• 제목/요약/키워드: gene ontology analysis

검색결과 244건 처리시간 0.042초

웹 기반 단일염기다형성 연관 패스웨이 분석 도구 (PRaDA : Web-based analyzer for Pathway Relation and Disease Associated SNP)

  • 유기진;박수호;류근호
    • 디지털콘텐츠학회 논문지
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    • 제19권9호
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    • pp.1795-1801
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    • 2018
  • 질환의 원인을 규명하기 위해 전장유전체 연관분석 (GWAS; Genome-Wide Association Study) 연구가 활발히 진행되고 유전체 레벨의 단일염기다형성 (SNP; Single-nucleotide polymorphism)이 많이 밝혀지고 있다. 그러나 단일염기다형성의 연관분석을 통해 질환이 발병하는 생물학적 메카니즘을 이해하기 어렵기 때문에 유전자, 생물학적 패스웨이 및 질환 등의 연관성 분석이 이전보다 더욱 중요하다. 본 논문에서는 단일염기다형성과 관련된 유전자와 패스웨이, 질환 정보를 검색하여 통합 분석하는 서비스를 제공하는 PRaDA 웹 시스템을 제안하였다. PRaDA는 사용자로부터 입력받은 유의한 몇몇의 단일염기다형성들과 관련된 유전자 및 패스웨이 뿐만 아니라, 유의하지 않은 다수의 단일염기다형성 집합의 간접적인 영향을 파악하기 위해 기능적으로 근접한 패스웨이를 검색하고 통계적 분석을 실행한다. 사용자들은 PRaDA가 제공하는 통합된 정보를 통해 질병의 전반적인 이해를 할 수 있다.

오미자(五味子) 클로로포름 분획물이 이상지질혈증 생쥐의 지질대사 및 간 조직 유전자 변화에 미치는 영향 (The Effects of Schizandrae Fructus Chloroform Fraction on Gene Expression in Liver Tissue of Dyslipidemic Mice)

  • 신윤리;김영균;김경민
    • 한방비만학회지
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    • 제15권2호
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    • pp.111-122
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    • 2015
  • Objectives: Schizandrae fructus (Schizandra chinensis) is one of very common herbs, it is known as natural antioxidants, anti-inflammatory agent. Also some reports show that its extract works to regulate of dyslipidemia. This study was designed to investigate the effects of Schizandrae fructus chloroform fraction (SFCF) on serum lipid levels in dyslipidemic mice. Methods: The levels of total cholesterol, high density lipoprotein-cholesterol, triglyceride, aspartate aminotransferase (AST), alanine aminotransferase (ALT), fasting blood glucose in serum were measured. Histopathological and gene expression changes in liver tissue were also observed. Results: Oral administration of SFCF lowered levels of total cholesterol and triglyceride, which were elevated by high-fat diet. But SFCF did not affect on weight changes and serum AST, ALT levels in dyslipidemic mice. After carrying out gene ontological analysis, large numbers of genes in high-fat diet group were up-(347) or down-regulated (235). In SFCF treated mice, some changed expression of the genes was restored to normal levels, with a recovery rate of 17%. And it seems that fatty acid biosynthesis pathway was one of important key pathways to recovery. Conclusions: SFCF has beneficial effect on dyslipidemia, and could be used to prevent and treat cardiovascular disease.

Comparative Transcriptome Analysis of Queen, Worker, and Larva of Asian Honeybee, Apis cerana

  • Kim, Woo Jin;Lee, Seok Hee;An, Saes Byeol;Kim, Song Eun;Liu, Qin;Choi, Jae Young;Je, Yeon Ho
    • International Journal of Industrial Entomology and Biomaterials
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    • 제27권2호
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    • pp.271-276
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    • 2013
  • The Asian honeybee, Apis cerana, is a native honeybee species in Korea which is important in agriculture for pollination and honey production. For better understanding of the physiology of A. cerana, high-throughput Illumina transcriptome sequencing was performed to analyze the gene expression profiles of queen, worker, and larva. A total of 219,799,682 clean reads corresponding to 22.2 Gb of nucleotide sequences was obtained from the whole body total RNA samples. The Apis mellifera reference mRNA sequence database was used to measure the gene expression level with Bowtie2 and eXpress software, and the Illumina short reads were then mapped to 11,459 out of 11,736 A. mellifera reference genes. Total of 9,221 genes with FPKM value greater than 5 of each sample group were subjected to eggNOG with BLASTX for gene ontology analysis. The differential gene expression between queen and worker, and worker and larva were analyzed to screen the overexpressed genes in each sample group. In the queen and worker sample group, total of 1,766 genes were differentially expressed with 887 and 879 genes overexpressed over two folds in queen and worker, respectively. In the worker and larva sample group, total of 1,410 genes were differentially expressed with 1,009 and 401 genes overexpressed over two folds in worker and larva, respectively.

