• Title/Summary/Keyword: Integrated omics

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Visualization for Integrated Analysis of Multi-Omics Data by Harmful Substances Exposed to Human (인체 유래 환경유해물질 노출에 따른 멀티 오믹스 데이터 통합 분석 가시화 시스템)

  • Shin, Ga-Hee;Hong, Ji-Man;Park, Seo-Woo;Kang, Byeong-Chul;Lee, Bong-Mun
    • Journal of Korea Multimedia Society
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    • v.25 no.2
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    • pp.363-373
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    • 2022
  • Multi-omics data is difficult to interpret due to the heterogeneity of information by the volume of data, the complexity of characteristics of each data, and the diversity of omics platforms. There is not yet a system for interpreting to visualize research data on environmental diseases concerning environmental harmful substances. We provide MEE, a web-based visualization tool, to comprehensively explore the complexity of data due to the interconnected characteristics of high-dimensional data sets according to exposure to various environmental harmful substances. MEE visualizes omics data of correlation between omics data, subjects and samples by keyword searches of meta data, multi-omics data, and harmful substances. MEE has been demonstrated the versatility by two examples. We confirmed the correlation between smoking and asthma with RNA-seq and Methylation-Chip data, it was visualized that genes (P HACTR3, PXDN, QZMB, SOCS3 etc.) significantly related to autoimmune or inflammatory diseases. To visualize the correlation between atopic dermatitis and heavy metals, we selected 32 genes related immune response by integrated analysis of multi-omics data. However, it did not show a significant correlation between mercury in blood and atopic dermatitis. In the future, should continuously collect an appropriate level of multi-omics data in MEE system, will obtain data to analyze environmental substances and diseases.

Classification of Colon Cancer Patients Based on the Methylation Patterns of Promoters

  • Choi, Wonyoung;Lee, Jungwoo;Lee, Jin-Young;Lee, Sun-Min;Kim, Da-Won;Kim, Young-Joon
    • Genomics & Informatics
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    • v.14 no.2
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    • pp.46-52
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    • 2016
  • Diverse somatic mutations have been reported to serve as cancer drivers. Recently, it has also been reported that epigenetic regulation is closely related to cancer development. However, the effect of epigenetic changes on cancer is still elusive. In this study, we analyzed DNA methylation data on colon cancer taken from The Caner Genome Atlas. We found that several promoters were significantly hypermethylated in colon cancer patients. Through clustering analysis of differentially methylated DNA regions, we were able to define subgroups of patients and observed clinical features associated with each subgroup. In addition, we analyzed the functional ontology of aberrantly methylated genes and identified the G-protein-coupled receptor signaling pathway as one of the major pathways affected epigenetically. In conclusion, our analysis shows the possibility of characterizing the clinical features of colon cancer subgroups based on DNA methylation patterns and provides lists of important genes and pathways possibly involved in colon cancer development.

ZNF204P is a stemness-associated oncogenic long non-coding RNA in hepatocellular carcinoma

  • Hwang, Ji-Hyun;Lee, Jungwoo;Choi, Won-Young;Kim, Min-Jung;Lee, Jiyeon;Chu, Khanh Hoang Bao;Kim, Lark Kyun;Kim, Young-Joon
    • BMB Reports
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    • v.55 no.6
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    • pp.281-286
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    • 2022
  • Hepatocellular carcinoma is a major health burden, and though various treatments through much research are available, difficulties in early diagnosis and drug resistance to chemotherapy-based treatments render several ineffective. Cancer stem cell model has been used to explain formation of heterogeneous cell population within tumor mass, which is one of the underlying causes of high recurrence rate and acquired chemoresistance, highlighting the importance of CSC identification and understanding the molecular mechanisms of CSC drivers. Extracellular CSC-markers such as CD133, CD90 and EpCAM have been used successfully in CSC isolation, but studies have indicated that increasingly complex combinations are required for accurate identification. Pseudogene-derived long non-coding RNAs are useful candidates as intracellular CSC markers - factors that regulate pluripotency and self-renewal - given their cancer-specific expression and versatile regulation across several levels. Here, we present the use of microarray data to identify stemness-associated factors in liver cancer, and selection of sole pseudogene-derived lncRNA ZNF204P for experimental validation. ZNF204P knockdown impairs cell proliferation and migration/invasion. As the cytosolic ZNF204P shares miRNA binding sites with OCT4 and SOX2, well-known drivers of pluripotency and self-renewal, we propose that ZNF204P promotes tumorigenesis through the miRNA-145-5p/OCT4, SOX2 axis.

