• 한국연초학회지
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• 제9권2호
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• pp.37-47
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• 1987

This experiment was conducted to obtain basic information on breeding of flue-cured tabacco varieties . Nine cultivars and partial diallel set of 36 Fl hybrids were grown at Daegu Experiment Station, Korea Ginseng & Tobacco Research Institute in 1983. Partial dominance with high additive gene effect was observed for yield, leaves per plant , days to flower, leaf weight, nicotine and reducing sugar content. partial dominance with additive and dominant gene effect was observed for stalk height , leaf width midrib weight Overdominance with high dominant gene effect was observed for leaf length and midrib width. The directions of dominance were positive for yield, stalk height, leaf weight, leaf length, leaf width, midrib weight, midrib width and reducing sugar content, and the negative was days to flower. The estimates of effective genes were 1 for leaves per plant, 2 for stalk height, days to flower and leaf shape. 3 to 6 for leaf length, leaf width, leaf weight and midrib weight.

• 정보처리학회논문지D
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• 제12D권5호
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• pp.755-764
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• 2005

생명체의 주된 기능 요소인 유전자를 모두 식별하는 작업의 중요성이 증가함에 따라, 최근에 유전자 예측도구들이 활발히 개발되고 있다. 그러나 유전자 예측 프로그램들은 예측 결과를 그들 고유의 형식으로 제공하여 사용자가 그 결과를 이해하기 위해서는 상당히 많은 추가적인 노력이 필요하다. 따라서 유전자 예측결과에 대한 표준화된 표현과 유전자 데이터 집합에 대한 예측결과를 자동으로 계산하는 방법을 지원하는 것이 바람직하다. 본 논문에서는 다양한 유전자 예측 정보에 대한 효과적인 XML 표현과 이를 바탕으로 예측된 유전자 결과를 자동으로 분석하는 in 기반 분석 도구에 대하여 기술한다. 개발된 도구는 유전자 예측도구를 사용하는 사용자들이 편리하게 예측결과를 분석하고 예측결과에 대한 통계결과를 자동으로 산출할 수 있도록 지원한다. 도구의 유용성을 보여주기 위하여 널리 사용되는 유전자 예측 도구인 GenScan과 GeneID의 처리결과를 개발된 도구에 적용시켜 보았다.

• BMB Reports
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• 제45권2호
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• pp.120-125
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• 2012

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

• Journal of Microbiology and Biotechnology
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• 제16권12호
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• pp.1912-1918
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• 2006

Marine bacterium Hahella chejuensis KCTC 2396 simultaneously produced red antibiotic prodigiosin and undecylprodiginine. A complete set of the prodigiosin biosynthetic gene cluster has been cloned, sequenced, and successfully expressed in a heterologous host. Sequence analysis of the gene cluster revealed 14 ORFs showing high similarity to pig and red genes from Serratia spp. and Streptomyces coelicolor A3(2), respectively, and the gene organization was almost: similar to that of pig genes. These genes were named hap for Hahella prodigiosin, and determined to be transcribed as a single operon, by RT-PCR experiment. Based on the hap gene mutagenesis experiments and comparative analysis with pig and red genes, we propose a prodigiosin-biosynthetic pathway in KCTC 2396.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.139-152
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• 2002

Gene-shaving(Hastie et al, 2000) is a very useful method to identify a meaningful group of genes when the variation of expression is large. By shaving off the low-correlated genes with the leading principal component, the primary genes with the coherent expression pattern can be identified. Gene-shaving method works well If expression levels are varied enough, but it may not catch the meaningful cluster in low expression level or different expression time even with coherent patterns. The sliding window gene-shaving method which is to apply gene-shaving in each sliding window after hierarchical clustering is to compensate losing a meaningful set of genes whose variation is not large but distinct. The performance to identify expression patterns is compared for the simulated profile data by the different variance and expression level.

• BMB Reports
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• 제39권4호
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• pp.441-447
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• 2006

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

• 생명과학회지
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• 제19권8호
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• pp.1159-1163
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• 2009

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOX04, AP-1, FOX03, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다.

• 대한본초학회지
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• 제38권1호
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• pp.45-53
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• 2023

Objectives : Network pharmacology-based research is one of useful tool to predict the possible efficacy and molecular mechanisms of natural materials with multi compounds-multi targeting effects. In this study, we investigated the functional underlying mechanisms of Astragalus membranaceus Bunge (AM) on its anti-obesity effects using a network pharmacology analysis. Methods : The constituents of AM were collected from public databases and its target genes were gathered from PubChem database. The target genes of AM were compared with the gene set of obesity to find the correlation. Then, the network was constructed by Cytoscape 3.9.1. and functional enrichment analysis was conducted to predict the most relevant pathway of AM. Results : The result showed that AM network contained the 707 nodes and 6867 edges, and 525 intersecting genes were exhibited between AM and obesity gene set, indicating that high correlation with the effects of AM on obesity. Based on GO biological process and KEGG Pathway, 'Response to lipid', 'Cellular response to lipid', 'Lipid metabolic process', 'Regulation of chemokine production', 'Regulation of lipase activity', 'Chemokine signaling pathway', 'Regulation of lipolysis in adipocytes' and 'PPAR signaling pathway' were predicted as functional pathways of AM on obesity. Conclusions : AM showed high relevance with the lipid metabolism related with the chemokine production and lipolysis pathways. This study could be a basis that AM has promising effects on obesity via network pharmacology analysis.

• Molecules and Cells
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• 제46권1호
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• pp.65-67
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• 2023

SMILES (simplified molecular-input line-entry system) information of small molecules parsed by one-hot array is passed to a convolutional neural network called black box. Outputs data representing a gene signature is then matched to the genetic signature of a disease to predict the appropriate small molecule. Efficacy of the predicted small molecules is examined by in vivo animal models. GSEA, gene set enrichment analysis.

• Animal cells and systems
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• 제6권2호
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• pp.145-151
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• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.