• Genomics & Informatics
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• 제5권4호
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• pp.143-151
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• 2007

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.

• 패션비즈니스
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• 제14권4호
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• pp.1-9
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• 2010

The study verified the regulatory fit effect of the message focus and propensity regulatory focus delivered in the sales promotion situation of beauty services and products on the basis of the self-regulatory focus theory being actively discussed in the consumer behavior area of marketing. As the result of ANOVA analysis on the experimental design 2 (chronic regulatory focus: promotion focus/prevention focus, between factor) ${\times}$ 2 (message regulatory focus: promotion focus/prevention focus, within factor), the promotion focus group showed more positive response to the promotion focus message(4.88) of beauty services than the prevention focus group(4.40) so that the effect of regulatory fit appeared(t=1.79, p<.1), but the regulatory fit effect didn't appear in the prevention focus message(t=.58, p>.1) so that the hypothesis was partially supported. However, as for the promotion focus message of beauty products, the promotion focus group(4.62) showed more positive response than the prevention focus group(4.16), and as for the prevention focus message, the prevention focus group(4.89) showed more positive results than the promotion focus group(4.33) so that the effect of regulatory fit appeared(t=2.07, p<.05). Therefore, the result of the study shows that as for the service consumers perceive high risk, the sales promotion activity of the prevention focus message can be effective for prevention focus consumers and for promotion focus consumers as well. Otherwise, it suggests the marketing approach that the consumer evaluation is more positive when the advertising message focus fit the consumer regulatory focus.

• 한국압력기기공학회 논문집
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• 제7권3호
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• pp.15-22
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• 2011

The chemistry factor and RTPTS margin for domestic reactor pressure vessel materials were analyzed by using the surveillance data which have been obtained from 8 nuclear power plants in Korea. The surveillance data have been used to assess the integrity of the pressure vessel under the pressurized thermal shock (PTS) event. The chemistry factor, which is determined by the Cu and Ni contents of vessel materials, is considered a proper tool to assess the $RT_{PTS}$. The chemistry factors, which were obtained from the surveillance data of domestic reactor pressure vessels, were investigated and compared with those of Regulatory Guide 1.99 in this study. Regressions for ${\Delta}RT_{NDT}$ were performed to expect the chemistry factor as a function of Cu and Ni, and to estimate $RT_{PTS}$ margin. The margin analysis was performed by comparing the regression graphs and standard deviations with those of Regulatory Guide 1.99. The standard deviations calculated by using the domestic surveillance data for base metal and welds are almost same as the standard deviations which are suggested on Regulatory Guide 1.99, Rev.2.

• Bioinformatics and Biosystems
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• 제2권1호
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).

• 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.

• BMB Reports
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• 제32권6호
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• pp.567-572
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• 1999

We have previously shown that a DNA fragment is responsible for the anticoagulatory effect of an earthworm, Lumbricus rubellus. The anticoagluant increased the activated partial thromboplastin time (APTT) and also inhibited the thrombin activity observed with either N-${\alpha}$-p-tosyl-L-arginine methyl ester (TAME) or H-D-phenyl-alanyl-L-pipecoil-L-arginine-p-nitroanilide (S-2238). Since trypsin digestion of the anticoagulant further increased the APTT, the possible presence of a regulatory protein for the anticoagulatory DNA was investigated by digesting the anticoagulant with trypsin and isolating the DNA fragment with C4-reversed phase HPLC. The DNA fragment lacking a regulatory protein was eluted in the flow-through fraction, and analyzed with thrombin and activated factor X. Activated factor X activity was more strongly inhibited than thrombin activity. For DNA digestion, we treated the anticoagulant with DNase and purified the DNA-binding protein with a FPLC Resource-S cation exchange column. The regulatory protein, with an $M_r$ of 55.0 kDa, reduced the anticoagulatory effect of the DNA fragment.

