• Genomics & Informatics
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• 제10권4호
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• pp.263-265
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• 2012

We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require any prior knowledge of scripting languages to carry out the data clustering and visualization. Furthermore, the heatmaps allow the selective display of data points satisfying user-defined criteria. For example, a clustered heatmap of experimental values can be differentially visualized based on statistical values, such as p-values. Including diverse menu-based display options, QCanvas provides a convenient graphical user interface for pattern analysis and visualization with high-quality graphics.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제10권6호
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• pp.2801-2816
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• 2016

Owing to their low scalability, weak support on big data, insufficient data collaborative analysis and inadequate situational awareness, the traditional methods fail to meet the needs of the security data analysis. This paper proposes visualization methods to fuse the multi-source security data and grasp the network situation. Firstly, data sources are classified at their collection positions, with the objects of security data taken from three different layers. Secondly, the Heatmap is adopted to show host status; the Treemap is used to visualize Netflow logs; and the radial Node-link diagram is employed to express IPS logs. Finally, the Labeled Treemap is invented to make a fusion at data-level and the Time-series features are extracted to fuse data at feature-level. The comparative analyses with the prize-winning works prove this method enjoying substantial advantages for network analysts to facilitate data feature fusion, better understand network security situation with a unified, convenient and accurate mode.

• Clinical and Experimental Pediatrics
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• 제64권7호
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• pp.355-363
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• 2021

Background: Nephrotic syndrome (NS) is a common renal disorder in children attributed to podocyte injury. However, children with the same diagnosis have markedly variable treatment responses, clinical courses, and outcomes, suggesting molecular heterogeneity. Purpose: This study aimed to explore the molecular responses of podocytes to nephrotic plasma to identify specific genes and signaling pathways differentiating various clinical NS groups as well as biological processes that drive injury in normal podocytes. Methods: Transcriptome profiles from immortalized human podocyte cell line exposed to the plasma of 8 subjects (steroid-sensitive nephrotic syndrome [SSNS], n=4; steroid-resistant nephrotic syndrome [SRNS], n=2; and healthy adult individuals [control], n=2) were generated using microarray analysis. Results: Unsupervised hierarchical clustering of global gene expression data was broadly correlated with the clinical classification of NS. Differential gene expression (DGE) analysis of diseased groups (SSNS or SRNS) versus healthy controls identified 105 genes (58 up-regulated, 47 down-regulated) in SSNS and 139 genes (78 up-regulated, 61 down-regulated) in SRNS with 55 common to SSNS and SRNS, while the rest were unique (50 in SSNS, 84 genes in SRNS). Pathway analysis of the significant (P≤0.05, -1≤ log2 FC ≥1) differentially expressed genes identified the transforming growth factor-β and Janus kinase-signal transducer and activator of transcription pathways to be involved in both SSNS and SRNS. DGE analysis of SSNS versus SRNS identified 2,350 genes with values of P≤0.05, and a heatmap of corresponding expression values of these genes in each subject showed clear differences in SSNS and SRNS. Conclusion: Our study observations indicate that, although podocyte injury follows similar pathways in different clinical subgroups, the pathways are modulated differently as evidenced by the heatmap. Such transcriptome profiling with a larger cohort can stratify patients into intrinsic subtypes and provide insight into the molecular mechanisms of podocyte injury.

• 생명과학회지
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• 제32권9호
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• pp.712-720
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• 2022

비록 PM_2.5 노출과 다양한 안구 표면 질환과 관련성이 많은 선행 연구에서 알려졌지만, PM_2.5 가 각막에 미치는 세포 독성에 대한 연구는 거의 수행되지 않았다. 본 연구의 목적은 PM에 의한 각막 상피세포의 유해성을 평가하기 위한 in vitro 모델로서 쥐의 각막유래 상피세포(primary rat corneal epithelial cells, RCE cells)의 효능을 조사하는 것이다. 이를 위하여 쥐의 눈에서 분리한 1차 배양 세포가 각막 상피세포임을 pan-cytokeratin 염색을 통하여 확인하였으며, PM_2.처리에 의한 각막 상피세포의 형태학적 변화를 동반한 생존율의 억제는 세포사멸 유도와 관련이 있었다. 또한 PM_2.가 처리된 각막 상피세포에서는 ROS의 생성이 증가되었으며, 이는 미토콘드리아 기능 장애와 연관성이 있었다. 이와 함께 PM_2.는 각막 상피세포에서 NO, TNF-α, IL-1β 및 IL-6를 포함한 염증 매개인자 및 사이토카인의 생성을 증가시켰다. 아울러 heatmap 분석을 통해 BLNK, IL-1RA, Itga2b, ABCb1a 및 Ptgs2가 미세먼지 유도 안구 질환의 임상 치료를 위한 잠재적인 표적 유전자로서 제시하였다. 결론적으로 본 연구의 결과는 1차 쥐의 각막 상피세포가 PM_2.에 의한 각막 상피세포 병리기전 연구에 유용한 모델일 수 있으며, 산화적 및 염증성 반응이 PM_2.유발 안구 표면 장애 유도에 핵심적인 역할을 함을 알 수 있었다.

