Beach; Rebecca Cullum; Sam Lee; Galina Soukhatcheva; Leping Li; Elizabeth D Wederell; Nina Thiessen; Mikhail Bilenky; Timothee Cezard; Angela Tam; Baljit Kamoh; Inanc Birol; Derek Dai; Yongjun Zhao; Martin Hirst; C Bruce Verchere; Cheryl D Helgason; Marco A Marra; Steven J M Jones; Pamela A Hoodless
Journal: Genome Res Date: 2010-06-15 Impact factor: 9.043

Review 2. The complexity of the mammalian transcriptome.

Authors: Stefano Gustincich; Albin Sandelin; Charles Plessy; Shintaro Katayama; Roberto Simone; Dejan Lazarevic; Yoshihide Hayashizaki; Piero Carninci
Journal: J Physiol Date: 2006-07-20 Impact factor: 5.182

3. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.

Authors: Jaswinder Khattra; Allen D Delaney; Yongjun Zhao; Asim Siddiqui; Jennifer Asano; Helen McDonald; Pawan Pandoh; Noreen Dhalla; Anna-Liisa Prabhu; Kevin Ma; Stephanie Lee; Adrian Ally; Angela Tam; Danne Sa; Sean Rogers; David Charest; Jeff Stott; Scott Zuyderduyn; Richard Varhol; Connie Eaves; Steven Jones; Robert Holt; Martin Hirst; Pamela A Hoodless; Marco A Marra
Journal: Genome Res Date: 2006-11-29 Impact factor: 9.043

Review 4. Sharing and reusing gene expression profiling data in neuroscience.

Authors: Xiang Wan; Paul Pavlidis
Journal: Neuroinformatics Date: 2007

5. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development.

Authors: Zhe Ji; Ju Youn Lee; Zhenhua Pan; Bingjun Jiang; Bin Tian
Journal: Proc Natl Acad Sci U S A Date: 2009-04-16 Impact factor: 11.205

Review 6. Noncoding RNA in development.

Authors: Paulo P Amaral; John S Mattick
Journal: Mamm Genome Date: 2008-10-07 Impact factor: 2.957

10. Integrative proteomic and transcriptomic analyses reveal multiple post-transcriptional regulatory mechanisms of mouse spermatogenesis.

Authors: Haiyun Gan; Tanxi Cai; Xiwen Lin; Yujian Wu; Xiuxia Wang; Fuquan Yang; Chunsheng Han
Journal: Mol Cell Proteomics Date: 2013-01-16 Impact factor: 5.911