• Genomics & Informatics
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• 제13권3호
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• pp.76-80
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• 2015

Type 2 diabetes mellitus is a complex metabolic disorder associated with multiple genetic, developmental and environmental factors. The recent advances in gene expression microarray technologies as well as network-based analysis methodologies provide groundbreaking opportunities to study type 2 diabetes mellitus. In the present study, we used previously published gene expression microarray datasets of human skeletal muscle samples collected from 20 insulin sensitive individuals before and after insulin treatment in order to construct insulin-mediated regulatory network. Based on a motif discovery method implemented by iRegulon, a Cytoscape app, we identified 25 candidate regulons, motifs of which were enriched among the promoters of 478 up-regulated genes and 82 down-regulated genes. We then looked for a hierarchical network of the candidate regulators, in such a way that the conditional combination of their expression changes may explain those of their target genes. Using Genomica, a software tool for regulatory network construction, we obtained a hierarchical network of eight regulons that were used to map insulin downstream signaling network. Taken together, the results illustrate the benefits of combining completely different methods such as motif-based regulatory factor discovery and expression level-based construction of regulatory network of their target genes in understanding insulin induced biological processes and signaling pathways.

• Molecules and Cells
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• 제44권5호
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• pp.342-355
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• 2021

The microphthalmia-associated transcription factor family (MiT family) proteins are evolutionarily conserved transcription factors that perform many essential biological functions. In mammals, the MiT family consists of MITF (microphthalmia-associated transcription factor or melanocyte-inducing transcription factor), TFEB (transcription factor EB), TFE3 (transcription factor E3), and TFEC (transcription factor EC). These transcriptional factors belong to the basic helix-loop-helix-leucine zipper (bHLH-LZ) transcription factor family and bind the E-box DNA motifs in the promoter regions of target genes to enhance transcription. The best studied functions of MiT proteins include lysosome biogenesis and autophagy induction. In addition, they modulate cellular metabolism, mitochondria dynamics, and various stress responses. The control of nuclear localization via phosphorylation and dephosphorylation serves as the primary regulatory mechanism for MiT family proteins, and several kinases and phosphatases have been identified to directly determine the transcriptional activities of MiT proteins. In different immune cell types, each MiT family member is shown to play distinct or redundant roles and we expect that there is far more to learn about their functions and regulatory mechanisms in host defense and inflammatory responses.

• Tuberculosis and Respiratory Diseases
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• 제48권6호
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• pp.879-886
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• 2000

연구배경: 폐특이 전사조절 유전자인 Thyroid Transcription Factor-1 (TTF-1)유전자는 폐에 선택적인 유전자의 표현의 조절에 중요한 전사인자로 작용하고 폐의 발생에서 morphogenic protein으로서 작용한다. 그러나 현재까지 이 TTF-1 유전자의 전사인자에 대한 연구는 거의 미미하다. DNase 1 hypersensitive(DH) regions은 활동적인 염색체에 대한 중요한 표식자이며 유전자를 조절하는 많은 DNA sequences와 밀접한 관계가 있다. 방법 : 추정적인 distal regulatory elements를 밝혀 내기 위해서 TTF-1을 표현하는 인간의 폐선암 세포주인 NCI-H441을 사용해 DNase 1 hypersensitive site assay를 이용하였다. 결과 : TTF-1 유전자에는 전사의 시작부위에서 +150, -450, -800, 그리고 -1500 base pair부위에 4곳의 DH sites가 있음을 할 수 있었다. 결론 : 이상의 결과로 전사 조절부위가 TTF-1 유전자 내에 그리고 5' prime부위에 위치함을 추정할 수 있었다.

• Journal of Photoscience
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• 제5권4호
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• pp.149-152
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• 1998

Expression of light-harvesting chlorophyll a/b-binding protein gene(cab) is repressed in the dark and activited by light. However, the detail of its regulatory mechanism is not characterized so far. To identify the interactions of cis-acting elements and trans-acting factors involvedin this regulation, nuclear extracts from the light-grown and dark-adapted Arabidopsis thaliana leaves were anlayzed for mobility shift assay against 134bp fragments had two retarded bands and one retardation band, respectively, both in light-grown and dark-adapted bands in the dark-adapted tissues. A new retardation the cab 3 expression in the dark. Several light regulatory motifs are scattered in the 146 bp region of cab 3 promoter. One of the light-regulatory motifs could be the binding site for the negative regulatory factor.