• Genomics & Informatics
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• 제20권4호
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• pp.49.1-49.7
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• 2022

Many packages for a meta-analysis of genome-wide association studies (GWAS) have been developed to discover genetic variants. Although variations across studies must be considered, there are not many currently-accessible packages that estimate between-study heterogeneity. Thus, we propose a python based application called Beta-Meta which can easily process a meta-analysis by automatically selecting between a fixed effects and a random effects model based on heterogeneity. Beta-Meta implements flexible input data manipulation to allow multiple meta-analyses of different genotype-phenotype associations in a single process. It provides a step-by-step meta-analysis of GWAS for each association in the following order: heterogeneity test, two different calculations of an effect size and a p-value based on heterogeneity, and the Benjamini-Hochberg p-value adjustment. These methods enable users to validate the results of individual studies with greater statistical power and better estimation precision. We elaborate on these and illustrate them with examples from several studies of infertility-related disorders.

• Asian-Australasian Journal of Animal Sciences
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• 제33권9호
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• pp.1400-1410
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• 2020

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB). Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multi-trait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874). Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits. Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

• Molecules and Cells
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• 제24권2호
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• pp.200-209
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• 2007

We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

• Genomics & Informatics
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• 제14권4호
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• pp.173-180
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• 2016

The meta-analysis has become a widely used tool for many applications in bioinformatics, including genome-wide association studies. A commonly used approach for meta-analysis is the fixed effects model approach, for which there are two popular methods: the inverse variance-weighted average method and weighted sum of z-scores method. Although previous studies have shown that the two methods perform similarly, their characteristics and their relationship have not been thoroughly investigated. In this paper, we investigate the optimal characteristics of the two methods and show the connection between the two methods. We demonstrate that the each method is optimized for a unique goal, which gives us insight into the optimal weights for the weighted sum of z-scores method. We examine the connection between the two methods both analytically and empirically and show that their resulting statistics become equivalent under certain assumptions. Finally, we apply both methods to the Wellcome Trust Case Control Consortium data and demonstrate that the two methods can give distinct results in certain study designs.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.245-250
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• 2003

There are currently about 6000 bacterial species with validly published names, but scientists assume that these may be less than 1% of bacterial species present on the earth. Microbial resource is one of the most important bioresources in bioinderstry and provides us with high economic values. To find missing ones, the studies of metagenome, metabolome, and proteome about microbes have started recently in developed countries. We construct the information system that integrates information on microbial genome resources and manages the information to support efficient research of microbial genome application, and name this system 'Bio-Meta Information System (Bio-MIS)'. Bio-MIS consists of integrated microbial genome resources database, microbial genome resources input system, integrated microbial genome resources search engine, microbial resources on-line distribution system, portal service and management via internet. In the future, we will include public database connection and implement useful bioinformatics software for analyzing microbial genome resources. The web-site is accessible at http://biomis.probionic.com

• Genomics & Informatics
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• 제12권4호
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• pp.236-239
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• 2014

The genetic regulation of glucose and insulin levels might be modified by adiposity. With regard to the genetic factors that are altered by adiposity, a large meta-analysis on the interactions between genetic variants and body mass index with regard to fasting glucose and insulin levels was reported by the Meta-Analyses of Glucose- and Insulin-related trait Consortium (MAGIC), based on European ancestry. Because no replication study has been performed in other ethnic groups, we first examined the link between reported single-nucleotide polymorphisms (SNPs) and fasting glucose and insulin levels in a large Korean cohort (Korean Genome and Epidemiology Study cohort [KoGES], n = 5,814). The MAGIC study reported 7 novel SNPs for fasting glucose levels and 6 novel SNPs for fasting insulin levels. In this study, we attempted to replicate the association of 5 SNPs with fasting glucose levels and 5 SNPs with fasting insulin levels. One SNP (rs2293941) in PDX1 was identified as a significant obesity-modifiable factor in Koreans. Our results indicate that the novel loci that were identified by MAGIC are poorly replicated in other ethnic groups, although we do not know why.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제5권3호
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• pp.86-93
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• 2024

Unintentional dispersal of organisms has explosively increased due to expansion of human activities. Among introduced organisms, some organisms are categorized as invasive species because of their effects on environmental risk, economic loss, and human health. In 2023, a leopard slug (Limax maximus) was reported in Suwon, Republic of Korea. This slug was designated as a potential invasive species because a wide range of plant species were identified as food sources for this slug in its original habitats. However, it is difficult to investigate the ecological risk of this newly introduced slug in Republic of Korea. Therefore, the potential ecological risk from this newly introduced slug was estimated by meta-genome analyses of its feces. Through meta-genome analyses, 22 Families, 28 Genera, and 26 Species of land plants were identified. Among these 26 identified plant species, six economically important crops - squash (Cucurbita maxima), tomato (Solanum lycopersicum), potato (Solanum tuberosum), cowpea (Vigna unguiculata), rice (Oryza sativa), and oriental melon (Cucumis melo) - were identified. Therefore, leopard slugs potentially could cause economic losses in Republic of Korea. Further study is required to build a control strategy against leopard slugs.

• 융합정보논문지
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• 제10권3호
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• pp.76-91
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• 2020

최근에 한국 고유종인 미선나무 (Abeliophyllum distichum Nakai; Oleaceae) 품종 옥황1호의 유전체가 성공적으로 해독되었다. Acteoside는 다양한 활성을 가지는 물질이며, 여러개의 생화학합성과정이 제시되어왔고, 이들을 통합 검토하여 정확한 생화학합성과정을 완성하였다. 유전체 데이터로부터 2차대사산물을 예측할 수 있는 MetaPre-AI^TM와 정확한 acteoside 생화학합성과정, InfoBoss Pathway Database를 활용하여, acteoside에 관여하는 모든 효소의 유전자를 옥황1호 유전체로부터 성공적으로 확인하였다. 이는 옥황1호는 acteoside 물질을 생산할 수 있는 가능성이 있음을 의미한다. 이에 고성능액체크로마토그래피를 사용하여 옥황1호의 캘러스 세포를 분석하여 acteoside과 이의 유도체인 isoacteoside를 확인하였다. 본 연구는 MetaPre-AI^TM은 유전체로부터 2차대사산물을 성공적으로 예측하였다. 이 방법은 화학물질보다 안정적인 DNA를 분석하여 2차 대사산물을 예측하는 효율적인 방법이 될 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권1호
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• pp.1-7
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• 2017

Objective: Three genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number. Methods: We performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc${\times}$Erhualian $F_2$ resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383). Results: We detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome-wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the $F_2$ resource population, corresponding to four loci for pig teat number. We highlighted vertnin (VRTN) and lysine demethylase 6B (KDM6B) as two interesting candidate genes at the loci on SSC7 and SSC12. No significant associated SNPs were identified in the meta-analysis of GWAS. Conclusion: The results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three populations