SOP (Search of Omics Pathway): A Web-based Tool for Visualization of KEGG Pathway Diagrams of Omics Data

  • Kim, Jun-Sub;Yeom, Hye-Jung;Kim, Seung-Jun;Kim, Ji-Hoon;Park, Hye-Won;Oh, Moon-Ju;Hwang, Seung-Yong
    • Molecular & Cellular Toxicology
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    • v.3 no.3
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    • pp.208-213
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    • 2007
  • With the help of a development and popularization of microarray technology that enable to us to simultaneously investigate the expression pattern of thousands of genes, the toxicogenomics experimenters can interpret the genome-scale interaction between genes exposed in toxicant or toxicant-related environment. The ultimate and primary goal of toxicogenomics identifies functional context among the group of genes that are differentially or similarly coexpressed under the specific toxic substance. On the other side, public reference databases with transcriptom, proteom, and biological pathway information are needed for the analysis of these complex omics data. However, due to the heterogeneous and independent nature of these databases, it is hard to individually analyze a large omics annotations and their pathway information. Fortunately, several web sites of the public database provide information linked to other. Nevertheless it involves not only approriate information but also unnecessary information to users. Therefore, the systematically integrated database that is suitable to a demand of experimenters is needed. For these reasons, we propose SOP (Search of Omics Pathway) database system which is constructed as the integrated biological database converting heterogeneous feature of public databases into combined feature. In addition, SOP offers user-friendly web interfaces which enable users to submit gene queries for biological interpretation of gene lists derived from omics experiments. Outputs of SOP web interface are supported as the omics annotation table and the visualized pathway maps of KEGG PATHWAY database. We believe that SOP will appear as a helpful tool to perform biological interpretation of genes or proteins traced to omics experiments, lead to new discoveries from their pathway analysis, and design new hypothesis for a next toxicogenomics experiments.

Multi-Omics Approaches to Improve Meat Quality and Taste Characteristics

  • Young-Hwa Hwang;Eun-Yeong Lee;Hyen-Tae Lim;Seon-Tea Joo
    • Food Science of Animal Resources
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    • v.43 no.6
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    • pp.1067-1086
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    • 2023
  • With rapid advances in meat science in recent decades, changes in meat quality during the pre-slaughter phase of muscle growth and the post-slaughter process from muscle to meat have been investigated. Commonly used techniques have evolved from early physicochemical indicators such as meat color, tenderness, water holding capacity, flavor, and pH to various omic tools such as genomics, transcriptomics, proteomics, and metabolomics to explore fundamental molecular mechanisms and screen biomarkers related to meat quality and taste characteristics. This review highlights the application of omics and integrated multi-omics in meat quality and taste characteristics studies. It also discusses challenges and future perspectives of multi-omics technology to improve meat quality and taste. Consequently, multi-omics techniques can elucidate the molecular mechanisms responsible for changes of meat quality at transcriptome, proteome, and metabolome levels. In addition, the application of multi-omics technology has great potential for exploring and identifying biomarkers for meat quality and quality control that can make it easier to optimize production processes in the meat industry.

Integration of metabolomics and transcriptomics in nanotoxicity studies

  • Shin, Tae Hwan;Lee, Da Yeon;Lee, Hyeon-Seong;Park, Hyung Jin;Jin, Moon Suk;Paik, Man-Jeong;Manavalan, Balachandran;Mo, Jung-Soon;Lee, Gwang
    • BMB Reports
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    • v.51 no.1
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    • pp.14-20
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    • 2018
  • Biomedical research involving nanoparticles has produced useful products with medical applications. However, the potential toxicity of nanoparticles in biofluids, cells, tissues, and organisms is a major challenge. The '-omics' analyses provide molecular profiles of multifactorial biological systems instead of focusing on a single molecule. The 'omics' approaches are necessary to evaluate nanotoxicity because classical methods for the detection of nanotoxicity have limited ability in detecting miniscule variations within a cell and do not accurately reflect the actual levels of nanotoxicity. In addition, the 'omics' approaches allow analyses of in-depth changes and compensate for the differences associated with high-throughput technologies between actual nanotoxicity and results from traditional cytotoxic evaluations. However, compared with a single omics approach, integrated omics provides precise and sensitive information by integrating complex biological conditions. Thus, these technologies contribute to extended safety evaluations of nanotoxicity and allow the accurate diagnoses of diseases far earlier than was once possible in the nanotechnology era. Here, we review a novel approach for evaluating nanotoxicity by integrating metabolomics with metabolomic profiling and transcriptomics, which is termed "metabotranscriptomics."

