Research Article

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10/31/2014
Abnormal chromosome diseases; Microarray; Prenatal diagnosis

The accuracy of prenatal diagnosis for abnormal chromosome diseases by chromosome microarray technology and karyotyping were compared. A literature search was carried out in the MEDLINE database with the keywords “chromosome” and “karyotype” and “genetic testing” and “prenatal diagnosis” and “oligonucleotide array sequence”. The studies obtained were filtered by using the QUADAS tool, ... more

H.B. Xu; H. Yang; G. Liu; H. Chen
02/20/2014
Anencephaly; Bioinformatics; MAPK signaling pathway; Microarray; MicroRNA; Neural tube defect

Anencephaly is one of the most serious forms of neural tube defects (NTDs), a group of congenital central nervous system (CNS) malformations. MicroRNAs (miRNAs) are involved in diverse biological processes via the post-transcriptional regulation of target mRNAs. Although miRNAs play important roles in the development of mammalian CNS, their function in human NTDs remains unknown. Using a ... more

W.D. Zhang; X. Yu; X. Fu; S. Huang; S.J. Jin; Q. Ning; X.P. Luo
03/01/2004
Chromobacterium violaceum; Gene expression; Gene regulation; RNA processing; Transcription; Translation

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
10/04/2007
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

L.S. Coelho; M.A. Mudado; B. Goertzel; C. Pennachin
10/04/2007
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

M.E. Cantão; J.E. Ferreira; E.G.M. Lemos
03/31/2006
Functional annotation; Gene expression; Tag classification; Web-based bioinformatics tool

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

G.S.P. Pereira; R.M. Brandão; S. Giuliatti; M.A. Zago; W.A. Silva
11/03/2009
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

C.M. Willis; J.L. Wrana; M. Klüppel
09/30/2008
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

S.A.P. Pinto; J.M. Ortega
10/25/2011
Cherax quadricarinatus; DEAD-box helicase; Eyestalk ablation; Gene expression; Spermatogenesis

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
11/17/2011
Cocoa; Cocoa butter; Fatty acid biosynthesis; Gene expression; Sterculiaceae

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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