• 대한임상검사과학회지
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• 제55권4호
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• pp.235-243
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• 2023

차세대 염기서열 분석이 개발되고 널리 사용됨에 따라 RNA-시퀀싱(RNA-sequencing, RNA-seq)이 글로벌 전사체 프로파일링을 검증하기 위한 도구의 첫번째 선택으로 급부상하게 되었다. RNA-seq의 상당한 발전으로 다양한 유형의 RNA-seq가 생물정보학(bioinformatics) 발전과 함께 진화했으나, 다양한 RNA-seq 기법 및 생물정보학에 대한 전반적인 이해 없이는 RNA-seq의 복잡한 데이터를 해석하여 생물학적 의미를 도출하기는 어렵다. 이와 관련하여 본 리뷰에서는 RNA-seq의 두 가지 주요 섹션을 논의하고 있다. 첫째, Standard RNA-seq과 주요하게 자주 사용되는 두 가지 RNA-seq variant method를 비교하였다. 이 비교는 어떤 RNA-seq 방법이 연구 목적에 가장 적절한지에 대한 시사점을 제공한다. 둘째, 가장 널리 사용되는 RNA-seq에서 생성된 데이터 분석; (1) 탐색적 자료 분석 및 (2) enriched pathway 분석에 대해 논의하였다. 데이터 세트의 전반적인 추세를 제공할 수 있는 주 성분 분석, Heatmap 및 Volcano plot과 같이 RNA-seq에 대해 가장 널리 사용되는 탐색적 자료 분석을 소개하였다. Enriched pathway 분석 섹션에서는 3가지 세대의 enriched pathway 분석에 대해 소개하고 각 세대가 어떤 식으로 RNA-seq 데이터 세트로부터 enriched pathway를 도출하는지를 소개하였다.

• Biomolecules & Therapeutics
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• 제30권1호
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• pp.98-116
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• 2022

The small GTPase RhoA has been studied extensively for its role in actin dynamics. In this study, multiple bioinformatics tools were applied cooperatively to the microarray dataset GSE64714 to explore previously unidentified functions of RhoA. Comparative gene expression analysis revealed 545 differentially expressed genes in RhoA-null cells versus controls. Gene set enrichment analysis (GSEA) was conducted with three gene set collections: (1) the hallmark, (2) the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and (3) the Gene Ontology Biological Process. GSEA results showed that RhoA is related strongly to diverse pathways: cell cycle/growth, DNA repair, metabolism, keratinization, response to fungus, and vesicular transport. These functions were verified by heatmap analysis, KEGG pathway diagramming, and direct acyclic graphing. The use of multiple gene set collections restricted the leakage of information extracted. However, gene sets from individual collections are heterogenous in gene element composition, number, and the contextual meaning embraced in names. Indeed, there was a limit to deriving functions with high accuracy and reliability simply from gene set names. The comparison of multiple gene set collections showed that although the gene sets had similar names, the gene elements were extremely heterogeneous. Thus, the type of collection chosen and the analytical context influence the interpretation of GSEA results. Nonetheless, the analyses of multiple collections made it possible to derive robust and consistent function identifications. This study confirmed several well-described roles of RhoA and revealed less explored functions, suggesting future research directions.