Quantitative and Comparative Analysis of Urinary Steroid Levels upon Treatment of an Anti-Diabetic Drug, CKD-501 using Gas Chromatography-Mass Spectrometry

  • Sadanala, Krishna Chaitanya;Jung, Byung-Hwa;Jang, In-Jin;Chung, Bong-Chul
    • Journal of Pharmaceutical Investigation
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    • v.41 no.1
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    • pp.37-43
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    • 2011
  • Urinary steroid levels were investigated in the treatment of CKD-501, a new anti-diabetic drug candidate. CKD-501 was administered orally at the dosage of 1, 2, 4 mg/day for 7 days to normal men (n=18). Urine was collected before, during and after stopping the drug administration and the urinary level of androgen, estrogen, progestin and corticoids were quantified using GC-MS (gas chromatography-mass spectrometry). Only urinary corticosteroid and an androgen, DHEA levels among all the analyzed steroids, have been found to increase progressively, reaching significant levels on the last day of drug treatment and later declined after the drug treatment is withdrawn. Therefore, it was thought that an increase in the urinary corticoid and DHEA levels could be a characteristic of CKD-501, since it prominently acts on the glucose sensitivity and suppresses the triglyceride levels. In conclusion, it was found that CKD-501, an anti-diabetic drug candidate, affects the glucocorticoid and DHEA levels and it plays a crucial role in glucose homeostasis.

Simultaneous Determination of Valproic Acid and its Toxic Metabolites, 4-ene-VPA and 2,4-diene-VPA in Rat Plasma using a Gas Chromatographic-mass Spectrometric Method

  • Lee, Min-Sun;Lee, Young-Joo;Chung, Bong-Chul;Jung, Byung-Hwa
    • Journal of Pharmaceutical Investigation
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    • v.40 no.3
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    • pp.155-160
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    • 2010
  • A gas chromatographic-mass spectrometric (GC-MS) method was developed for the simultaneous determination of valproic acid (VPA) and its toxic metabolites, 4-ene-VPA and 2,4-diene-VPA in rat plasma. Extraction was performed in weak acidic condition (pH 5.2) to avoid degradation of 4-ene-VPA and 2,4-diene-VPA. The recoveries for 4-ene-VPA and 2,4-diene-VPA were more than 70% and that for VPA was 33-42%. R value for each compounds exceeded 0.998 in calibration curve during all the analysis. Accuracy and precision ranged from 88.3 to 113.2% and from 2.16 to 14.2%, respectively The method was successfully applied to monitor plasma concentrations of VPA, 4-ene-VPA and 2,4-diene-VPA after intravenous administration of VPA at the dose of 100 mg/kg, suggesting that these toxic metabolites may involved in the hepatotoxicity induced by VPA.

Mutation of the lbp-5 gene alters metabolic output in Caenorhabditis elegans

  • Xu, Mo;Choi, Eun-Young;Paik, Young-Ki
    • BMB Reports
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    • v.47 no.1
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    • pp.15-20
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    • 2014
  • Intracellular lipid-binding proteins (LBPs) impact fatty acid homeostasis in various ways, including fatty acid transport into mitochondria. However, the physiological consequences caused by mutations in genes encoding LBPs remain largely uncharacterized. Here, we explore the metabolic consequences of lbp-5 gene deficiency in terms of energy homeostasis in Caenorhabditis elegans. In addition to increased fat storage, which has previously been reported, deletion of lbp-5 attenuated mitochondrial membrane potential and increased reactive oxygen species levels. Biochemical measurement coupled to proteomic analysis of the lbp-5(tm1618) mutant revealed highly increased rates of glycolysis in this mutant. These differential expression profile data support a novel metabolic adaptation of C. elegans, in which glycolysis is activated to compensate for the energy shortage due to the insufficient mitochondrial ${\beta}$-oxidation of fatty acids in lbp-5 mutant worms. This report marks the first demonstration of a unique metabolic adaptation that is a consequence of LBP-5 deficiency in C. elegans.