• Asian Pacific Journal of Cancer Prevention
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• 제15권5호
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• pp.2345-2351
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• 2014

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2- delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.

• Asian Pacific Journal of Cancer Prevention
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• 제16권13호
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• pp.5445-5451
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• 2015

Fascin-1 (FSCN1) is an actin-bundling protein that induces cell membrane protrusions, increases cell motility, and is overexpressed in various human epithelial cancers, including esophageal squamous cell carcinoma (ESCC). We analyzed various protein-protein interactions (PPI) of differentially-expressed genes (DEGs), in fascin knockdown ESCC cells, to explore the role of fascin overexpression. The node-degree distributions indicated these PPI sub-networks to be characterized as scale-free. Subcellular localization analysis revealed DEGs to interact with other proteins directly or indirectly, distributed in multiple layers of extracellular membrane-cytoskeleton/ cytoplasm-nucleus. The functional annotation map revealed hundreds of significant gene ontology (GO) terms, especially those associated with cytoskeleton organization of FSCN1. The Random Walk with Restart algorithm was applied to identify the prioritizations of these DEGs when considering their relationship with FSCN1. These analyses based on PPI network have greatly expanded our comprehension of the mRNA expression profile following fascin knockdown to future examine the roles and mechanisms of fascin action.

• 미생물학회지
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• 제39권2호
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• pp.67-75
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• 2003

비교유전체학의 주요 주제 중 유전자서열을 분류하고 단백질기능을 예측하는 연구가 있으며, 이를 위해 단백질 구조, 공통서열 및 바인딩 위치 예측등의 방법과 함께, 전유전체 서열에서 구해지는 유사도 그래프를 분석해 상동유전자를 검색하는 계산학적인 접근방법이 있다. 유사도그래프를 사용한 방법은 서열에 대한 기존 지식에 의존하지 않는 장점이 있지만 유사도 하한값과 같은 주관적인 임계값이 필요한 단점이 있다. 본 논문에서는 반복적으로 그래프를 분해하는 이전의 방법을 일반화시켜, 유사도 그래프에 기반한 유전자 서열군집분석 방법론과 객관적이고 안정적인 파라미터 임계값 계산 방법을 제안한다. 제시된 방법으로 알려진 미생물 유전체 서 열을 분석하여 이전의 방법인 BAG 알고리즘 결과와 비교했다.

• Journal of Microbiology and Biotechnology
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• 제26권6호
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• pp.1124-1131
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• 2016

In this study, the global proteome of the IPEC-J2 cell line was evaluated using ultra-high performance liquid chromatography coupled to a quadrupole Q Exactive^™ Orbitrap mass spectrometer. Proteins were isolated from highly confluent IPEC-J2 cells in biological replicates and analyzed by label-free mass spectrometry prior to matching against a porcine genomic dataset. The results identified 1,517 proteins, accounting for 7.35% of all genes in the porcine genome. The highly abundant proteins detected, such as actin, annexin A2, and AHNAK nucleoprotein, are involved in structural integrity, signaling mechanisms, and cellular homeostasis. The high abundance of heat shock proteins indicated their significance in cellular defenses, barrier function, and gut homeostasis. Pathway analysis and annotation using the Kyoto Encyclopedia of Genes and Genomes database resulted in a putative protein network map of the regulation of immunological responses and structural integrity in the cell line. The comprehensive proteome analysis of IPEC-J2 cells provides fundamental insights into overall protein expression and pathway dynamics that might be useful in cell adhesion studies and immunological applications.

• 융합신호처리학회논문지
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• 제6권1호
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• pp.27-32
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• 2005

유전자 서열 분석기의 발달로 유전체 서열 데이터는 급속도로 증가하여 자동적으로 유전체에 주석을 첨부하는 과정이 필요하다. 유전체에 주석을 다는 작업 중 가장 어려운 과정이 유전체내에 존재하는 단백질을 코드화하고 있는 유전자의 탐색이다. 진핵생물과 원핵생물은 유전자 구조에서 현격한 차이를 보이고 있으므로 유전자를 예측하는 방법도 각각 달라야 한다. 지금까지 전체 유전체 서열이 밝혀진 231종의 생물에서 200종이 원핵생물이다. 그러므로 비교 유전체학을 통한 생물공학 연구에서 진핵생물보다 원핵생물이 더 적합하다 할 것이다. 게다가 원핵생물의 경우 intron이라는 구조를 가지고 있지 않아 유전자 예측이 더 간단하다. 이전에 연구된 원핵생물의 유전자 예측 정확성은 80%～90%에 이르고 있고 최근의 연구에서는 유전자 예측 정확도 100%를 목표로 하고 있고, 본 논문에서는 E. coli K-12와 S. typhi 유전체의 경우, 유전체 예측 정확도가 각각 98.5%와 98.7%를 보여 기존의 GLIMMER보다 더 우수한 결과를 나타내었다.

• Genomics & Informatics
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• 제13권2호
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• pp.53-59
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• 2015

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

• BMB Reports
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• 제42권12호
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• Genomics & Informatics
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• 제5권4호
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• pp.194-195
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• 2007

We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.

• Journal of the Korean Data and Information Science Society
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• 제18권2호
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• pp.489-506
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• 2007

Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is the most important process in annotating genes and greatly affects gene analysis and genome annotation. As eukaryotic genes have more complicated structures in DNA sequences than those of prokaryotic genes, analysis programs for eukaryotic gene structure prediction have more diverse and more complicated computational models. There are Ab Initio method, Similarity-based method, and Ensemble method for gene prediction method for eukaryotic genes. Each Method use various algorithms. This paper introduce how to predict genes using HMM(Hidden Markov Model) algorithm and present the process of gene prediction with well-known gene prediction programs.

• Journal of Genetic Medicine
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• 제10권1호
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• pp.27-32
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• 2013

Post-transcriptional nucleotide sequence modification of transcripts by RNA editing is an important molecular mechanism in the regulation of protein function and is associated with a variety of human disease phenotypes. Identification of RNA editing sites is the basic step for studying RNA editing. Databases and bioinformatics resources are used to annotate and evaluate as well as identify RNA editing sites. No method is free of limitations. Correctly establishing an analytic pipeline and strategic application of both experimental and bioinformatics methods constitute the first step in investigating RNA editing. This review summarizes modern bioinformatics approaches and related resources for RNA editing research.