Assessment of SAGE in transcript identification

Genome Research

Volumn 13, Issue 6 A, 2003, Pages 1203-1215

  Pleasance, Erin D ^a   Marra, Marco A ^a   Jones, Steven J M ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAG; GENE EXPRESSION SYSTEM; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; UNTRANSLATED REGION;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; DROSOPHILA MELANOGASTER; GENE EXPRESSION PROFILING; GENES, HELMINTH; GENES, INSECT; GENOME; TRANSCRIPTION, GENETIC;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; MELANOGASTER; SALVIA;

EID: 0037803473     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.873003     Document Type: Article

References (39)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Andrews, J., Bouffard, G.G., Cheadle, C., Lu, J., Becker, K.G., and Oliver, B. 2000. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 10: 2030-2043.
4. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
5. Chen, J.J., Rowley, J.D., and Wang, S.M. 2000. Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proc. Natl. Acad. Sci. 97: 349-353.
6. Durbin, R. and Thierry-Mieg, J. 1991. A C. elegans Database.
7. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
8. FlyBase Consortium. 2002. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 30: 106-108.
9. Friedman, R. and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11: 373-381.
10. Fujii, S. and Amrein, H. 2002. Genes expressed in the Drosophila head reveal a role for fat cells in sex-specific physiology. EMBO J. 21: 5353-5363.
11. Gorski, S.M., Chittaranjan, S., Pleasance, E.D., Freeman, J.D., Anderson, C.L., Varhol, R.J., Coughlin, S.M., Zuyderduyn, S.D., Jones, S.J.M., and Marra, M.A. 2003. A SAGE approach to discovery of genes involved in autophagic cell death. Curr. Biol. 13: 358-363.
12. Graber, J.H., Cantor, C.R., Mohr, S.C., and Smith, T.F. 1999. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl. Acad. Sci. 96: 14055-14060.
13. Jasper, H., Benes, V., Schwager, C., Sauer, S., Clauder-Munster, S., Ansorge, W., and Bohmann, D. 2001. The genomic response of the Drosophila embryo to JNK signaling. Dev. Cell 1: 579-586.
14. Jones, S.J., Riddle, D.L., Pouzyrev, A.T., Velculescu, V.E., Hillier, L., Eddy, S.R., Stricklin, S.L., Baillie, D.L., Waterston, R., and Marra, M.A. 2001. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res. 11: 1346-1352.
15. Kent, W.J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
16. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
17. Lash, A.E., Tolstoshev, C.M., Wagner, L., Schuler, G.D., Strausberg, R.L., Riggins, G.J., and Altschul, S.F. 2000. SAGEmap: A public gene expression resource. Genome Res. 10: 1051-1060.
18. Lee, S., Clark, T., Chen, J., Zhou, G., Scott, L.R., Rowley, J.D., and Wang, S.M. 2002. Correct identification of genes from serial analysis of gene expression tag sequences. Genomics 79: 598-602.
19. Madden, S.L., Galella, E.A., Zhu, J., Bertelsen, A.H., and Beaudry, G.A. 1997. SAGE transcript profiles for p53-dependent growth regulation. Oncogene 15: 1079-1085.
20. Mott, R. 1997. ESTNOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci. 13: 477-478.
21. Nacht, M., Dracheva, T., Gao, Y., Fujii, T., Chen, Y., Player, A., Akmaev, V., Cook, B., Dufault, M., Zhang, M., et al. 2001. Molecular characteristics of non-small cell lung cancer. Proc. Natl. Acad. Sci. 98: 15203-15208.
22. Pauws, E., van Kampen, A.H., van de Graaf, S.A., de Vijlder, J.J., and Ris-Stalpers, C. 2001. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: Implications for SAGE analysis. Nucleic Acids Res. 29: 1690-1694.
23. Riddle, D.L., Blumenthal, T., Meyer, B.J., and Preiss, J.R. 1997. C. Elegans II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
24. Rogic, S., Mackworth, A.K., and Ouellette, F.B. 2001. Evaluation of gene-finding programs on mammalian sequences. Genome Res. 11: 817-832.
25. Ryo, A., Kondoh, N., Wakatsuki, T., Hada, A., Yamamoto, N., and Yamamoto, M. 2000. A modified serial analysis of gene expression that generates longer sequence tags by nonpalindromic cohesive linker ligation. Anal. Biochem. 277: 160-162.
26. Saha, S., Sparks, A.B., Rago, C., Akmaev, V., Wang, C.J., Vogelstein, B., Kinzler, K.W., and Velculescu, V.E. 2002. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20: 508-512.
27. Schuler, G.D. 1997. Pieces of the puzzle: Expressed sequence tags and the catalog of human genes. J. Mol. Med. 75: 694-698.
28. Sonnhammer, E.L. and Durbin, R. 1994. A workbench for large-scale sequence homology analysis. Comput. Appl. Biosci. 10: 301-307.
29. Stapleton, M., Liao, G., Brokstein, P., Hong, L., Carninci, P., Shiraki, T., Hayashizaki, Y., Champe, M., Pacleb, J., Wan., K., et al. 2002. The Drosophila gene collection: Identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 12: 1294-1300.
30. Steen, B.R., Lian, T., Zuyderduyn, S., MacDonald, W.K., Marra, M., Jones, S.J., and Kronstad, J.W. 2002. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 12: 1386-1400.
31. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., and Spieth, J. 2001. WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29: 82-86.
32. Stein, L.D. and Thierry-Mieg, J. 1998. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res. 8: 1308-1315.
33. Strausberg, R.L., Feingold, E.A., Klausner, R.D., and Collins, F.S. 1999. The mammalian gene collection. Science 286: 455-457.
34. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. 1995. Serial analysis of gene expression. Science 270: 484-487.
35. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett Jr., D.E., Hieter, P., Vogelstein, B., and Kinzler, K.W. 1997. Characterization of the yeast transcriptome. Cell 88: 243-251.
36. Velculescu, V.E., Madden, S.L., Zhang, L., Lash, A.E., Yu, J., Rago, C., Lal, A., Wang, C.J., Beaudry, G.A., Ciriello, K.M., et al. 1999. Analysis of human transcriptomes. Nat. Genet. 23: 387-388.
37. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
38. Virlon, B., Cheval, L., Buhler, J.M., Billon, E., Doucet, A., and Elalouf, J.M. 1999. Serial microanalysis of renal transcriptomes. Proc. Natl. Acad. Sci. 96: 15286-15291.
39. Waghray, A., Schober, M., Feroze, F., Yao, F., Virgin, J., and Chen, Y.Q. 2001. Identification of differentially expressed genes by serial analysis of gene expression in human prostate cancer. Cancer Res. 61: 4283-4286.