XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Sczyrba, Alexander ^a   Beckstette, Michael ^a   Brivanlou, Ali H ^b   Giegerich, Robert ^a   Altmann, Curtis R ^c  

^a BIELEFELD UNIVERSITY   (Germany)

^b ROCKEFELLER UNIVERSITY   (United States)

^c FLORIDA STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; XENOPUS PROTEIN;

BIOINFORMATICS; COMPUTER MODEL; COMPUTER PROGRAM; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENETIC DATABASE; INFORMATION PROCESSING; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN DATABASE; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; XENDB; XENOPUS LAEVIS;

VERTEBRATA; XENOPUS LAEVIS;

EID: 25444444800     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-123     Document Type: Review

References (104)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H et al.: Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991, 252: 1651-1656.
2. Zhang MQ: Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 2002, 3: 698-709.
3. Henderson J, Salzberg S, Fasman KH: Finding genes in DNA with a Hidden Markov Model. J Comput Biol 1997, 4: 127-141.
4. Besemer J, Borodovsky M: Heuristic approach to deriving models for gene finding. Nucleic Acids Res 1999, 27: 3911-3920.
5. Pontius JU, Wagner L, Schuler GD: UniGene: a unified view of the transcriptome. In The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information; 2003:21-1-21-12.
6. Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W: STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res 2001, 29: 234-238.
7. Mironov AA, Fickett JW, Gelfand MS: Frequent alternative splicing of human genes. Genome Res 1999, 9: 1288-1293.
8. Ladd AN, Cooper TA: Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol 2002, 3: reviews0008.
9. Lipscombe D, Pan JQ, Gray AC: Functional diversity in neuronal voltage-gated calcium channels by alternative splicing of Ca(v)alpha1. Mol Neurobiol 2002, 26: 21-44.
10. Stamm S: Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome. Hum Mol Genet 2002, 11: 2409-2416.
11. Venables JP: Alternative splicing in the testes. Curr Opin Genet Dev 2002, 12: 615-619.
12. Roberts GC, Smith CW: Alternative splicing: combinatorial output from the genome. Curr Opin Chem Biol 2002, 6: 375-383.
13. Oklu R, Hesketh R: The latent transforming growth factor beta binding protein (LTBP) family. Biochem J 2000, 352 Pt 3: 601-610.
14. Tarone G, Hirsch E, Brancaccio M, De Acetis M, Barberis L, Balzac F et al.: Integrin function and regulation in development. Int J Dev Biol 2000, 44: 725-731.
15. Klint P, Claesson-Welsh L: Signal transduction by fibroblast growth factor receptors. Front Biosci 1999, 4: D165-D177.
16. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T et al.: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14: 1147-1159.
17. Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H et al.: Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 2003, 270: 24-33.
18. Useche FJ, Gao G, Harafey M, Rafalski A: High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Inform Ser Workshop Genome Inform 2001, 12:194-203.: 194-203.
19. Nekrutenko A: Reconciling the numbers: ESTs versus protein-coding genes. Mol Biol Evol 2004, 21: 1278-1282.
20. Wang JP, Lindsay BG, Leebens-Mack J, Cui L, Wall K, Miller WC et al.: EST clustering error evaluation and correction. Bioinformatics 2004.
21. Genome-Consortium: Finishing the euchromatic sequence of the human genome. Nature 2004, 431: 931-945.
22. Ewing B, Green P: Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet 2000, 25: 232-234.
23. Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL et al.: Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res 2004, 32 Database issue:D35-40.: D35-D40.
24. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU et al.: Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31: 28-33.
25. Schuler GD: Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J Mol Med 1997, 75: 694-698.
26. Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K et al.: A gene map of the human genome. Science 1996, 274: 540-546.
27. Boguski MS, Schuler GD: ESTablishing a human transcript map. Nat Genet 1995, 10: 369-371.
28. Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9: 868-877.
29. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8: 186-194.
30. Phrap sequence assember website. 2005. http://www.phrap.org/], Laboratory of Phil Green, HHMI Genome Sciences Department, University of Washington.
31. Burke J, Davison D, Hide W: d2_cluster: a validated method for clustering EST and full-length cDNAsequences. Genome Res 1999, 9: 1135-1142.
