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DNA arrays have been a rich source of data for the study of genomic expression of a wide variety of biological systems. Gene clustering is one of the paradigms quite used to assess the significance of a gene (or group of genes). However, most of the gene clustering techniques are applied to cDNA array data without a corresponding statistical error measure. We propose an easy-to-implement and simple-to-use technique that uses bootstrap re-sampling to evaluate the statistical error of the nodes provided by SOM-based clustering. Comparisons between SOM and parametric clustering are presented for simulated as well as for two real data sets. We also implement a bootstrap-based pre-processing procedure for SOM, that improves the false discovery ratio of differentially expressed genes. Code in Matlab is freely available, as well as some supplementary material, at the following address: https://ipe.cbmeg.unicamp.br/pub/abreu.gcg. Code implementation in R is in progress. Udgivelsesdato: February DNA arrays have been a rich source of data for the study of genomic expression of a wide variety of biological systems. Gene clustering is one of the paradigms quite used to assess the significance of a gene (or group of genes). However, most of the gene clustering techniques are applied to cDNA array data without a corresponding statistical error measure. We propose an easy-to-implement and simple-to-use technique that uses bootstrap re-sampling to evaluate the statistical error of the nodes provided by SOM-based clustering. Comparisons between SOM and parametric clustering are presented for simulated as well as for two real data sets. We also implement a bootstrap-based pre-processing procedure for SOM, that improves the false discovery ratio of differentially expressed genes. Code in Matlab is freely available, as well as some supplementary material, at the following address: https://ipe.cbmeg.unicamp.br/pub/abreu.gcg. Code implementation in R is in progress.

Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs.

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

International audience

28 ref.; International audience