Searching journal content for articles similar to Nikaido et al. 13 (6b): 1402.

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Methods: Genome-wide prediction of imprinted murine genes
- Philippe P. Luedi,
- Alexander J. Hartemink,
- and Randy L. Jirtle
Genome Res. June 2005 15: 875-884; doi:10.1101/gr.3303505
.... This approach can lead to a false-positive rate as high as 42% because the transcription of nonimprinted genes may be regulated by the products of imprinted control genes ( Mizuno et al. 2002 ). Given the high false-positive rate associated with expression profiling, our estimate seems realistic. Computational...
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Research: Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
- Alexis Battle,
- Sara Mostafavi,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Courtney McCormick,
- Christian D. Haudenschild,
- Kenneth B. Beckman,
- Jianxin Shi,
- Rui Mei,
- Alexander E. Urban,
- Stephen B. Montgomery,
- Douglas F. Levinson,
- and Daphne Koller
Genome Res. January 2014 24: 14-24; Published in Advance October 3, 2013, doi:10.1101/gr.155192.113
...Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals Alexis Battle 1 , Sara Mostafavi 1 , Xiaowei Zhu 2 , James B. Potash 3 , Myrna M. Weissman 4 , Courtney McCormick 5...
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PERSPECTIVE: Origin of phenotypes: Genes and transcripts
- Thomas R. Gingeras
Genome Res. June 2007 17: 682-690; doi:10.1101/gr.6525007
...to chromosome 21 were located in introns, exons, and intergenic regions ( Cawley et al. 2004 ; Euskirchen et al. 2004 ). Many of these sites contained evidence of unannotated transcription in close proximity. The large-scale sequencing of more than 12 million CAGE tags from multiple mouse and human tissues...
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Research: Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
- Xu Wang,
- Kory C. Douglas,
- John L. VandeBerg,
- Andrew G. Clark,
- and Paul B. Samollow
Genome Res. January 2014 24: 70-83; Published in Advance September 24, 2013, doi:10.1101/gr.161919.113
...modifications in fetal brain and extra-embryonic membranes in the gray, short-tailed opossum (Monodelphis domestica). Themajority of X-linked genes (152 of 176 genes with trackable SNP variants) exhibited paternally imprinted expression, with nearly 100% of transcripts derived from the maternal allele; whereas...
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LETTER: Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
- 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,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1318-1323; doi:10.1101/gr.1075103
...Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays Hidemasa Bono 1 , Ken Yagi 1 , Takeya Kasukawa 1 , 2 , Itoshi Nikaido 1 , 3 , Naoko Tominaga 1 , Rika Miki 1 , Yosuke Mizuno 1...
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Resource: Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
- Alexandra C. Nica,
- Halit Ongen,
- Jean-Claude Irminger,
- Domenico Bosco,
- Thierry Berney,
- Stylianos E. Antonarakis,
- Philippe A. Halban,
- and Emmanouil T. Dermitzakis
Genome Res. September 2013 23: 1554-1562; Published in Advance May 28, 2013, doi:10.1101/gr.150706.112
...will likely explain a proportion of these associations, but uncovering them is entirely dependent on first describing the transcriptional profile of the beta cell and understanding its genetic determinants. In this context, we interrogate here the human beta cell transcriptome in multiple whole- sequenced...
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Research: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
- Claire Vandiedonck,
- Martin S. Taylor,
- Helen E. Lockstone,
- Katharine Plant,
- Jennifer M. Taylor,
- Caroline Durrant,
- John Broxholme,
- Benjamin P. Fairfax,
- and Julian C. Knight
Genome Res. July 2011 21: 1042-1054; Published in Advance May 31, 2011, doi:10.1101/gr.116681.110
...al. 2010). In this study, we show how gene expression profiling of individuals homozygous for the region has allowed us to identify extensive haplotype-related transcriptional differences and highlight the importance of alternative splicing in this transcriptional diversity. Results The MHC array...
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ARTICLE: Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized
- Hidenori Kiyosawa,
- Nathan Mise,
- Shigeru Iwase,
- Yoshihide Hayashizaki,
- and Kuniya Abe
Genome Res. April 2005 15: 463-474; Published in Advance March 21, 2005, doi:10.1101/gr.3155905
...., et al. 2003 . Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res. 13 : 1402 -1409. ↵ Osato, N., Yamada, H., Satoh, K., Ooka, H., Yamamoto, M., Suzuki, K., Kawai, J., Carninci, P., Ohtomo, Y., Murakami, K., et al. 2003 . Antisense...
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Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
- Markus Brosch,
- Gary I. Saunders,
- Adam Frankish,
- Mark O. Collins,
- Lu Yu,
- James Wright,
- Ruth Verstraten,
- David J. Adams,
- Jennifer Harrow,
- Jyoti S. Choudhary,
- and Tim Hubbard
Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
...matching with genome-wide protein-coding predictions to perform large-scale gene validation and discovery in the mouse genome for the first time. In searching an excess of 10 million spectra, we have been able to validate 32%, 17%, and 7% of all protein-coding genes, exons, and splice boundaries...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...for transcriptome studies. The most unique benefit of RNA-PET is the ability to identify unconventional fusion transcripts. A large-scale RNA-PET program to investigate fusion genes could lead to discoveries of new candidate biomarkers for diagnostic and therapeutic options. ChIP-PET for identifying regulatory...
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