Expressed sequence tags: An overview

Methods in Molecular Biology

Volumn 533, Issue , 2009, Pages 1-12

  Parkinson, John ^a,b   Blaxter, Mark ^c  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

cDNA libraries; database resources; dbEST; EST; Expressed sequence tags; gene discovery; transcript profiling

Indexed keywords

EUKARYOTA;

COMPLEMENTARY DNA;

ANIMAL; BIOLOGICAL MODEL; EXPRESSED SEQUENCE TAG; GENE LIBRARY; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; HUMAN; METABOLISM; PHYLOGENY; REPRODUCIBILITY; REVIEW;

ANIMALS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENETIC TECHNIQUES; HUMANS; MODELS, GENETIC; PHYLOGENY; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION, GENETIC;

EID: 84970020970     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-136-3_1     Document Type: Article

References (40)

1. Putney, S. D., Herlihy, W. C., and Schimmel, P. (1983) A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302, 718-21. (Pubitemid 13120277)
2. Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M., Polymeropoulos, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Moreno, R. F., et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-6. (Pubitemid 21917081)
3. Boguski, M. S., Lowe, T. M., and Tol-stoshev, C. M. (1993) dbEST-database for "expressed sequence tags". Nat Genet 4, 332-3.
4. Bernal, A., Ear, U., and Kyrpides, N. (2001) Genomes online database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 29, 126-7. (Pubitemid 32054425)
5. Ranjit, N., Jones, M. K., Stenzel, D. J., Gasser, R. B., and Loukas, A. (2006) A survey of the intestinal transcriptomes of the hookworms, necator americanus and ancy-lostoma caninum, using tissues isolated by laser microdissection microscopy. Int J Parasitol 36, 701-10. (Pubitemid 43765726)
6. Parkinson, J., Anthony, A., Wasmuth, J., Schmid, R., Hedley, A., and Blaxter, M. (2004) Partigene-constructing partial genomes. Bioinformatics 20, 1398-404.
7. Wasmuth, J. D., and Blaxter, M. L. (2004) prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioin-formatics 5, 187.
8. Koski, L. B., Gray, M. W., Lang, B. F., and Burger, G. (2005) Autofact: an automatic functional annotation and classification tool. BMC Bioinformatics 6, 151.
9. Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755-63. (Pubitemid 28552108)
10. Parkinson, J., Whitton, C., Schmid, R., Thomson, M., and Blaxter, M. (2004) NEMBASE: a resource for parasitic nema-tode ESTs. Nucleic Acids Res 32, D427-30. (Pubitemid 38081691)
11. Wylie, T., Martin, J. C., Dante, M., Mitreva, M. D., Clifton, S. W., Chinwalla, A., Waterston, R. H., Wilson, R. K., and McCarter, J. P. (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res 32, D423-6. (Pubitemid 38081690)
12. Wheeler, D. L., Church, D. M., Federhen, S., Lash, A. E., Madden, T. L., Pontius, J. U., Schuler, G. D., Schriml, L. M., Sequeira, E., Tatusova, T. A., and Wagner, L. (2003) Database resources of the national center for biotechnology. Nucleic Acids Res 31, 28-33. (Pubitemid 36150327)
13. Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R., Antonescu, V., Chan, A., Cheung, F., and Quackenbush, J. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 33, D71-4. (Pubitemid 40207833)
14. Peregrin-Alvarez, J. M., Yam, A., Sivakumar, G., and Parkinson, J. (2005) Partigenedb-collating partial genomes. Nucleic Acids Res 33, D303-7.
15. Parkinson, J., and Blaxter, M. (2003) SimiTri-visualizing similarity relationships for groups of sequences. Bioinfor-matics 19, 390-5. (Pubitemid 36284938)
16. Kenyon, F., Welsh, M., Parkinson, J., Whitton, C., Blaxter, M. L., and Knox, D. P. (2003) Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis-allergens, proteases and free-radical scavengers. Parasitology 126, 451-60. (Pubitemid 36649298)
17. Fernandez, C., Gregory, W. F., Loke, P., and Maizels, R. M. (2002) Full-length-enriched cdna libraries from echinococcus granulosus contain separate populations of oligo-capped and trans-spliced transcripts and a high level of predicted signal peptide sequences. Mol Biochem Parasitol 122, 171-80. (Pubitemid 34775086)
18. Luo, M., Dang, P., Guo, B. Z., He, G., Holbrook, C. C., Bausher, M. G., and Lee, R. D. (2005) Generation of Expressed Sequence Tags (ESTs) for gene discovery and marker development in cultivated peanut. Crop Sci 45, 346-53. (Pubitemid 40118408)
19. Wong, C. E., Li, Y., Whitty, B. R., Diaz-Camino, C., Akhter, S. R., Brandle, J. E., Golding, G. B., Weretilnyk, E. A., Moffatt, B. A., and Griffith, M. (2005) Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Plant Mol Biol 58, 561-74. (Pubitemid 41125985)
