• Molecules and Cells
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• 제42권2호
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Asian-Australasian Journal of Animal Sciences
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• 제26권1호
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• pp.19-29
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• 2013

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

• Genomics & Informatics
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• 제21권4호
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• pp.45.1-45.11
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• 2023

Nonalcoholic fatty liver disease (NAFLD) is a common type of chronic liver disease, with severity levels ranging from nonalcoholic fatty liver to nonalcoholic steatohepatitis (NASH). The extent of liver fibrosis indicates the severity of NASH and the risk of liver cancer. However, the mechanism underlying NASH development, which is important for early screening and intervention, remains unclear. Weighted gene co-expression network analysis (WGCNA) is a useful method for identifying hub genes and screening specific targets for diseases. In this study, we utilized an mRNA dataset of the liver tissues of patients with NASH and conducted WGCNA for various stages of liver fibrosis. Subsequently, we employed two additional mRNA datasets for validation purposes. Gene set enrichment analysis (GSEA) was conducted to analyze gene function enrichment. Through WGCNA and subsequent analyses, complemented by validation using two additional datasets, we identified five genes (BICC1, C7, EFEMP1, LUM, and STMN2) as hub genes. GSEA analysis indicated that gene sets associated with liver metabolism and cholesterol homeostasis were uniformly downregulated. BICC1, C7, EFEMP1, LUM, and STMN2 were identified as hub genes of NASH, and were all related to liver metabolism, NAFLD, NASH, and related diseases. These hub genes might serve as potential targets for the early screening and treatment of NASH.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.185-192
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• 2013

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

• Animal Bioscience
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• 제35권6호
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• pp.814-825
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• 2022

Objective: This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland. Methods: According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of genome wide association study (GWAS) signals, functional annotation and weighted gene co-expression network analysis (WGCNA). Results: We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from day -2 to day +1. Further, the GWAS signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted WGCNA, we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day -14, day -2, and day +1, in which, 35 lncRNAs and 319 mRNAs were involved. Conclusion: This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

• 융합보안논문지
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• 제13권3호
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• pp.39-46
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• 2013

최근 지구 온난화 문제는 전 세계적으로 중요한 이슈가 되고 있으며, 이와 같은 문제해결을 위한 방안으로 그린 IT에 대한 관심이 높아지고 있다. 이러한 가운데 IT분야는 다양한 서비스들과 해킹기술도 함께 진화하고 있어, 다양하고, 더 많은 보안시스템의 사용이 불가피하게 됨에 따라, $CO_2$배출량의 증가가 예상되고 있다. 따라서 본 논문은 보안시스템의 $CO_2$배출에 대한 실험 및 사례연구를 통해 요인들을 분석하고, 보안 시스템의 기능적 구조 개선을 통한, $CO_2$배출량의 경감 여부를 알아봄으로써, 향후, 보안 네트워크의 설계와 성능 향상, IT분야의 탄소배출량 경감을 위한 자료로 활용될 것으로 기대한다.

• 한국산업정보학회논문지
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• 제22권4호
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• pp.29-43
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• 2017

Innovation Cosystems are Conceptualized as Organizational Networks of Economic Actors, Technologies and Social Contexts that Interact for Knowledge Production, use, and Adaptation. This Paper Proposed a Conceptual Framework to Describe Value Co-creation of Organizational Networks Engaged in Technology Innovation. We Adopted Theory-Based Approach by Integrating the Perspective of Service-Dominant (S-D) Logic Into the Evolutionary Model of the Triple Helix. The Framework Gives a Plausible Explanation on how Actors Collaborate to Create Value in Dynamic Contexts of an Innovation Ecosystem. The Innovation Ecosystem can be Considered as a Composite of Sub-Ecosystems, Including Knowledge, Sectoral, and Business Ecosystems. When these Sub-Ecosystems are Recursively Transformed by Coordination of Functional Mechanisms that Serve Value Co-creation in the Innovation Process, the Innovation Ecosystem will be Re-Organized and Evolve. The case of the Digital Living Network Alliance (DLNA) was Examined to Demonstrate the Fundamental Mechanisms for Value Co-creation that was Described in the Framework. The case Study Indicates Features of Value Co-creation when Implementing Innovation in Organizational Networks.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제15권4호
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• pp.284-288
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• 2009

