• 전자공학회논문지CI
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• 제45권4호
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• pp.19-26
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• 2008

Gene set enrichment analysis (GSEA)는 두 개의 클래스를 가지는 마이크로어레이 실험 데이터 분석을 위해 생물학적 특징을 기반으로 구성된 다양한 유전자-집합 중에서 두 클래스의 발현값들이 통계적으로 중요한 차이를 나타내는 유의한 유전자-집합을 추출하기 위한 분석 방법이다. 특히, 유전자에 대한 다양한 생물학적인 정보를 지닌 유전자 주석 데이터베이스(Cytogenetic Band, KEGG pathway, Gene Ontology 등)를 이용하여 마이크로어레이 실험에 사용된 전체 유전자 중 특정 기능을 가지는 유전자들을 그룹화하여 다양한 유전자-집합을 발굴하고, 각 유전자-집합 내에서 두 클래스간에 발현값의 차이를 참조하여 유의한 유전자들을 결정하여, 이를 기반으로 통계적으로 유의한 유전자-집합들을 최종 검출하는 방법이다. 본 논문에서는 GSEA 분석 과정에서 현재 주로 사용되고 있는 signal-to-noise ratio 기반 유전자 서열화(gene ranking) 방법 대신에, Fisher criterion을 이용한 유전자 서열화 방법을 적용함으로써 기존의 GSEA 방법에서 추출하지 못한 생물학적으로 의미 있는 새로운 유의 유전자-집합을 추출하는 방법을 제안하고자 한다. 또한, 제안한 방법의 성능을 고찰하기 위하여 공개된 Leukemia 관련 마이크로어레이 실험 데이터 분석에 적용하였으며, 기존의 알려진 결과와 비교 분석함으로써 제안한 방법의 유용성을 검증하고자 하였다.

• 정보처리학회논문지B
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• 제15B권4호
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• pp.365-374
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• 2008

본 논문에서는 패턴의 다변화를 통하여 관계를 점진적으로 추출함으로써 온톨로지를 확장하는 모델을 제안한다. 패턴 다변화 과정에서 위키피디아로부터 추출한 관계 패턴 후보를 자질별로 다변화시킨다. 다변화된 패턴 후보로부터 말뭉치 빈도수에 따른 신뢰도를 이용하여 패턴을 선별한다. 선별된 패턴은 위키피디아로부터 관계를 추출하는 데 사용되며, 추출된 관계는 다시 관계 패턴 확장에 사용된다. 본 논문에서는 점진적 학습 과정에서의 패턴 다변화를 통하여 패턴 선택의 범위를 확장함으로써, 선택되는 패턴이 점진적으로 정제되는 모델을 제시한다. 이를 통하여, 관계의 확장성과 정확도를 향상시키고자 하였다. 단일 자질 패턴 모델에 대한 실험을 통하여, 어휘, 중심어, 상위어 정보는 신뢰도에, 품사, 구문 정보는 확장성에 유리하며, 구문 단위 유형별로 필요한 자질 유형이 다름을 관찰하였다. 이와 같은 특성에 기반하여 현재 연구 진행 중인복합 자질 패턴 모델을 제안한다.

• Biomolecules & Therapeutics
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• 제30권1호
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• pp.98-116
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• 2022

The small GTPase RhoA has been studied extensively for its role in actin dynamics. In this study, multiple bioinformatics tools were applied cooperatively to the microarray dataset GSE64714 to explore previously unidentified functions of RhoA. Comparative gene expression analysis revealed 545 differentially expressed genes in RhoA-null cells versus controls. Gene set enrichment analysis (GSEA) was conducted with three gene set collections: (1) the hallmark, (2) the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and (3) the Gene Ontology Biological Process. GSEA results showed that RhoA is related strongly to diverse pathways: cell cycle/growth, DNA repair, metabolism, keratinization, response to fungus, and vesicular transport. These functions were verified by heatmap analysis, KEGG pathway diagramming, and direct acyclic graphing. The use of multiple gene set collections restricted the leakage of information extracted. However, gene sets from individual collections are heterogenous in gene element composition, number, and the contextual meaning embraced in names. Indeed, there was a limit to deriving functions with high accuracy and reliability simply from gene set names. The comparison of multiple gene set collections showed that although the gene sets had similar names, the gene elements were extremely heterogeneous. Thus, the type of collection chosen and the analytical context influence the interpretation of GSEA results. Nonetheless, the analyses of multiple collections made it possible to derive robust and consistent function identifications. This study confirmed several well-described roles of RhoA and revealed less explored functions, suggesting future research directions.

• International Journal of Computer Science & Network Security
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• 제23권12호
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• pp.199-203
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• 2023

In recent decades, the growth of communication technology has resulted in an explosion of data-related information. Ontology perception is being used as a growing requirement to integrate data and unique functionalities. Ontologies are not only critical for transforming the traditional web into the semantic web but also for the development of intelligent applications that use semantic enrichment and machine learning to transform data into smart data. To address these unclear facts, several researchers have been focused on expanding ontologies and semantic web technologies. Due to the lack of clear-cut limitations, ontologies would not suffice to deliver uncertain information among domain ideas, conceptual formalism supplied by traditional. To deal with this ambiguity, it is suggested that fuzzy ontologies should be used. It employs Ontology to introduce fuzzy logical policies for ambiguous area concepts such as darkness, heat, thickness, creaminess, and so on in a device-readable and compatible format. This survey efforts to provide a brief and conveniently understandable study of the research directions taken in the domain of ontology to deal with fuzzy information; reconcile various definitions observed in scientific literature, and identify some of the domain's future research-challenging scenarios. This work is hoping that this evaluation can be treasured by fuzzy ontology scholars. This paper concludes by the way of reviewing present research and stating research gaps for buddy researchers.

