• Genomics & Informatics
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• v.19 no.1
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• pp.4.1-4.9
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• 2021

Lip and oral cavity cancer, which can occur in any part of the mouth, is the 11th most common type of cancer worldwide. The major obstacles to patients' survival are the poor prognosis, lack of specific biomarkers, and expensive therapeutic alternatives. This study aimed to identify the main genes and pathways associated with lip and oral cavity carcinoma using network analysis and to analyze its molecular mechanism and prognostic significance further. In this study, 472 genes causing lip and oral cavity carcinoma were retrieved from the DisGeNET database. A protein-protein interaction network was developed for network analysis using the STRING database. VEGFA, IL6, MAPK3, INS, TNF, MAPK8, MMP9, CXCL8, EGF, and PTGS2 were recognized as network hub genes using the maximum clique centrality algorithm available in cytoHubba, and nine potential drug candidates (ranibizumab, siltuximab, sulindac, pomalidomide, dexrazoxane, endostatin, pamidronic acid, cetuximab, and apricoxib) for lip and oral cavity cancer were identified from the DGIdb database. Gene enrichment analysis was also performed to identify the gene ontology categorization of cellular components, biological processes, molecular functions, and biological pathways. The genes identified in this study could furnish a new understanding of the underlying molecular mechanisms of carcinogenesis and provide more reliable biomarkers for early diagnosis, prognostication, and treatment of lip and oral cavity cancer.

• Journal of Life Science
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• v.26 no.10
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• pp.1137-1152
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• 2016

Cells sense, respond, and adapt to a low oxygen environment called hypoxia, which is widely involved in a variety of human diseases. Adaptation to low oxygen concentrations includes gene expression changes by inducing hypoxic genes and reducing aerobic genes. Recently, the mitochondrial respiratory chain has been implicated in the control of these oxygen-regulated genes when cells experience hypoxia. In order to obtain an insight into an effect of the mitochondrial respiratory chain on cellular response to hyxpoxia, we here examined whole genome transcript signatures of respiration-proficient and respiration-deficient budding yeasts exposed to hypoxia using DNA microarrays. By comparing whole transcriptomes to hypoxia in respiration-proficient and respiration-deficient yeasts, we found that there are several classes of oxygen-regulated genes. Some of them require the mitochondrial respiratory chain for their expression under hypoxia while others do not. We found that the majority of hypoxic genes and aerobic genes need the mitochondrial respiratory chain for their expression under hypoxia. However, we also found that there are some hypoxic and aerobic genes whose expression under hypoxia is independent of the mitochondrial respiratory chain. These results indicate a key involvement of the mitochondrial respiratory chain in oxygen-regulated gene expression and multiple mechanisms for controlling oxygen-regulated gene expression. In addition, we provided gene ontology analyses and computational promoter analyses for hypoxic genes identified in the study. Together with differentially regulated genes under hypoxia, these post-analysis data will be useful resources for understanding the biology of response to hypoxia.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.871-884
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• 2009

Gene expression profiling is a useful tool for identifying critical genes and pathways in metabolism. The objective of this study was to determine the major differences in the expression of genes associated with metabolism and metabolic regulation in liver and mammary tissues of lactating cows. We used the Michigan State University bovine metabolism (BMET) microarray; previously, we have designed a bovine metabolism-focused microarray containing known genes of metabolic interest using publicly available genomic internet database resources. This is a high-density array of 70mer oligonucleotides representing 2,349 bovine genes. The expression of 922 genes was different at p<0.05, and 398 genes (17%) were differentially expressed by two-fold or more with 222 higher in liver and 176 higher in mammary tissue. Gene ontology categories with a high percentage of genes more highly expressed in liver than mammary tissues included carbohydrate metabolism (glycolysis, glucoenogenesis, propanoate metabolism, butanoate metabolism, electron carrier and donor activity), lipid metabolism (fatty acid oxidation, chylomicron/lipid transport, bile acid metabolism, cholesterol metabolism, steroid metabolism, ketone body formation), and amino acid/nitrogen metabolism (amino acid biosynthetic process, amino acid catabolic process, urea cycle, and glutathione metabolic process). Categories with more genes highly expressed in mammary than liver tissue included amino acid and sugar transporters and MAPK, Wnt, and JAK-STAT signaling pathways. Real-time PCR analysis showed consistent results with those of microarray analysis for all 12 genes tested. In conclusion, microarray analyses clearly identified differential gene expression profiles between hepatic and mammary tissues that are consistent with the differences in metabolism of these two tissues. This study enables understanding of the molecular basis of metabolic adaptation of the liver and mammary gland during lactation in bovine species.