20. Jenny, M. J., Ringwood, A. H., Lacy, E. R., Lewitus, A. J., Kempton, J. W., Gross, P. S., Warr, G. W., and Chapman, R. W. (2002) Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica. Mar Biotechnol (NY) 4, 81-93. (Pubitemid 34253816)
21. Sturzenbaum, S., Parkinson, J., Blaxter, M., Morgan, A., Kille, P., and Georgiev, O. (2003) The earthworm EST sequencing project. Pedobiologia 47, 447-51.
22. Li, L., Brunk, B. P., Kissinger, J. C., Pape, D., Tang, K., Cole, R. H., Martin, J., Wylie, T., Dante, M., Fogarty, S. J., Howe, D. K., Liberator, P., Diaz, C., and erson, J., White, M., Jerome, M. E., Johnson, E. A., Radke, J. A., Stoeckert, C. J., Jr., Waterston, R. H., Clifton, S. W., Roos, D. S., and Sibley, L. D. (2003) Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res 13, 443-54. (Pubitemid 36395402)
23. Hughes, J., Longhorn, S. J., Papadopoulou, A., Theodorides, K., de Riva, A., Mejia-Chang, M., Foster, P. G., and Vogler, A. P. (2006) Dense taxonomic EST sampling and its applications for molecular systema-tics of the coleoptera (beetles). Mol Biol Evol 23, 268-78. (Pubitemid 43100041)
24. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R. H., McCarter, J. P., and Blaxter, M. L. (2004) A transcriptomic analysis of the phylum nematoda. Nat Genet 36, 1259-67. (Pubitemid 39577933)
25. Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M., McCarter, J. P., McRey-nolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrin-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L., and Scott, A. L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science 317, 1756-60. (Pubitemid 47461841)
26. LoVerde, P. T., Hirai, H., Merrick, J. M., Lee, N. H., and El-Sayed, N. (2004) Schis-tosoma mansoni genome project: an update. Parasitol Int 53, 183-92. (Pubitemid 38479893)
27. Philippe, H., Lartillot, N., and Brinkmann, H. (2005) Multigene analyses of bilaterian animals corroborate the monophyly of ecdysozoa, lophotrochozoa, and protosto-mia. Mol Biol Evol 22, 1246-53. (Pubitemid 40577762)
28. Peregrin-Alvarez, J. M., and Parkinson, J. (2007) The global landscape of sequence diversity. Genome Biol 8, R238.
29. Zhang, Y., Eberhard, D. A., Frantz, G. D., Dowd, P., Wu, T. D., Zhou, Y., Watanabe, C., Luoh, S. M., Polakis, P., Hillan, K. J., Wood, W. I., and Zhang, Z. (2004) GEPIS-quantitative gene expression profiling in normal and cancer tissues Bioinformatics 20, 2390-8. (Pubitemid 39429910)
30. Ferguson, D. A., Chiang, J. T., Richardson, J. A., and Graff, J. (2005) eXPRESSION: an in silico tool to predict patterns of gene expression. Gene Expr Patterns 5, 619-28. (Pubitemid 40796607)
31. Stanton, J. A., Macgregor, A. B., and Green, D. P. (2003) Identifying tissue-enriched gene expression in mouse tissues using the NIH UniGene database. Appl Bioinfor-matics 2, S65-73.
32. Ramsey, J. S., Wilson, A. C., de Vos, M., Sun, Q., Tamborindeguy, C., Winfield, A., Malloch, G., Smith, D. M., Fenton, B., Gray, S. M., and Jander, G. (2007) Geno-mic resources for Myzus persicae: EST sequencing, SNP identification, and micro-array design. BMC Genomics 8, 423.
33. Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A., and Cossins, A. R. (2004) Coping with cold: an integrative, multitissue analysis of the tran-scriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101, 16970-5. (Pubitemid 39601348)
34. Owen, J., Hedley, B., Svendsen, C., Wren, J., Jonker, M. J., Hankard, P. K., Lister, L. J., Stürzenbaum, S. R., Morgan, A. J., Spurgeon, D. J., Blaxter, M. L., and Kille, P. (2008) Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics. 9, 266.
35. Edwards, N. J. (2007) Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 3, 102.
36. Gupta, S., Zink, D., Korn, B., Vingron, M., and Haas, S. A. (2004) Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 20, 2579-85. (Pubitemid 39530144)
37. Ner-Gaon, H., Leviatan, N., Rubin, E., and Fluhr, R. (2007) Comparative cross-species alternative splicing in plants. Plant Physiol 144, 1632-41. (Pubitemid 47037463)
38. Panitz, F., Stengaard, H., Hornshoj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B., Madsen, L. B., Hoj, A., Vingborg, R. K., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jorgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B. J., Havgaard, J. H., Brunak, S., Fredholm, M., and Bendixen, C. (2007) SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinfor-matics 23, i387-91. (Pubitemid 47244424)
39. Tang, J., Vosman, B., Voorrips, R. E., van der Linden, C. G., and Leunissen, J. A. (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 7, 438.
40. Huntley, D., Baldo, A., Johri, S., and Ser-got, M. (2006) SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics 22, 495-6. (Pubitemid 43231427)