• 한국가금학회:학술대회논문집
• /
• 한국가금학회 2005년도 제22차 정기총회 및 학술발표회
• /
• pp.53-59
• /
• 2005

본 연구에서는 닭의 정소 및 정자에 대한 기능 유전체 연구를 위한 자원을 확보할 수 있도록 정소 특이적유전자로 예상되는 후보 염기서열을 분석하였다. TIGR Gallus gallus Gene Index 상의 데이터베이스에서 닭의 정소에서만 나타나는 것으로 공개된 EST 염기서열을 검색하여 나온 총 292개의 서열을 선택하였으며, 이와 같이 선별된 서열들에 대하여 닭의 정소와 난소를 포함한 다양한 조직에서 전사체의 발현을 검증하였다. 결과에서, 총 292개의 염기서열 중 110개가 정소 특이적인 발현을 나타내었다. Tentative consensus sequence (TC) 상에서 집합된 EST의 수와 정소 특이적으로 발현하는 TCs의 수 사이의 상관관계는 발견되지 않았다. Gene Ontology 데이터베이스 용어를 이용하여 분류한 결과에서는 정소특이적인 TC는 닭의 전체 TC를 분류한 것과 비교하면 catalytic activity (Molecular Functionbranch)의 카테고리에 많은 수의 TC가 포함된 것으로 나타났다. 본 연구의 결과는 닭의 정소 특이적 유전자에 대한 연구와 그 기능 분석을 보다 더욱 촉진시킬 수 있을 것이다.

• The Plant Pathology Journal
• /
• 제29권3호
• /
• pp.249-259
• /
• 2013

Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin biosynthesis and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNAseq of the wild-type B. glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::${\Omega}$) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::${\Omega}$). A comparison of gene expression profiling among the wild-type BGR1 and the two mutants before and after QS onset as well as gene ontology (GO) enrichment analysis from differential expressed genes (DEGs) revealed that genes involved in motility were highly enriched in TofI-dependent DEGs, whereas genes for transport and DNA polymerase were highly enriched in QsmR-dependent DEGs. Further, a combination of pathways with these DEGs and phenotype analysis of mutants pointed to a couple of metabolic processes, which are dependent on QS in B. glumae, that were directly or indirectly related with bacterial motility. The consistency of observed bacterial phenotypes with GOs or metabolic pathways in QS-regulated genes implied that integration RNAseq with GO enrichment or pathways would be useful to study bacterial physiology and phenotypes.

• 운동영양학회지
• /
• 제25권3호
• /
• pp.28-35
• /
• 2021

[Purpose] As Panax ginseng C. A. Meyer (ginseng) exhibits various physiological activities and is associated with exercise, we investigated the potential active components of ginseng and related target genes through network pharmacological analysis. Additionally, we analyzed the association between ginseng-related genes, such as the G-protein-coupled receptors (GPCRs), and improved exercise capacity. [Methods] Active compounds in ginseng and the related target genes were searched in the Traditional Chinese Medicine Database and Analysis Platform (TCMSP). Gene ontology functional analysis was performed to identify biological processes related to the collected genes, and a compound-target network was visualized using Cytoscape 3.7.2. [Results] A total of 21 ginseng active compounds were detected, and 110 targets regulated by 17 active substances were identified. We found that the active compound protein was involved in the biological process of adrenergic receptor activity in 80%, G-protein-coupled neurotransmitter in 10%, and leucocyte adhesion to arteries in 10%. Additionally, the biological response centered on adrenergic receptor activity showed a close relationship with G protein through the beta-1 adrenergic receptor gene reactivity. [Conclusion] According to bioavailability analysis, ginseng comprises 21 active compounds. Furthermore, we investigated the ginseng-stimulated gene activation using ontology analysis. GPCR, a gene upregulated by ginseng, is positively correlated to exercise. Therefore, if a study on this factor is conducted, it will provide useful basic data for improving exercise performance and health.

• Journal of Plant Biotechnology
• /
• 제43권2호
• /
• pp.189-203
• /
• 2016

Brassica oleraceae var capitata is a member of the Brassicaceae family and is widely used as an horticultural crop. In the present study, transcriptome analysis of B. oleraceae L. var capitata was done for the first time using eight-week old seedlings treated with $50{\mu}m$ MeJA, versus mock-treated samples. The complete transcripts for both samples were obtained using the GS-FLX sequencer. Overall, we obtained 275,570 and 266,457 reads from seedlings treated with or without $50{\mu}m$ MeJA, respectively. All the obtained reads were annotated using biological databases and functionally classified using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomics (KEGG). By using GO analyses, putative transcripts were examined in terms of biotic and abiotic stresses, cellular component organization, biogenesis, and secondary metabolic processes. The KEGG pathways for most of the transcripts were involved in carbohydrate metabolism, energy metabolism, and secondary metabolite synthesis. In order to double the sequenced data, we randomly chose two putative genes involved in terpene biosynthetic pathways and studied their transcript patterns under MeJA treatment. This study will provide us a platform to further characterize the genes in B. oleracea var capitata.