• Korean Journal of Ichthyology
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• v.32 no.3
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• pp.117-129
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• 2020

The body color pattern in fish is a distinctive feature for species identification. The blass bloched rockfish Sebastes pachycephalus is a commercially important marine fish species, distributed in the central and southern parts of Korea and south Hokkaido of Japan. It has a morphological feature divided into four subspecies according to with or lacking distinct spots on the body surface, and to the location of markings on the body surface. However, the genetic basis of body color pattern of S. pachycephalus is still unknown. Thus we analyzed the transcriptome of S. pachycephalus skin samples using RNA-seq analysis to investigate functional genes related to body color patterns. The experimental skin samples were prepared by classified into 'Wild type' (lacking distinct spots and markings) and 'Color type' (with distinct spots and marking). Two skin sample transcriptomes were compared pairwise and the results revealed that were 164 differentially expressed unigenes in the skin samples of 'Wild type' and 'Color type'. Gene Ontology analysis of 164 differentially expressed unigenes showed that these genes were included in the functional group of molecular function (2 genes), biological process (46 genes), and cellular component (6 genes). There were several genes that body color type skin specific expression and the genes were CTL (Galactose-specific lectin nattectin), CUL1 (Cullin-1), CMAS (N-acylneuraminate cytidylyltransferase), NMRK2 (Nicotinamide riboside kinase 2), ALOXE3 (Hydroperoxide isomerase ALOXE3), SLC4A7 (sodium bicarbonate cotransporter 3). Our study is the first attempt to search for functional genes involved in the formation of body color patterns in S. pachycephalus. The differentially expressed unigenes obtained in this study can be used as candidate genes for functional gene study related to body coloration of fish.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.5-5
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• 2018

Ginseng (Panax ginseng C.A. Meyer), one of the most widely used medicinal plants in traditional oriental medicine, is used for the treatment of various diseases. It has been classified according to its cultivation environment, such as field cultivated ginseng (FCG) and mountain cultivated ginseng (MCG). However, little is known about differences in gene expression in ginseng roots between field cultivated and mountain cultivated ginseng. In order to investigate the whole transcriptome landscape of ginseng, we employed High-Throughput sequencing technologies using the Illumina HiSeqTM2500 system, and generated a large amount of sequenced transcriptome from ginseng roots. Approximately 77 million and 87 million high-quality reads were produced in the FCG and MCG roots transcriptome analyses, respectively, and we obtained 256,032 assembled unigenes with an average length of 1,171 bp by de novo assembly methods. Functional annotations of the unigenes were performed using sequence similarity comparisons against the following databases: the non-redundant nucleotide database, the InterPro domains database, the Gene Ontology Consortium database, and the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 4,207 unigenes were assigned to specific metabolic pathways, and all of the known enzymes involved in starch and sucrose metabolism pathways were also identified in the KEGG library. This study indicated that alpha-glucan phosphorylase 1, putative pectinesterase/pectinesterase inhibitor 17, beta-amylase, and alpha-glucan phosphorylase isozyme H might be important factors involved in starch and sucrose metabolism between FCG and MCG in different environments.

• Nutrition Research and Practice
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• v.14 no.4
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• pp.412-422
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• 2020