• 한국축산식품학회지
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• 제44권4호
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• pp.934-950
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• 2024

This study addresses the prevalent issue of meat species authentication and adulteration through a chemometrics-based approach, crucial for upholding public health and ensuring a fair marketplace. Volatile compounds were extracted and analyzed using headspace-solid-phase-microextraction-gas chromatography-mass spectrometry. Adulterated meat samples were effectively identified through principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA). Through variable importance in projection scores and a Random Forest test, 11 key compounds, including nonanal, octanal, hexadecanal, benzaldehyde, 1-octanol, hexanoic acid, heptanoic acid, octanoic acid, and 2-acetylpyrrole for beef, and hexanal and 1-octen-3-ol for pork, were robustly identified as biomarkers. These compounds exhibited a discernible trend in adulterated samples based on adulteration ratios, evident in a heatmap. Notably, lipid degradation compounds strongly influenced meat discrimination. PCA and PLS-DA yielded significant sample separation, with the first two components capturing 80% and 72.1% of total variance, respectively. This technique could be a reliable method for detecting meat adulteration in cooked meat.

• 유통과학연구
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• 제20권6호
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• pp.1-10
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• 2022

Purpose: This research proposes a new modified Recency-Frequency-Monetary (RFM) model by extending the model with spatial analysis for supporting decision-makers in discovering the promotional target market. Research design, data and methodology: This quantitative research utilizes data-mining techniques and the RFM model to cluster a university's provider schools. The RFM model was modified by adapting its variables to the university's marketing context and adding a district's potential (D) variable based on heatmap analysis using Geographic Information System (GIS) and K-means clustering. The K-prototype algorithm and the Elbow method were applied to find provider school clusters using the proposed RFM-D model. After profiling the clusters, the target segment was assigned. The model was validated using empirical data from an Indonesian university, and its performance was compared to the Customer Lifetime Value (CLV)-based RFM utilizing accuracy, precision, recall, and F1-score metrics. Results: This research identified five clusters. The target segment was chosen from the highest-value and high-value clusters that comprised 17.80% of provider schools but can contribute 75.77% of students. Conclusions: The proposed model recommended more targeted schools in higher-potential districts and predicted the target segment with 0.99 accuracies, outperforming the CLV-based model. The empirical findings help university management determine the promotion location and allocate resources for promotional information distribution and student recruitment.

• 한국측량학회지
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• 제40권3호
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• pp.169-175
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• 2022

우리나라 건설 산업은 건설 인력의 부족 및 노령화, 타 산업분야에 비해 낮은 생산성, 높은 산업재해율 등이 있다. 국토교통부에서는 4차 산업혁명을 대비하고, 건설산업의 생산성 향상을 위해 건설자동화, 혁신성장동력을 정하고 이에 대한 투자를 확대하고 있다. 도로건설 분야에서 새로운 기술들이 활용되기 위해서는 기술에 대한 정확도 검증과 공종별 적용성에 대한 평가가 이루어져야 한다. 본 연구에서는 관련 작업규정을 기준으로 모바일맵핑시스템의 정확도를 검증하고, 도로 시공현장에 대한 데이터 취득 및 분석을 통해 도로 시공측량에 대한 모바일맵핑시스템의 적용성을 제시하고자 하였다. 정밀도로지도 제작 작업규정에 따라 연구에 활용한 장비의 정확도를 검증하였으며, 수평 및 수직 방향에 대한 최대 오차가 10cm 이내로 연구에 활용한 모바일맵핑시스템의 도로 시공측량 적용 가능성을 제시하였다. 또한 시공측량을 위한 데이터 취득 시간에 대한 기존 방법과의 비교와 시공측량 성과물 제작과 heatmap 및 토공량 산정을 통해 모바일맵핑시스템을 이용한 도로 시공측량 활용의 가능성을 제시하였다. 향후, 모바일맵핑시스템의 도로 시공측량 활용은 건설공사의 효율성을 크게 향상시킬 수 있을 것이다.

• 한국컴퓨터정보학회논문지
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• 제21권5호
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• pp.19-29
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• 2016

This paper suggests a method to refine a massive collective intelligence data, and visualize with multilevel sentiment network, in order to understand information in an intuitive and semantic way. For this study, we first calculated a frequency of sentiment words from each movie review. Second, we designed a Heatmap visualization to effectively discover the main emotions on each online movie review. Third, we formed a Sentiment-Movie Network combining the MDS Map and Social Network in order to fix the movie network topology, while creating a network graph to enable the clustering of similar nodes. Finally, we evaluated our progress to verify if it is actually helpful to improve user cognition for multilevel analysis experience compared to the existing network system, thus concluded that our method provides improved user experience in terms of cognition, being appropriate as an alternative method for semantic understanding.