differential gene expression

Expression of drought tolerance genes in tropical upland rice cultivars (Oryza sativa)

R. D. D. Silveira, Abreu, F. R. M., Mamidi, S., McClean, P. E., Vianello, R. P., Lanna, A. C., Carneiro, N. P., and Brondani, C., Expression of drought tolerance genes in tropical upland rice cultivars (Oryza sativa), vol. 14, pp. 8181-8200, 2015.

Gene expression related to drought response in the leaf tissues of two Brazilian upland cultivars, the drought-tolerant Douradão and the drought-sensitive Primavera, was analyzed. RNA-seq identified 27,618 transcripts in the Douradão cultivar, with 24,090 (87.2%) homologous to the rice database, and 27,221 transcripts in the Primavera cultivar, with 23,663 (86.9%) homologous to the rice database. Gene-expression analysis between control and water-deficient treatments revealed 493 and 1154 differentially expressed genes in Douradão and Primavera cultivars, respectively.

Screening and identification of peritoneal metastasis-related genes of gastric adenocarcinoma using a cDNA microarray

F. H. Bai, Wang, N. J., Wang, J., Yang, L., Zhang, F. M., Yin, F., Liang, J., Wu, K. C., and Fan, D. M., Screening and identification of peritoneal metastasis-related genes of gastric adenocarcinoma using a cDNA microarray, vol. 11, pp. 1682-1689, 2012.

With the aim of identifying peritoneal metastasis-related genes in gastric cancer, we performed a broad analysis of differential gene expression between the parental cell line GC9811 and its highly metastatic peritoneal counterpart, cell line GC9811-P. Two fluorescent cDNA probes, labeled with Cy3 and Cy5 dyes, were prepared from GC9811 and GC9811-P mRNA samples by the reverse transcription method. The two color probes were then mixed and hybridized to a cDNA chip constructed with double-dots from 11,901 human genes; this was scanned at two wavelengths.

Electrophoresis and spectrometric analyses of adaptation-related proteins in thermally stressed Chromobacterium violaceum

I. B. Cordeiro, Castro, D. P., Nogueira, P. P. O., Angelo, P. C. S., Nogueira, P. A., Gonçalves, J. F. C., Pereira, A. M. R. F., Garcia, J. S., Souza, G. H. M. F., Arruda, M. A. Z., Eberlin, M. N., Astolfi-Filho, S., Andrade, E. V., and López-Lozano, J. L., Electrophoresis and spectrometric analyses of adaptation-related proteins in thermally stressed Chromobacterium violaceum, vol. 12, pp. 5057-5071, 2013.

Chromobacterium violaceum is a Gram-negative proteobacteria found in water and soil; it is widely distributed in tropical and subtropical regions, such as the Amazon rainforest. We examined protein expression changes that occur in C. violaceum at different growth temperatures using electrophoresis and mass spectrometry. The total number of spots detected was 1985; the number ranged from 99 to 380 in each assay.

Combining P values to improve classification of differential gene expression in the HTself software

D. A. Cortez, Tonon, A. P., Colepicolo, P., and Vêncio, R. Z. N., Combining P values to improve classification of differential gene expression in the HTself software, vol. 10, pp. 3586-3595, 2011.

HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression in low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. We developed an extension of HTself, originally released in 2005, by calculating P values instead of using a fixed acceptance level α. As before, the statistic used to compute single-spot P values is obtained from the Gaussian kernel density estimator method applied to self-self data.

Identification of COL6A1 as a differentially expressed gene in human astrocytomas

A. Fujita, Sato, J. R., Festa, F., Gomes, L. R., Oba-Shinjo, S. M., Marie, S. K. N., Ferreira, C. E., and Sogayar, M. C., Identification of COL6A1 as a differentially expressed gene in human astrocytomas, vol. 7, pp. 371-378, 2008.

Diffuse infiltrating gliomas are the most common tumors of the central nervous system. Gliomas are classified by the WHO according to their histopathological and clinical characteristics into four classes: grade I (pilocytic astrocytoma), grade II (diffuse astrocytoma), grade III (anaplastic astrocytoma), and grade IV (glioblastoma multiforme). Several genes have already been correlated with astrocytomas, but many others are yet to be uncovered.

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