Tag-based approaches for transcriptome research and genome annotation
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Ruan, Y., Le Ber, P., Ng, H.H. & Liu, E.T. Interrogating the transcriptome. Trends Biotechnol. 22, 23–30 (2004).
Gerhard, D.S. et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 14, 2121–2127 (2004).
Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002).
Landry, J.R., Mager, D.L. & Wilhelm, B.T. Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet. 19, 640–648 (2003).
Black, D.L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291–336 (2003).
Garcia-Blanco, M.A., Baraniak, A.P. & Lasda, E.L. Alternative splicing in disease and therapy. Nat. Biotechnol. 22, 535–546 (2004).
Brasch, M.A., Hartley, J.L. & Vidal, M. ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res. 14, 2001–2009 (2004).
Tan, P.K. et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31, 5676–5684 (2003).
Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242–2246 (2004).
Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).
Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).
Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484–487 (1995).
Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630–634 (2000).
Saha, S. et al. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–512 (2002).
Matsumura, H. et al. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. USA 100, 15718–15723 (2003).
Powell, J. SAGE. The serial analysis of gene expression. Methods Mol. Biol. 99, 297–319 (2000).
Wang, S.M. SAGE: Current Technologies an Applications. (Horizon Bioscience, Norwich; 2005).
Man, M.Z., Wang, X. & Wang, Y. POWER_SAGE: comparing statistical tests for SAGE experiments. Bioinformatics 16, 953–959 (2000).
Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1998).
Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).
Silva, A.P. et al. The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucleic Acids Res. 32, 6104–6110 (2004).
Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 100, 15776–15781 (2003).
Hwang, B.J., Muller, H.M. & Sternberg, P.W. Genome annotation by high-throughput 5′ RNA end determination. Proc. Natl. Acad. Sci. USA 101, 1650–1655 (2004).
Hashimoto, S. et al. 5′-end SAGE for the analysis of transcriptional start sites. Nat. Biotechnol. 22, 1146–1149 (2004).
Wei, C.L. et al. 5′ long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl. Acad. Sci. USA 101, 11701–11706 (2004).
Schnoor, M. et al. Characterization of the synthetic compatible solute homoectoine as a potent PCR enhancer. Biochem. Biophys. Res. Commun. 322, 867–872 (2004).
Das, M., Harvey, I., Chu, L.L., Sinha, M. & Pelletier, J. Full-length cDNAs: more than just reaching the ends. Physiol. Genomics 6, 57–80 (2001).
Sugahara, Y. et al. Comparative evaluation of 5′-end-sequence quality of clones in CAP trapper and other full-length cDNA libraries. Gene 263, 93–102 (2001).
Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Kasai, Y. et al. 5′ SAGE: 5′-end Serial Analysis of Gene Expression database. Nucleic Acids Res. 33, D550–D552 (2005).
Tateno, Y., Saitou, N., Okubo, K., Sugawara, H. & Gojobori, T. DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res. 33, D25–D28 (2005).
Harbers, M. & Carninci, P. in SAGE: Current Technologies and Applications. (ed. S.M. Wang) 29–76 (Horizon Bioscience, Norwich; 2005).
Ideker, T., Galitski, T. & Hood, L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343–372 (2001).
Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C.M. & Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144–2148 (2000).
Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929–934 (2001).
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207–210 (2002).
Kodzius, R. et al. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Lett. 559, 22–26 (2004).
Carninci, P. et al. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res. 13, 1273–1289 (2003).
Pleasance, E.D., Marra, M.A. & Jones, S.J. Assessment of SAGE in transcript identification. Genome Res. 13, 1203–1215 (2003).
Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods 2, 105–111 (2005).
Macevicz, S.C. US patent 6, 136,537 (2000).
Salditt-Georgieff, M., Harpold, M.M., Wilson, M.C. & Darnell, J.E., Jr. Large heterogeneous nuclear ribonucleic acid has three times as many 5′ caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1, 179–187 (1981).
Carninci, P. et al. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10, 1617–1630 (2000).
Sabo, P.J. et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc. Natl. Acad. Sci. USA 101, 16837–16842 (2004).
Kim, J., Bhinge, A.A., Morgan, X.C. & Iyer, V.R. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat. Methods 2, 47–53 (2004).
Shibata, Y. et al. Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing. Biotechniques 31, 1042, 1044, 1048–1049 (2001).
Carninci, P. & Hayashizaki, Y. High-efficiency full-length cDNA cloning. Methods Enzymol. 303, 19–44 (1999).
Carninci, P. et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327–336 (1996).
Maruyama, K. & Sugano, S. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171–174 (1994).
Edery, I., Chu, L.L., Sonenberg, N. & Pelletier, J. An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture). Mol. Cell. Biol. 15, 3363–3371 (1995).
Theissen, H. et al. Cloning of the human cDNA for the U1 RNA-associated 70K protein. EMBO J. 5, 3209–3217 (1986).
Merenkova, I., Milne, E. & Jean-Baptiste, D. US patent 6, 136,537 (2000).