Research Article

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Mutations in the fibroblast growth factor receptor-3 (FGFR3) gene are frequently found in bladder cancer, but their prognostic value remains controversial. To globally summarize the association between FGFR3 mutations and the grade and stage of bladder cancer, and to analyze the predictive role of FGFR3 mutations with respect to survival, eligible studies were ... more

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B7 homolog 1 (B7-H1), which is also known as programmed death-L1, is an important member of the B7/CD28 costimulatory factor superfamily, which are emerging as important mediators of various host immune responses. B7-H1 is differentially expressed in various cell subsets and to different extents in human and murine cells. Human B7-H1 is constitutively expressed at low levels in dendritic ... more

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The repertoire of 4,431 open reading frames (ORFs), eight rRNA operons and 98 tRNA genes of Chromobacterium violaceum must be expressed in a regulated manner for successful adaptation to a wide variety of environmental conditions. To accomplish this feat, the organism relies on protein machineries involved in transcription, RNA processing and translation. Analysis of the C. violaceum ... more

R. Silva; J.R. Araripe; E. Rondinelli; T.P. Ürményi
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Clustering; Gene expression; Gene-gene interactions; Supervised learning

We show here an example of the application of a novel method, MUTIC (model utilization-based clustering), used for identifying complex interactions between genes or gene categories based on gene expression data. The method deals with binary categorical data which consist of a set of gene expression profiles divided into two biologically meaningful categories. It does not require data ... more

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Bioinformatics tool; Comparative genomic hybridization; DNA microarray; Gene expression; Genomic shotgun libraries; Optimal clones

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the ... more

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Serial analysis of gene expression (SAGE) technology produces large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in these gene sets. We present an interactive web-based tool, called Gene Class, which allows functional annotation of SAGE data using the Gene Ontology (GO) database. This tool ... more

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C4ST-1; Chondroitin sulfate; CHST11; cis-regulatory modules; Gene expression; TGFβ

Chondroitin-4-sulfotransferase-1(C4ST-1)/carbohydrate sul­fotransferase 11 (CHST11) is a Golgi-bound enzyme involved in the biosyn­thesis of the glycosaminoglycan chondroitin sulfate. The sulfation pattern of chondroitin is tightly regulated during development, injury and disease, with the temporal and spatial expression of chondroitin sulfotransferase genes be­lieved to be a crucial ... more

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Clustering; Gene expression; Most expressed sequences; Similarity measure

Following sequence alignment, clustering algorithms are among the most utilized techniques in gene expression data analysis. Clustering gene expression patterns allows researchers to determine which gene expression patterns are alike and most likely to participate in the same biological process being investigated. Gene expression data also allow the clustering of whole samples of data, which ... more

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The freshwater crayfish Cherax quadricarinatus, originally from Australia, is an invasive species that is also widely used in aquaculture. DEAD-box helicase family genes are found throughout evolution and encode RNA-binding proteins. The human DDX5 (p68) is important for normal cell growth, differentiation and proliferation. We identified a C. quadricarinatus homolog of ... more

D.A. Fang; Q. Wang; J. Wang; L. He; L.H. Liu; Y. Wang
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Lack of continuous progress in Theobroma cacao (Malvaceae) breeding, especially associated with seed quality traits, requires more efficient selection methods based on genomic information. Reverse transcript quantitative PCR (RT-qPCR) has become the method of choice for gene expression analysis, but relative expression analysis requires various reference genes, which must be ... more

T.T. Pinheiro; C.G. Litholdo; M.L. Sereno; G.A. Leal; P.S.B. Albuquerque; A. Figueira

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