BACKGROUND/OBJECTIVES: This study investigates correlations between circulating microRNAs (miRNAs) and obesity-related parameters among young women (aged 20-30 years old) in Korea. SUBJECTS/METHODS: We analyzed TaqMan low density arrays (TLDAs) of circulating miRNAs in 9 lean (body mass index [BMI] < 25 kg/㎡) and 15 obese (BMI > 25 kg/㎡) women. We also performed gene ontology (GO) analyses of the biological functions of predicted miRNA target genes, and clustered the results using the database for annotation, visualization and integrated discovery. RESULTS: The TLDA cards contain 754 human miRNAs; of these, the levels of 8 circulating miRNAs significantly declined (> 2-fold) in obese subjects compared with those in lean subjects, including miR-1227, miR-144-5p, miR-192, miR-320, miR-320b, miR-484, miR-324-3p, and miR-378. Among them, miR-484 and miR-378 displayed the most significant inverse correlations with BMI (miR-484, r = -0.5484, P = 0.0056; miR-378, r = -0.5538, P = 0.0050) and visceral fat content (miR-484, r = -0.6141, P = 0.0014; miR-378, r = -0.6090, P = 0.0017). GO analysis indicated that genes targeted by miR-484 and miR-378 had major roles in carbohydrate and lipid metabolism. CONCLUSION: Our result showed the differentially expressed circulating miRNAs in obese subjects compared to lean subjects. Although the mechanistic study to reveal the causal role of miRNAs remains, these miRNAs may be novel biomarkers for obesity.

• Journal of KIISE:Computing Practices and Letters
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• v.15 no.5
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• pp.375-379
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• 2009

Protein domain is the conserved unit of compact tree-dimensional structure and evolution, which carries specific function. Domains may appear in patterns in proteins, since they have been conserved through the evolution for functional formation of proteins. In this paper, we propose a formulated method for conservation analysis of domain combination based on association rule. Proposed method measures mutual dependency of domains in a combination, as well as co-occurrence frequency of them, which is conventionally used. Based on the method, we extracted conserve domain combinations in S.cerevisiae proteins and analyzed their functions based on Gene Ontology. From the results, we drew conclusions that domains in S.cerevisiae proteins form patterns whose members are highly affiliated to one another, and that extracted patterns tend to be associated with molecular function. Moreover, the results testified to proposed method superior to conventional ones for identifying domain combinations conserved for functional cooperation.

• Genes and Genomics
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• v.40 no.12
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• Journal of Acupuncture Research
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• v.37 no.2
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• pp.128-135
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• 2020

Background: Classical acupuncture is being used in the treatment of rheumatoid arthritis (RA). To explore the biological response to acupuncture, a network-based analysis was performed on gene expression data collected from an animal model of RA treated with acupuncture. Methods: Gene expression data were obtained from published microarray studies on blood samples from rats with collagen induced arthritis (CIA) and non-CIA rats, both treated with manual acupuncture. The weighted gene co-expression network analysis was performed to identify gene clusters expressed in association with acupuncture treatment time and RA status. Gene ontology and pathway analyses were applied for functional annotation and network visualization. Results: A cluster of 347 genes were identified that differentially downregulated expression in association with acupuncture treatment over time; specifically in rats with CIA with module-RA correlation at 1 hour after acupuncture (-0.27; p < 0.001) and at 34 days after acupuncture (-0.33; p < 0.001). Functional annotation showed highly significant enrichment of porphyrin-containing compound biosynthetic processes (p < 0.001). The network-based analysis also identified a module of 140 genes differentially expressed between CIA and non-CIA in rats (p < 0.001). This cluster of genes was enriched for antigen processing and presentation of exogenous peptide antigen (p < 0.001). Other functional gene clusters previously reported in earlier studies were also observed. Conclusion: The identified gene expression networks and their hub-genes could help with the understanding of mechanisms involved in the pathogenesis of RA, as well understanding the effects of acupuncture treatment of RA.

• Biomedical Science Letters
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• v.18 no.3
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• pp.313-318
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• 2012

Acanthamoeba is an opportunistic pathogen known to cause granulomatous amoebic encephalitis and amebic keratitis. Acanthamoeba exhibits life cycle consisting of trophozoite and cyst, and the cyst is highly resistant to variable antibiotics and therapeutic agents. To understand the encystation mechanism of Acanthamoeba, the expression profiles of trophozoite and cyst were compared by gene ontology (GO) analysis. Ribosomal proteins and cytoskeletal proteins were highly expressed in trophozoite. In cyst, various protease, and signal transduction - and protein turnover - related proteins were highly expressed. These results correlated with eukaryotic orthologous groups (KOG) assignment and microarray analysis of Acanthamoeba trophozoite and cyst ESTs. The information of differential expression profiles of trophozoite and cyst would provide important clues for research on encystation mechanism of cyst forming protozoa including Acanthamoeba.