32. Abouelhoda MI, Ohlebusch E, Kurtz S: Optimal exact string matching based on suffix arrays. In Proceeding of the Ninth International Symposium on String Processing and Information Retieval. Springer Verlag; 2002:31-43.
33. Abouelhoda MI, Kurtz S, Ohlebusch E: The Enhanced Suffix Array and its Applications to Genome Analysis. In Proceedings of the Second Workshop on Algorithms in Bioinformatics. Springer Verlag; 2002:449-463.
34. Abouelhoda MI, Kurtz S, Ohlebusch E: Replacing Suffix Trees with Enhanced Suffix Arrays. Journal of Discrete Algorithms 2004, 2: 53-86.
35. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J: An optimized protocol for analysis of EST sequences. Nucleic Acids Res 2000, 28: 3657-3665.
36. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2005, 33: D39-D45.
37. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S et al.: The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 2001, 29: 159-164.
38. Vector Database Website. 2005. http://genome-www2.stanford.edu/vectordb/].
39. The Vmatch large scale sequence analysis software website. 2005. http://www.vmatch.de/].
40. Jurka J: Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 2000, 16: 418-420.
41. Smit A, Green P. Repeat Masker Website and Server. 2005. http://www.repeatmasker.org/].
42. Beckstette M, Strothmann D, Homann R, Giegerich R, Kurtz S: PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices Using Enhanced Suffix Arrays. In: Proceedings of the German Conference on Bioinformatics (GCB 2004); 2004; 53-64.
43. Kruger J, Sczyrba A, Kurtz S, Giegerich R: e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. Nucleic Acids Res 2004, 32: W301-W304.
44. Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7: 203-214.
45. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389-3402.
46. Pearson WR, Wood T, Zhang Z, Miller W: Comparison of DNA sequences with protein sequences. Genomics 1997, 46: 24-36.
47. Beckstette M, Mailänder J, Marhöfer RJ, Sczyrba A, Ohlebusch E, Giegerich R et al.: Genlight: Interactive high-throughput sequence analysis and comparative genomics. Journal of Integrative Bioinformatics 2004, 8: 79-94.
48. European Bioinformatics Institute International Protein Index Website. 2005. http://www.ebi.ac.uk/IPI.
49. Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R: The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4: 1985-1988.
50. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S et al.: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 2004, 32 Database issue:D115-9.: D115-D119.
51. Aaronson JS, Eckman B, Blevins RA, Borkowski JA, Myerson J, Imran S et al.: Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res 1996, 6: 829-845.
52. Hillier LD, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S et al.: Generation and analysis of 280,000 human expressed sequence tags. Genome Res 1996, 6: 807-828.
53. Komar AA, Hatzoglou M: Internal ribosome entry sites in cellular mRNAs: The mystery of their existence. J Biol Chem 2005.
54. The Mammalian Gene Collection. 2005. http://mgc.nci.nih.gov/.
55. The Xenopus Gene Collection. 2005. http://xgc.nci.nih.gov/.
56. The Zebrafish Gene Collection. 2005. http://zgc.nci.nih.gov/.
57. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25-29.
58. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS et al.: A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004, 5: R7.
59. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340: 783-795.
60. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, %19;305: 567-580.
61. Sonnhammer EL, von Heijne G, Krogh A: A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 1998, 6: 175-182.
62. Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ et al.: SAGEmap: a public gene expression resource. Genome Res 2000, 10: 1051-1060.
63. Strausberg RL, Buetow KH, Greenhut SF, Grouse LH, Schaefer CF: The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer. Cancer Invest 2002, 20: 1038-1050.
64. Gehring WJ, Affolter M, Burglin T: Homeodomain proteins. Annu Rev Biochem 1994, 63: 487-526.
65. Cox WG, Hemmati-Brivanlou A: Caudalization of neural fate by tissue recombination and bFGF. dev 1995, 121: 4349-4358.
66. Wright CV, Morita EA, Wilkin DJ, De Robertis EM: The Xenopus XIHbox 6 homeo protein, a marker of posterior neural induction, is expressed in proliferating neurons. dev 1990, 109: 225-234.
67. Isaacs HV, Pownall ME, Slack JM: Regulation of Hox gene expression and posterior development by the Xenopus caudal homologue Xcad3. EMBO J 1998, 17: 3413-3427.
68. JGI Xenopus tropicalis Web Site. 2005. http://genome.jgi-psf.org/Xentr3/Xentr3.home.html.
69. Cancer Genome Anatomy Project. 2005. http://cgap.nci.nih.gov/].
70. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270: 484-487.
71. Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K et al.: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A 2002, 99: 11287-11292.
72. Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE et al.: A public database for gene expression in human cancers. Cancer Res 1999, 59: 5403-5407.
73. Kuhlbrodt K, Herbarth B, Sock E, Hermans-Borgmeyer I, Wegner M: Sox10, a novel transcriptional modulator in glial cells. J Neurosci 1998, 18: 237-250.
74. Yoshida M: Intermediate filament proteins define different glial subpopulations. J Neurosci Res 2001, 63: 284-289.
75. Yoshida M, Colman DR: Glial-defined rhombomere boundaries in developing Xenopus hindbrain. J Comp Neurol 2000, 424: 47-57.
76. Gaiano N, Fishell G: The role of notch in promoting glial and neural stem cell fates. Annu Rev Neurosci 2002, 25. Epub002 Mar 25.: 471-490.
77. Konig R, Baldessari D, Pollet N, Niehrs C, Eils R: Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res 2004, 32: e29.
78. Crump D, Werry K, Veldhoen N, Van Aggelen G, Helbing CC: Exposure to the herbicide acetochlor alters thyroid hormone-dependent gene expression and metamorphosis in Xenopus Laevis. Environ Health Perspect 2002, 110: 1199-1205.
79. Munoz-Sanjuan I, Bell E, Altmann CR, Vonica A, Brivanlou AH: Gene profiling during neural induction in Xenopus laevis: regulation of BMP signaling by post-transcriptional mechanisms and TAB3, a novel TAK1-binding protein. dev 2002, 129: 5529-5540.
80. Tran PH, Peiffer DA, Shin Y, Meek LM, Brody JP, Cho KW: Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res 2002, 30: e54.
81. Altmann CR, Bell E, Sczyrba A, Pun J, Bekiranov S, Gaasterland T et al.: Microarray-based analysis of early development in Xenopus laevis. Dev Biol 2001, 236: 64-75.
82. Arima K, Shiotsugu J, Niu R, Khandpur R, Martinez M, Shin Y et al.: Global analysis of RAR-responsive genes in the Xenopus neurula using cDNA microarrays. Dev Dyn 2005, 232: 414-431.
83. Peiffer DA, von Bubnoff A, Shin Y, Kitayama A, Mochii M, Ueno N et al.: A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development. Dev Dyn 2005, 232: 445-456.
84. Shin Y, Kitayama A, Koide T, Peiffer DA, Mochii M, Liao A et al.: Identification of neural genes using Xenopus DNA microarrays. Dev Dyn 2005, 232: 432-444.
85. Chung HA, Hyodo-Miura J, Kitayama A, Terasaka C, Nagamune T, Ueno N: Screening of FGF target genes in Xenopus by microarray: temporal dissection of the signalling pathway using a chemical inhibitor. Genes Cells 2004, 9: 749-761.
86. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30: 207-210.
87. Michaut L, Flister S, Neeb M, White KP, Certa U, Gehring WJ: Analysis of the eye developmental pathway in Drosophila using DNA microarrays. Proc Natl Acad Sci U S A 2003, 100: 4024-4029.
88. Glaser T, Walton DS, Maas RL: Genomic structure, evolutionary conservation and aniridia mutations in the human PAX6 gene. Nat Genet 1992, 2: 232-239.
89. Gehring WJ, Ikeo K: Pax 6: mastering eye morphogenesis and eye evolution. Trends Genet 1999, 15: 371-377.
90. Gehring WJ: The genetic control of eye development and its implications for the evolution of the various eye-types. Int J Dev Biol 2002, 46: 65-73.
91. Halder G, Callaerts P, Gehring WJ: Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila [see comments]. Science 1995, 267: 1788-1792.
92. Chow RL, Altmann CR, Lang RA, Hemmati-Brivanlou A: Pax6 induces ectopic eyes in a vertebrate. dev 1999, 126: 4213-4222.
93. The NCBI Gene Expression Omnibus. 2005. www.ncbi.nlm.nih.gov/geo/.
94. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D et al.: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004, 101: 6062-6067.
95. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P et al.: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420: 520-562.
96. Finishing the euchromatic sequence of the human genome. Nature 2004, 431: 931-945.
97. Morey C, Avner P: Employment opportunities for non-coding RNAs. FEBS Lett 2004, 567: 27-34.
98. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116: 281-297.
99. Gupta S, Zink D, Korn B, Vingron M, Haas SA: Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 2004, 20: 2579-2585.
100. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A et al.: Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 2003, 21: 379-386.
101. Mattick JS: Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 2: 986-991.
102. Sammut B, Marcuz A, Pasquier LD: The fate of duplicated major histocompatibility complex class Ia genes in a dodecaploid amphibian, Xenopus ruwenzoriensis. Eur J Immunol 2002, 32: 1593-1604.
103. Trans-NIH Xenopus Initiative Website. 2005. http://www.nih.gov/science/models/Xenopus/].
104. Xenbase Xenopus Web Resource Website. 2005. http://xenbase.org.