1. A transcript finishing initiative for closing gaps in the human transcriptome
- Author
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Sogayar, M. C., Camargo, A. A., Bettoni, F., Carraro, D. M., Pires, L. C., Parmigiani, M. B., Ferreira, E. N., Moreira, E. S., Latorre, MRDO, Simpson, AJG, Cruz, L. O., Degaki, T. L., Festa, F., Massirer, K. B., Camargo, F., Camargo, L. P., Cunha, MAV, De Souza, S. J., Faria, M., Giuliatti, S., Kopp, Oliviera, PSL, Paiva, P. B., Pereira, A. A., Pinheiro, D. G., Puga, R. D., Souza, JES, Albuquerque, D. M., Andrade, LEC, Baia, G. S., Briones, MRS, Cavaleiro-Luna, AMS, Cerutti, J. M., Costa, F. F., Constanzi-Strauss, E., Espreafico, E. M., Ferrasi, A. C., Ferro, E. S., Fortes, MAHZ, Furchi, JRF, Gianella-Neto, D., Goldman, G. H., Goldman, MHS, Gruber, A., Guimaraes, G. S., Hackel, C., Henrique-Silva, F., Kimura, E. T., Leoni, S. G., Macedo, C., Malnic, B., Manzini, C. V., Marie, SKN, Martinez-Rossi, N. M., Menossi, M., Miracca, E. C., Nagai, M. A., Nobrega, F. G., Nobrega, M. P., Oba-Shinjo, S. M., Oliviera, M. K., Orabona, G. M., Otsuke, A. Y., Paco-Larson, M. L., Paixao, BMC, Pandolfi, JRC, Pardini, MIMC, Passos-Bueno, M. R., Passos, GAS, Pesquero, J. B., Pessoa, J. G., Rahal, Paula [UNESP], Rainho, C. A., Reis, C. P., Ricca, T. I., Rodriguez, V, Rogatto, Silvia Regina [UNESP], Romano, C. M., Romeiro, J. G., Rossi, A., Sa, R. G., Sales, M. M., SantAnna, S. C., Santarosa, P. L., Segato, F., Silva, W. A., Silva, IDCG, Silva, N. P., Soares-Costa, A., Sonati, M. F., Strauss, B. E., Tajara, E. H., Valentini, Sandro Roberto [UNESP], Villanova, F. E., Ward, L. S., Zanette, D. L., Universidade de São Paulo (USP), Ludwig Inst Canc Res, Univ Ribeirao Preto, Inst Ludwig, Universidade Federal de São Paulo (UNIFESP), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista (Unesp), Universidade Federal de São Carlos (UFSCar), and Univ Vale Paraiba
- Subjects
Transcription, Genetic ,Software Validation ,Molecular Sequence Data ,Biology ,Cell Line ,Open Reading Frames ,Exon ,Software Design ,Cell Line, Tumor ,Complementary DNA ,Consensus Sequence ,Databases, Genetic ,Methods ,Genetics ,Consensus sequence ,Humans ,Gene ,Genetics (clinical) ,Expressed Sequence Tags ,Expressed sequence tag ,Genome, Human ,Alternative splicing ,Computational Biology ,DNA, Neoplasm ,U937 Cells ,HISTOLOGIA ,Alternative Splicing ,Open reading frame ,Genes ,Human genome ,Software ,HeLa Cells - Abstract
Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2014-02-26T17:19:33Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-02-26T17:19:33Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T13:50:12Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-05-20T13:50:12Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST Clusters, mapped against the genomic sequence. Each pair of EST Clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted Set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms. Univ São Paulo, Inst Quim, BR-05513970 São Paulo, Brazil Ludwig Inst Canc Res, BR-01509010 São Paulo, Brazil Univ São Paulo, Dept Epidemiol, Sch Publ Hlth, BR-01246904 São Paulo, SP, Brazil Univ Ribeirao Preto, Dept Quim Informat Bioinformat, BR-14096380 Ribeirao Preto, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Centro Terapia Celular, Hemocentro, BR-14051140 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Clin Med, BR-14051140 Ribeirao Preto, SP, Brazil Inst Ludwig, Lab Biol Computacional, BR-01509010 São Paulo, SP, Brazil Univ São Paulo, Lab Genet Cardiol Mol, Inst Coracao, BR-05403000 São Paulo, SP, Brazil Univ Fed São Paulo, Bioinform Lab, Hlth Informatics Dept, BR-04039032 São Paulo, Brazil Univ Estad Campinas, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Fed São Paulo, Rheumatol Div, BR-04113001 São Paulo, Brazil Univ São Paulo, Dept Histol Embriol, Inst Ciências Biomed, BR-05508900 São Paulo, Brazil Univ Fed São Paulo, Dept Microbiol Immunol Parasitol, BR-04023062 São Paulo, Brazil Univ São Paulo, Lab Cellular Mol Endocrinol, Sch Med, BR-01246903 São Paulo, Brazil Univ Fed São Paulo, Dept Med, Disciplina Endocrinol, Lab Endocrinol Mol, BR-04039002 São Paulo, Brazil Univ São Paulo, Inst Ciências Biomed, Lab Transferencia Genica, BR-05508900 São Paulo, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Biol Celular Mol Bioagentes Patogenicas, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil Univ Fed Sao Carlos, Dept Genet Evol, BR-13565905 Sao Carlos, SP, Brazil Univ São Paulo, Fac Ciências Farmaceuticas Ribeirao Preto, BR-14040903 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Filosofia Ciências Letras Ribeirao Preto, Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Patol, Fac Med Vet Zootecnia, BR-05508000 São Paulo, Brazil Univ Estadual Campinas, Dept Genet Med, Fac Ciências Med, BR-13081970 Campinas, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Genet, BR-14040900 Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Bioquim, Inst Quim, BR-05599970 São Paulo, Brazil Univ São Paulo, Dept Neurol, Fac Med, BR-01246903 São Paulo, Brazil Univ Estadual Campinas, Lab Genoma Funcional, Centro Biol Mol Engenharia Genet, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Genet Evol, Inst Biol, Campinas, SP, Brazil Univ São Paulo, Dept Radiol, Disciplina Oncol, Fac Med, BR-01246903 São Paulo, Brazil Univ Vale Paraiba, Inst Pesquisa Desenvolvimento, BR-12244000 Sao Jose Dos Campos, SP, Brazil Univ São Paulo, Inst Biociencias, Centro Estudios Genoma Humano, Dept Biol, BR-055508900 São Paulo, Brazil Univ Fed São Paulo, Lab Mol Gynecol, Dept Gynecol, BR-04039001 São Paulo, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ São Paulo, Discipl Genet, Fac Odontol, BR-14040900 Ribeirao Preto, SP, Brazil Univ Fed São Paulo, Dept Biofisica, BR-04023062 São Paulo, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil Univ São Paulo, Dept Bioquim Imunol, Fac Med Ribeirao Preto, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Campinas, Lab Genet Mol Cancer, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Patol Clin, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ São Paulo, Setor Vetores Virals, Lab Cardiol Mol, Inst Coracao, BR-15403000 São Paulo, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil
- Published
- 2004