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A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

Faulkner, Geoffrey J., Forrest, Alistair R.R., Chalk, Alistair M., Schroder, Kate, Hayashizaki, Yoshihide, Carninci, Piero, Hume, David A., Grimmond, Sean M.·2008·Genomics
DOI 10.1016/j.ygeno.2007.11.003
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Research works printed but not linked: 22

  1. Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014 · DOI
  2. Carninci, 2003, Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia, Genome Res., 13, 1273, 10.1101/gr.1119703 · DOI
  3. Hayashizaki, 2006, Genome Network and FANTOM3: assessing the complexity of the transcriptome, PLoS Genet., 2, e63, 10.1371/journal.pgen.0020063 · DOI
  4. Kawai, 2001, Functional annotation of a full-length mouse cDNA collection, Nature, 409, 685, 10.1038/35055500 · DOI
  5. Okazaki, 2002, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563, 10.1038/nature01266 · DOI
  6. Carninci, 1999, High-efficiency full-length cDNA cloning, Methods Enzymol., 303, 19, 10.1016/S0076-6879(99)03004-9 · DOI
  7. Carninci, 1996, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37, 327, 10.1006/geno.1996.0567 · DOI
  8. Carninci, 2000, Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes, Genome Res., 10, 1617, 10.1101/gr.145100 · DOI
  9. Shiraki, 2003, Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage, Proc. Natl. Acad. Sci. U. S. A., 100, 15776, 10.1073/pnas.2136655100 · DOI
  10. Bajic, 2006, Mice and men: their promoter properties, PLoS Genet., 2, e54, 10.1371/journal.pgen.0020054 · DOI
  11. Engstrom, 2006, Complex loci in human and mouse genomes, PLoS Genet., 2, e47, 10.1371/journal.pgen.0020047 · DOI
  12. Frith, 2006, Evolutionary turnover of mammalian transcription start sites, Genome Res., 16, 713, 10.1101/gr.5031006 · DOI
  13. Sandelin, 2007, Mammalian RNA polymerase II core promoters: insights from genome-wide studies, Nat. Rev., Genet., 8, 424, 10.1038/nrg2026 · DOI
  14. Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 · DOI · Paper page
  15. Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102 · DOI · Paper page
  16. Bailey, 2006, MEME: discovering and analyzing DNA and protein sequence motifs, Nucleic Acids Res., 34, W369, 10.1093/nar/gkl198 · DOI
  17. Birney, 2007, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, 447, 799, 10.1038/nature05874 · DOI · Paper page
  18. Forrest, 2006, Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases, Genome Biol., 7, R5, 10.1186/gb-2006-7-1-r5 · DOI
  19. Wells, 2006, Alternate transcription of the Toll-like receptor signaling cascade, Genome Biol., 7, R10, 10.1186/gb-2006-7-2-r10 · DOI
  20. van Ruissen, 2005, Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips, BMC Genomics, 6, 91, 10.1186/1471-2164-6-91 · DOI
  21. Kasukawa, 2004, Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis, Genomics, 84, 913, 10.1016/j.ygeno.2004.08.011 · DOI
  22. Irizarry, 2003, Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Res., 31, e15, 10.1093/nar/gng015 · DOI

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Metadata

Authors
Faulkner, G. J., Forrest, A. R. R., Chalk, A. M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D. A., & Grimmond, S. M.
Venue
Genomics
Publisher
Elsevier BV
Published
2008-03
Volume
91
Issue
3
Pages
281-288
ISSN
0888-7543
DOI
10.1016/j.ygeno.2007.11.003
Cited by
82
References
2
Language
en
Licence

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