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

• Animal Bioscience
• /
• 제37권3호
• /
• pp.451-460
• /
• 2024

Objective: The objective is to identify genomic regions and candidate genes associated with age to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) in Yorkshire pig. Methods: This study used a total of 104,380 records and 11,854 single nucleotide polymorphism (SNP) data obtained from Illumina porcine 60K chip. The estimated genomic breeding values (GEBVs) and SNP effects were estimated by single-step genomic best linear unbiased prediction (ssGBLUP). Results: The heritabilities of AGE, ADG, BF, and EMA were 0.50, 0.49, 0.49, and 0.23, respectively. We identified significant SNP markers surpassing the Bonferroni correction threshold (1.68×10^-6), with a total of 9 markers associated with both AGE and ADG, and 4 markers associated with BF and EMA. Genome-wide association study (GWAS) analyses revealed notable chromosomal regions linked to AGE and ADG on Sus scrofa chromosome (SSC) 1, 6, 8, and 16; BF on SSC 2, 5, and 8; and EMA on SSC 1. Additionally, we observed strong linkage disequilibrium on SSC 1. Finally, we performed enrichment analyses using gene ontology and Kyoto encyclopedia of genes and genomes (KEGG), which revealed significant enrichments in eight biological processes, one cellular component, one molecular function, and one KEGG pathway. Conclusion: The identified SNP markers for productive traits are expected to provide valuable information for genetic improvement as an understanding of their expression.

• Interdisciplinary Bio Central
• /
• 제3권2호
• /
• pp.7.1-7.6
• /
• 2011

Background: Published manuscripts are the main source of biological knowledge. Since the manual examination is almost impossible due to the huge volume of literature data (approximately 19 million abstracts in PubMed), intelligent text mining systems are of great utility for knowledge discovery. However, most of current text mining tools have limited applicability because of i) providing abstract-based search rather than sentence-based search, ii) improper use or lack of ontology terms, iii) the design to be used for specific subjects, or iv) slow response time that hampers web services and real time applications. Results: We introduce an advanced text mining system called PubMine that supports intelligent knowledge discovery based on diverse bio-ontologies. PubMine improves query accuracy and flexibility with advanced search capabilities of fuzzy search, wildcard search, proximity search, range search, and the Boolean combinations. Furthermore, PubMine allows users to extract multi-dimensional relationships between genes, diseases, and chemical compounds by using OLAP (On-Line Analytical Processing) techniques. The HUGO gene symbols and the MeSH ontology for diseases, chemical compounds, and anatomy have been included in the current version of PubMine, which is freely available at http://pubmine.kobic.re.kr. Conclusions: PubMine is a unique bio-text mining system that provides flexible searches and analysis of biological entity relationships. We believe that PubMine would serve as a key bioinformatics utility due to its rapid response to enable web services for community and to the flexibility to accommodate general ontology.

• Asian Pacific Journal of Cancer Prevention
• /
• 제14권1호
• /
• pp.457-461
• /
• 2013

Prostate cancer is a leading cause of death in male populations across the globe. With the advent of gene expression arrays, many microarray studies have been conducted in prostate cancer, but the results have varied across different studies. To better understand the genetic and biologic mechanisms of prostate cancer, we conducted a meta-analysis of two studies on prostate cancer. Eight key genes were identified to be differentially expressed with progression. After gene co-expression analysis based on data from the GEO database, we obtained a co-expressed gene list which included 725 genes. Gene Ontology analysis revealed that these genes are involved in actin filament-based processes, locomotion and cell morphogenesis. Further analysis of the gene list should provide important clues for developing new prognostic markers and therapeutic targets.

• 디지털융복합연구
• /
• 제13권2호
• /
• pp.153-158
• /
• 2015

생물학자들은 특정 암이나 선천성 질병을 이해하는데 핵심정보를 제공할 수 있는 유전자관련 연구를 진행하고 있다. 하지만 생물학적 실험은 실험당시의 여러 가지 요소나 상황의 차이 또는 해석의 차이에 의해 서로 다른 결과를 생성하기도 한다. 따라서 현존하는 연구 결과들은 서로 상이한 정보를 제공할 수 있다. 유전자 정보의 통합을 통하여 이러한 불일치를 찾을 수 있다. 유전자 정보들이 불일치가 없이 통합 된다면 생물학자들은 어떤 유전자 정보를 알기 위해서 여러 연구 결과를 검토하지 않아도 되어 시간과 노력을 절감할 수 있게 된다. 이를 위하여 본 논문에서는 서로 다른 연구에 의해 구축된 유전자 정보를 하나의 정보로 통합 및 확장하는 기법을 소개한다.

• 동의생리병리학회지
• /
• 제18권5호
• /
• pp.1291-1300
• /
• 2004

Baicalin, a biologically active flavonoid form the roots of Scutallaria baicalensis (Skullcap), have been reported to not only function as anti-oxidants but also cause anticancer effect. We investigated the mechanism of baicalin-induced cytotoxicity and the macro scale gene expression analysis in leukemia cell line, HL-60 cells. Baicalin (10 μM) were used to treat the cells for 6h, 12h, 24h, 48h and 72h. In a human cDNAchip study of 65,000 genes evaluated 6, 12, 24, 48. 72 hours after treated with Baicalin in HL-60 cells. Hierarchical cluster against the genes which showed expression changes by more than two fold. One hundred one genes were grouped into 6 clusters according to their profile of expression by a hierarchical clustering algorithm. For genes differentially expressed in response to baicalin treatment, we tested functional classes based on Gene Ontology (GO) terms. This study provides the most comprehensive available survey of gene expression changes in response to baicalin treatment in HL-60 cell line.