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1.
Genomics & Informatics ; : 128-135, 2017.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-192020

RESUMO

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.


Assuntos
Animais , Arabidopsis , Brassica rapa , Células Clonais , Genoma , Métodos , Sintenia
2.
Genomics & Informatics ; : 178-182, 2017.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-192013

RESUMO

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.


Assuntos
Conjunto de Dados , Genoma , Estudo de Associação Genômica Ampla , Genômica , Humanos , Desequilíbrio de Ligação , Análise de Sequência de RNA
3.
Genomics & Informatics ; : 90-95, 2016.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-117342

RESUMO

Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.


Assuntos
DNA Mitocondrial , Éxons , Genoma , Genoma Mitocondrial , Plantas
4.
Genomics & Informatics ; : 211-215, 2016.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-172198

RESUMO

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.


Assuntos
Processamento Alternativo , Arabidopsis , Conjunto de Dados , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
5.
Genomics & Informatics ; : 29-33, 2016.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-193407

RESUMO

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.


Assuntos
Biotecnologia , Quimera , DNA , DNA de Cadeia Simples , Genoma Bacteriano , Retroelementos , Transcrição Reversa , RNA , DNA Polimerase Dirigida por RNA
6.
Genomics & Informatics ; : 76-80, 2015.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-216095

RESUMO

Type 2 diabetes mellitus is a complex metabolic disorder associated with multiple genetic, developmental and environmental factors. The recent advances in gene expression microarray technologies as well as network-based analysis methodologies provide groundbreaking opportunities to study type 2 diabetes mellitus. In the present study, we used previously published gene expression microarray datasets of human skeletal muscle samples collected from 20 insulin sensitive individuals before and after insulin treatment in order to construct insulin-mediated regulatory network. Based on a motif discovery method implemented by iRegulon, a Cytoscape app, we identified 25 candidate regulons, motifs of which were enriched among the promoters of 478 up-regulated genes and 82 down-regulated genes. We then looked for a hierarchical network of the candidate regulators, in such a way that the conditional combination of their expression changes may explain those of their target genes. Using Genomica, a software tool for regulatory network construction, we obtained a hierarchical network of eight regulons that were used to map insulin downstream signaling network. Taken together, the results illustrate the benefits of combining completely different methods such as motif-based regulatory factor discovery and expression level-based construction of regulatory network of their target genes in understanding insulin induced biological processes and signaling pathways.


Assuntos
Fenômenos Biológicos , Conjunto de Dados , Diabetes Mellitus Tipo 2 , Expressão Gênica , Humanos , Insulina , Métodos , Músculo Esquelético , Regulon , Fatores de Transcrição
7.
Genomics & Informatics ; : 165-170, 2014.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-61847

RESUMO

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.


Assuntos
Índice de Massa Corporal , Conjunto de Dados , Estudo de Associação Genômica Ampla , Haplótipos , Coreia (Geográfico) , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único
8.
Genomics & Informatics ; : 171-180, 2014.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-61846

RESUMO

Aberrant DNA methylation, as an epigenetic marker of cancer, influences tumor development and progression. We downloaded publicly available DNA methylation and gene expression datasets of matched cancer and normal pairs from the Cancer Genome Atlas Data Portal and performed a systematic computational analysis. This study has three aims to screen genes that show hypermethylation and downregulated patterns in colorectal cancers, to identify differentially methylated regions in one of these genes, SFRP1, and to test whether the SFRP genes affect survival or not. Our results show that 31 hypermethylated genes had a negative correlation with gene expression. Among them, SFRP1 had a differentially methylated pattern at each methylation site. We also show that SFRP1 may be a potential biomarker for colorectal cancer survival.


Assuntos
Neoplasias Colorretais , Simulação por Computador , Conjunto de Dados , Metilação de DNA , Epigenômica , Expressão Gênica , Genoma , Metilação , Análise de Sobrevida
9.
Genomics & Informatics ; : 163-163, 2013.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-11260

RESUMO

No abstract available.

