• Genomics & Informatics
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• v.5 no.3
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• pp.129-132
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• 2007

arraylmpute is a software for exploratory analysis of missing data and imputation of missing values in microarray data. It also provides a comparative analysis of the imputed values obtained from various imputation methods. Thus, it allows the users to choose an appropriate imputation method for microarray data. It is built on R and provides a user-friendly graphical interface. Therefore, the users can easily use arraylmpute to explore, estimate missing data, and compare imputation methods for further analysis.

• Journal of Interdisciplinary Genomics
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• v.5 no.2
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• pp.24-28
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• 2023

Chromosomal microarray (CMA) is primarily recommended for detecting clinically significant copy number variants (CNVs) in the genetic diagnosis of developmental delay, intellectual disability, autism, and congenital malformations. Prenatal CMA is recommended when a fetus has major congenital malformations. The main principles of CMA can be divided into array comparative genomic hybridization and single-nucleotide polymorphism arrays. In the current CMA platforms, these two principles are combined, and detection of genetic abnormalities including CNVs and absence of heterozygosity is facilitated. In this review, I described practical assessment of CMA testing regarding to laboratory management of CMA, interpretation of CNVs, and special considerations for comprehensive genetic counseling.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1649-1659
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• 2012

Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.

• Journal of Ginseng Research
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• v.41 no.4
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• pp.469-476
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• 2017

Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

• Biomolecules & Therapeutics
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• v.25 no.1
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• pp.57-68
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• 2017

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.197-200
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• 2003

Scalable Vector Graphics (SVG) has enabled a visually appealing, browser-based application for the display of Brassica sequences relative to Arabidopsis thaliana, and there are currently more than 70,000 B. napus Expressed Sequence Tags (ESTs) displayed. The client side of this browser is based on a Custom Graphical User Interface (CGUI) library which uses SVG, a new web graphics standard, to provide windowing functionality inside the web browser. This windowing functionality, combined with asynchronous data retrieval and client side rendering overcomes two of the key technology imposed drawbacks of current web based browsers: Fixed displays and frequent page reloads. The end result is an intuitive and enjoyable browsing experience. The browser is accessible online from the Brassica / Arabidopsis Genomics Initiative (http://brassica.agr.gc.ca). Inquiries about the browser should be directed to LewisCT@agr.gc.ca.

• Genomics & Informatics
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• v.15 no.1
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• pp.38-47
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• 2017

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

• Journal of Genetic Medicine
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• v.12 no.1
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• pp.6-11
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• 2015

Intellectual disability (ID) is the most common disability among people under the age of 20 years. In the absence of obvious non-genetic causes of ID, the majority of cases of severe ID are thought to have a genetic cause. The advent of technologies such as array comparative genomic hybridization, single nucleotide polymorphism genotyping arrays, and massively parallel sequencing has shown that de novo copy number variations and single nucleotide variations affecting coding regions are major causes of severe ID. This article reviews the genetic causes of ID along with diagnostic approaches for this disability.

• BMB Reports
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• v.37 no.1
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• pp.107-113
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• 2004

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.

• Current Research on Agriculture and Life Sciences
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• v.32 no.1
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• pp.43-52
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• 2014

Reactive oxygen and nitrogen species (ROS and RNS, respectively) are messengers that carry signals to alter the redox state in order to activate plant responses and other physiological processes, such as differentiation, aging, senescence, and pathogen defense. Quite a large number of genes are involved in this signaling and lead to oxidative stress in plants. Although the role of ROS/RNS during stress conditions is well documented, a comprehensive list of genes and comparative study of these genes has not yet been completed. Accordingly, the in silico identification of oxidative stress-related genes was performed for soybeans and Arabidopsis. These genes were also studied in relation to multiple domain prediction. The presence of domains like dehydogenase and ATPase suggests that these genes are involved in various metabolic processes, as well as the transportation of ions under optimal environmental conditions. In addition to a sequence analysis, a phylogenetic analysis was also performed to identify orthologous pairs among the soybean and Arabidopsis oxidative stress-related genes based on neighbor joining. This study was also conducted with the objective of further understanding the complex molecular signaling mechanism in plants under various stress conditions.