단백질 상호작용의 예측 및 실험 결과가 대용량으로 배포되면서 바이오 정보 기술 연구자들은 생명체 내의 단백질 상호작용 네트워크를 구성하기 위해 노력하여 왔다. 일반적으로 대용량의 상호작용 데이터들은 많은 오류를 포함한다고 알려져 있으나, 최근 단백질의 물리 화학적 특성 및 구조를 기반으로 한 방법들이 실제 실험과 병행되어 고화질(High resolution)의 결과를 제공하게 되면서, 특정 종에 대한 단백질 상호작용 네트워크가 점차 완성되고 있다. 그러나, 단순 물리적 링크 수준의 단백질 상호작용 네트워크만으로는 특정 병원체의 발병 메커니즘 규명 등과 같은 응용분야의 활용에 한계가 있다. 본 논문에서는 실험을 통하여 보고된 신호 전달 경로(signaling transduction pathway)를 이용하여 단백질 기능 간의 관계를 방향성이 있는 그래프로 표현한 단백질 기능 흐름 모델을 제시한다. 제안하는 모델은 Gene Ontology에서 정의된 molecular function을 정점(vertex)으로 가지고 이들 사이의 관계를 간선(edge)으로 표현함으로써 특정 기능의 전이를 살펴볼 수 있다. 이러한 기능 흐름 모델은 수 만개의 정점(vertex)으로 구성된 단백질 상호작용 네트워크에서 의미 있는 경로를 추출하는 데에 제약 혹은 참조 조건으로 사용될 수 있어 향후 활용도가 클 것으로 기대한다. 평가는 KEGG에서 제공되는 11개의 인간 신호 전달 경로 각각에 대하여 대상 경로를 제외한 나머지로부터 생성된 모델과의 크론바하 알파 계수(Cronbach's alpha)를 측정하였고(${\alpha}=0.67$), 총 1023개의 흐름 중 ${\alpha}=0.6$ 이상의 신뢰도에 대하여 총 765개의 흐름을 가지는 기능 흐름 모델을 최종 구성하였다.

• Macromolecular Research
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• 제11권3호
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• pp.163-171
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• 2003

For the pervaporation of water-ethanol mixtures, new composite membranes having poly(acrylic acid)-poly (butyl methacrylate-co-methyl methacrylate) interpenetrati ng polymer network [PAA-P(BMA-co-MMA) IPN] skin layer supported on porous and crosslinked poly(BMA-co-MMA) were prepared. The morphology of the sub-layer of the composite membrane prepared in the presence of 60 wt% solvent showed cellular structure, on the other hand that of sublayer prepared in the presence of 70 wt% solvent presented very porous interconnected pore structure with macrovoids. Permeation rates of the composite membranes were largely influenced by the morphology of the sublayer. Separation factors increased with the increase of the degree of crosslinking of the PAA network. It was found that permeation rates could be increased by introducing anionic charges on carboxyl groups of the PAA. The permeation rate changes of the PAA-P(BMA-co-MMA) IPN composite membranes according to the feed compositions showed quite similar pattern with the swelling behavior in water-ethanol mixtures.

• Composites Research
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• 제28권6호
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• pp.333-339
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• 2015

무전해 도금을 통해 제조한 FeCo 자성 금속 중공형 섬유와 EPDM 고분자를 이용하여 전자파 차폐 복합재를 제작하였다. 열처리 공정을 통하여 섬유의 종횡비를 제어하였으며 중공형 구조로 섬유를 제조한 후, 이를 EPDM 수지에 첨가하여 복합재를 제조하였다. 자성 금속 중공형 섬유의 종횡비가 클수록 낮은 표면 저항 특성과 우수한 전자파 차폐 성능을 나타내었다. 약 $100{\mu}m$ 길이의 자성 금속 중공형 섬유를 이용한 두께 $150{\mu}m$ 전자파 차폐 복합재의 경우 밀도 $1.18g/cm^3$, 약 30 ohm/sq의 표면 저항, 그리고 30 dB의 전자파 차폐 성능을 나타내었다. 이는 종횡비가 큰 섬유에 의한 퍼콜레이션 임계치 이상의 전도성 네트워크 형성과 더불어, 낮은 표면 저항에 기인한 임피던스 차이에 의한 반사 손실 증가, 흡수 손실, 그리고 다중 내부 반사 손실에 의하여 우수한 전자파 차폐 성능을 나타내는 것으로 판단된다.