Single-Cell RNA Sequencing of Bone Marrow Mesenchymal Stem Cells from the Elderly People

  • Dezhou Zhu;Jie Gao;Chengxuan Tang;Zheng Xu;Tiansheng Sun
    • International Journal of Stem Cells
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    • 제15권2호
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    • pp.173-182
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    • 2022
  • Background and Objectives: Bone marrow mesenchymal stem cells (BMSCs) show considerable promise in regenerative medicine. Many studies demonstrated that BMSCs cultured in vitro were highly heterogeneous and composed of diverse cell subpopulations, which may be the basis of their multiple biological characteristics. However, the exact cell subpopulations that make up BMSCs are still unknown. Methods and Results: In this study, we used single-cell RNA sequencing (scRNA-Seq) to divide 6,514 BMSCs into three clusters. The number and corresponding proportion of cells in clusters 1 to 3 were 3,766 (57.81%), 1,720 (26.40%), and 1,028 (15.78%). The gene expression profile and function of the cells in the same cluster were similar. The vast majority of cells expressed the markers defining BMSCs by flow cytometry and gene expression analysis. Each cluster had at least 20 differentially expressed genes (DEGs). We conducted Gene Ontology enrichment analysis on the top 20 DEGs of each cluster and found that the three clusters had different functions, which were related to self-renewal, multilineage differentiation and cytokine secretion, respectively. In addition, the function of the top 20 DEGs of each cluster was checked by the National Center for Biotechnology Information gene database to further verify our hypothesis. Conclusions: This study indicated that scRNA-Seq can be used to divide BMSCs into different subpopulations, demonstrating the heterogeneity of BMSCs.

네트워크 약리학을 이용한 윤폐환(潤肺丸)의 COPD 치료 효능 및 작용기전 연구 (Network Pharmacology-based Prediction of Efficacy and Mechanism of Yunpye-hwan Acting on COPD)

  • 김민주;양아람;권빛나;김동욱;배기상
    • 대한본초학회지
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    • 제39권3호
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    • pp.37-47
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    • 2024
  • Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

특수 목적견으로서의 품성 및 능력 관련 유전자들에 관한 생물정보학적 분석 (Bioinformatic Analysis of the Canine Genes Related to Phenotypes for the Working Dogs)

  • 권윤정;어정우;최봉환;최유리;김정안;김다희;김태헌;성환후;김희수
    • 생명과학회지
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    • 제23권11호
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    • pp.1325-1335
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    • 2013
  • 특수 목적견(구조견, 군견, 안내견 및 탐지견)은 집중력, 소유욕, 대담성 등을 기반으로 한 훈련시험을 통해 선별된다. 최근 특수견으로서의 특수한 능력 및 품성에 대해 유전적인 정보가 중요한 인자로 다뤄지고 있다. 본 연구에서는 특수견으로서의 개의 특수한 능력 및 품성과 관련된 유전자들의 분자적인 특징을 고찰하고자 하였다. 이전 연구에서 보고된 24개의 유전자(AR, BDNF, DAT, DBH, DGCR2, DRD4, MAOA, MAOB, SLC6A4, TH, TPH2, IFT88, KCNA3, TBR2, TRKB, ACE, GNB1, MSTN, PLCL1, SLC25A22, WFIKKN2, APOE, GRIN2B, PIK3CG)를 선택하여 품성, 후각, 운동 및 학습능력 관련 유전자, 네 가지 카테고리로 분류하였다. 본 연구에서는 생물학적인 기법을 이용하여 이 유전자들의 염색체상의 위치, 유전자들 간의 네트워크를 통한 상호관계를 조사하였으며, 어떤 생물학적 기능과 관련이 있는지 Gene Ontology 분석과 데이터베이스를 기반으로 in silico 발현 양상을 살펴보았다. 또한 이전 연구를 통하여 품성 관련 유전자들의 다양한 유전적 다형성에 대한 보고를 조사하였다. 본 연구는 특수 견으로서 주요하게 고려되는 개의 고유한 능력 및 품성 관련된 유전자에 대해 분자적 특징을 제시하고 있다. 이 후보 유전자들은 개의 특수한 표현형과의 관계를 밝힐 수 있는 연구의 기초자료로서 이용될 수 있을 뿐만 아니라 핵심적인 유전인자로 응용되어 신속하고 정확한 특수견 선발에 기여할 수 있을 것으로 전망된다.

Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress

  • Kim, Ji-Eun;Choe, Junkyung;Lee, Jeong Hee;Kim, Woong Bom;Cho, Whan;Ha, Ji Hong;Kwon, Ki Jin;Han, Kook Il;Jo, Sung-Hwan
    • Journal of Animal Science and Technology
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    • 제58권4호
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    • pp.17.1-17.7
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    • 2016
  • Background: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance. Results: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type ($p{\leq}0.05$). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized. Conclusions: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

StrokeBase: A Database of Cerebrovascular Disease-related Candidate Genes

  • Kim, Young-Uk;Kim, Il-Hyun;Bang, Ok-Sun;Kim, Young-Joo
    • Genomics & Informatics
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    • 제6권3호
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    • pp.153-156
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    • 2008
  • Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

KUGI: A Database and Search System for Korean Unigene and Pathway Information

  • Yang, Jin-Ok;Hahn, Yoon-Soo;Kim, Nam-Soon;Yu, Ung-Sik;Woo, Hyun-Goo;Chu, In-Sun;Kim, Yong-Sung;Yoo, Hyang-Sook;Kim, Sang-Soo
    • 한국생물정보학회:학술대회논문집
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    • 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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    • pp.407-411
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    • 2005
  • KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

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Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies

  • Meng, Qingli;Wang, Kejun;Liu, Xiaolei;Zhou, Haishen;Xu, Li;Wang, Zhaojun;Fang, Meiying
    • Asian-Australasian Journal of Animal Sciences
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    • 제30권4호
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    • pp.462-469
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    • 2017
  • Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.