• Journal of Information Science Theory and Practice
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• 제11권1호
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• pp.61-78
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• 2023

Ontological knowledge modelling of epic texts, though being an established research arena backed by concrete multilingual and multicultural works, still suffers from two key shortcomings. Firstly, all epic ontological models developed till date have been designed following ad-hoc methodologies, most often combining existing general purpose ontology development methodologies. Secondly, none of the ad-hoc methodologies consider the potential reuse of existing epic ontological models for enrichment, if available. This paper presents, as a unified solution to the above shortcomings, the design and development of GOMME - the first dedicated methodology for iterative ontological modelling of epics, potentially extensible to works in different research arenas of digital humanities in general. GOMME is grounded in transdisciplinary foundations of canonical norms for epics, knowledge modelling best practices, application satisfiability norms, and cognitive generative questions. It is also the first methodology (in epic modelling but also in general) to be flexible enough to integrate, in practice, the options of knowledge modelling via reuse or from scratch. The feasibility of GOMME is validated via a first brief implementation of ontological modelling of the Indian epic Mahabharata by reusing an existing ontology. The preliminary results are promising, with the GOMME-produced model being both ontologically thorough and competent performance-wise.

• Genomics & Informatics
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• 제5권3호
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• pp.133-136
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• 2007

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2004년도 봄 학술발표논문집 Vol.31 No.1 (B)
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• pp.553-555
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• 2004

최근 인터넷의 급속한 성장과 더불어 전자메일(I-Mail)은 의사교환의 필수적인 매체로 사용 되어지고 있다. 그러나 편리하고 비용이 들지 앉는 장정을 이용해 엄청난 양의 스맴 메일이 매일같이 솎아져 오고, 이를 해결하기 위한 다양한 연구들이 제시되어져 왔다. 특히. 문서 분류에 널리 쓰이는 베이지안 분류자(Bayesian classifier)가 가장 널리 이용되어지고 있는데, 정확도와 재현율에서 비교적 우수한 성능을 보이고 있다. 그러나 몇 가지 문제점을 갖고 있는데, 첫째, 사전에 사용자에 의해 스팸. 논스팸 메일에 대한 충분한 학습이 선행되어야 하는 정, 둘째, 필터링을 위한 연산시간이 소요되는 점, 셋째, 필터링의 대상이 되는 메일 본문의 내용이 적을 경우 정확한 필터링이 어렵다는 정 등의 문제점이 있다. 본 논문에서는 마지막 문제점으로 지적된 메일 본문의 내용이 적을 경우 즉, 연산을 위한 특징적인 단어들의 부족으로 정확한 분류가 불가능한 경우의 해결방안으로 온틀로지와 Semantic Enrichment 기법을 이용한 스팸 메일 필터링 시스템을 제안한다. 실험 결과, 제안하는 시스템이 베이지안 분류자를 이용한 분류 시스템보다 정확도에서 4.1%, 재현율에서 10.5%. 그리고 F-measure에서 7.64%의 성능향상을 보였다.

• Genomics & Informatics
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• 제18권4호
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• pp.39.1-39.8
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• 2020

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

• 한국언어정보학회지:언어와정보
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• 제14권1호
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• pp.165-196
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• 2010

The primary goal of this paper is to propose methods of enriching two heterogeneous ontologies: Sejong Semantic Classes (SJSC) and KorLexNoun 1.5 (KLN). In order to achieve this goal, this study introduces the pros and cons of two ontologies, and analyzes the error patterns found during the fine-grained manual mapping processes between them. Error patterns can be classified into four types: (1) structural defectives involved in node branching, (2) errors in assigning the semantic classes, (3) deficiency in providing linguistic information, and (4) lack of the lexical units representing specific concepts. According to these error patterns, we propose different solutions in order to correct the node branching defectives and the semantic class assignment, to complement the deficiency of linguistic information, and to increase the number of lexical units suitably allotted to their corresponding concepts. Using the results of this study, we can obtain more enriched ontologies by correcting the defects and errors in each ontology, which will lead to the enhancement of practicality for syntactic and semantic analysis.

• Asian-Australasian Journal of Animal Sciences
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• 제26권5호
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• pp.609-624
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• 2013

The objective of this study was to get a comprehensive understanding of how genes in chicken shell gland modulate eggshell strength at the early stage of active calcification. Four 32-week old of purebred Xianju hens with consistent high or low shell breakage strength were grouped into two pairs. Using Affymetrix Chicken Array, a whole-transcriptome analysis was performed on hen's shell gland at 9 h post oviposition. Gene ontology enrichment analysis for differentially expressed (DE) transcripts was performed using the web-based GOEAST, and the validation of DE-transcripts was tested by qRT-PCR. 1,195 DE-transcripts, corresponding to 941 unique genes were identified in hens with strong eggshell compared to weak shell hens. According to gene ontology annotations, there are 77 DE-transcripts encoding ion transporters and secreted extracellular matrix proteins, and at least 26 DE-transcripts related to carbohydrate metabolism or post-translation glycosylation modification; furthermore, there are 88 signaling DE-transcripts. GO term enrichment analysis suggests that some DE-transcripts mediate reproductive hormones or neurotransmitters to affect eggshell quality through a complex suite of biophysical processes. These results reveal some candidate genes involved with eggshell strength at the early stage of active calcification which may facilitate our understanding of regulating mechanisms of eggshell quality.