• Genomics & Informatics
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• v.10 no.4
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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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• v.10 no.6
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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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• v.64 no.7
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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.

• Journal of Life Science
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• v.32 no.9
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• pp.712-720
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• 2022

The purpose of this study was to investigate the efficacy of rat corneal-derived epithelial cells as an in vitro model to evaluate the harmfulness of the cornea caused by particulate matter 2.5 (PM_2.5). To establish an experimental model for the effect of PM_2.5 on corneal epithelial cells, it was confirmed that primary cultured cells isolated from rat eyes were corneal epithelial cells through pan-cytokeratin staining. Our results showed that PM_2.5 treatment reduced cell viability of primary rat corneal epithelial (RCE) cells, which was associated with the induction of apoptosis. PM_2.5 treatment also increased the generation of reactive oxygen species due to mitochondrial dysfunction. In addition, the production of nitric oxide and inflammatory cytokines was increased in PM_2.5-treated RCE cells. Furthermore, through heatmap analysis showing various expression profiling between PM_2.5-exposed and unexposed RCE cells, we proposed five genes, including BLNK, IL-1RA, Itga2b, ABCb1a and Ptgs2, as potential targets for clinical treatment of PM-related ocular diseases. These findings indicate that the primary RCE cell line is a useful in vitro model system for the study of PM_2.5-mediated pathological mechanisms and that PM2.5-induced oxidative and inflammatory responses are key factors in PM2.5-induced ocular surface disorders.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.235-243
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• 2023

As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling. With the significant advances in RNA-seq, various types of RNA-seq have evolved in conjunction with the progress in bioinformatic tools. On the other hand, it is difficult to interpret the complex data underlying the biological meaning without a general understanding of the types of RNA-seq and bioinformatic approaches. In this regard, this paper discusses the two main sections of RNA-seq. First, two major variants of RNA-seq are described and compared with the standard RNA-seq. This provides insights into which RNA-seq method is most appropriate for their research. Second, the most widely used RNA-seq data analyses are discussed: (1) exploratory data analysis and (2) pathway enrichment analysis. This paper introduces the most widely used exploratory data analysis for RNA-seq, such as principal component analysis, heatmap, and volcano plot, which can provide the overall trends in the dataset. The pathway enrichment analysis section introduces three generations of pathway enrichment analysis and how they generate enriched pathways with the RNA-seq dataset.

• Biomolecules & Therapeutics
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• v.30 no.1
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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.

• Food Science of Animal Resources
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• v.44 no.4
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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.

• Journal of Distribution Science
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• v.20 no.6
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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.

• Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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• v.40 no.3
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• pp.169-175
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• 2022

Korea's construction industry has a shortage and aging of construction manpower, low productivity compared to other industries, and a high rate of industrial accidents. The Ministry of Land, Infrastructure and Transport is preparing for the 4th industrial revolution and is expanding investment in construction automation and innovative growth engines to improve productivity in the construction industry. In order for new technologies to be utilized in the road construction field, the accuracy of the technologies and the applicability of each type of work must be evaluated. In this study, the accuracy of the mobile mapping system was tried to verify based on the relevant work regulations, and to suggest the applicability of the mobile mapping system to high-speed driving tracks through data acquisition and analysis on road construction sites. The accuracy of the equipment used in the study was verified in accordance with the relevant work regulations, and the possibility of applying the mobile mapping system used for the study to road construction surveying was presented with a maximum error of less than 10cm in the horizontal and vertical directions. In addition, the possibility of utilizing the road construction survey using the mobile mapping system was presented through comparison with the existing method for data acquisition time for construction surveying, production of construction status survey results, and calculation of heatmap and earthworks. In the future, the use of construction status surveying of the mobile mapping system will greatly improve the efficiency of construction work.

• Journal of the Korea Society of Computer and Information
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• v.21 no.5
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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.