10.
Genomics & Informatics ; : 101-101, 2013.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-58528

RESUMO

No abstract available.

11.
Genomics & Informatics ; : 135-141, 2013.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-58523

RESUMO

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.


Assuntos
Estudo de Associação Genômica Ampla , Genótipo , Concentração de Íons de Hidrogênio , Coreia (Geográfico) , Epidemiologia Molecular , Neurônios , Polimorfismo de Nucleotídeo Único , Semântica
12.
Genomics & Informatics ; : 59-59, 2013.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-164845

RESUMO

No abstract available.

13.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-177972

RESUMO

No abstract available.

14.
Genomics & Informatics ; : 213-213, 2012.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-11763

RESUMO

No abstract available.

15.
Genomics & Informatics ; : 234-238, 2012.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-11759

RESUMO

Genetic epidemiology studies have established that the natural variation of gene expression profiles is heritable and has genetic bases. A number of proximal and remote DNA variations, known as expression quantitative trait loci (eQTLs), that are associated with the expression phenotypes have been identified, first in Epstein-Barr virus-transformed lymphoblastoid cell lines and later expanded to other cell and tissue types. Integration of the eQTL information and the network analysis of transcription modules may lead to a better understanding of gene expression regulation. As these network modules have relevance to biological or disease pathways, these findings may be useful in predicting disease susceptibility.


Assuntos
Linhagem Celular , Suscetibilidade a Doenças , DNA , Regulação da Expressão Gênica , Metagenômica , Epidemiologia Molecular , Fenótipo , Locos de Características Quantitativas , Transcriptoma
16.
Genomics & Informatics ; : 123-127, 2012.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-57571

RESUMO

Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.


Assuntos
Artefatos , Diabetes Mellitus Tipo 2 , Genoma , Estudo de Associação Genômica Ampla , Genótipo , Mãos , Polimorfismo de Nucleotídeo Único
17.
Genomics & Informatics ; : 9-15, 2012.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-155520

RESUMO

Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. Cryptosporidium parvum is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that C. parvum CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.


Assuntos
Apicomplexa , Bactérias , Doenças Transmissíveis , Cryptosporidium , Cryptosporidium parvum , Eucariotos , Transferência Genética Horizontal , Genoma , Humanos , Inositol , Monoéster Fosfórico Hidrolases , Proteínas , Proteobactérias
18.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-171929

RESUMO

Genome-wide association (GWA) studies are the method of choice for discovering loci associated with common diseases. More than a thousand GWA studies have reported successful identification of statistically significant association signals in human genomes for a variety of complex diseases. In this review, I discuss some of the issues related to the future of GWA studies and their biomedical applications.


Assuntos
Genoma Humano , Estudo de Associação Genômica Ampla , Humanos
19.
Genomics & Informatics ; : 138-141, 2011.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-7986

RESUMO

Here, we report a computer program written in Python, which phases SNP genotypes and infers inherited deletions based on the pattern of Mendelian inheritance within a trio pedigree. When tiered trio genotypes that encompass three generations are available, it narrows a recombination event down to a region between two consecutive heterozygous markers. In addition, the phase information that is inferred from the upper trio that is formed by one of the parents and grandparents can be propagated to phase the genotypes of the lower trio that is formed by the parents and an offspring.


Assuntos
Boidae , Características da Família , Genótipo , Humanos , Pais , Linhagem , Recombinação Genética , Software , Testamentos
20.
Genomics & Informatics ; : 181-188, 2011.
Artigo em Inglês | WPRIM (Pacífico Ocidental) | ID: wprim-73131

RESUMO

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.


Assuntos
Grupo com Ancestrais do Continente Asiático , Consenso , Grupos Étnicos , Genótipo , Humanos , Filogenia , Polimorfismo de Nucleotídeo Único
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