• Journal of Applied Biological Chemistry
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• v.58 no.4
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• pp.355-361
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• 2015

The rice protein profiles of Oryza sativa L (Koshihikari) grown under organic and conventional cultivation regimes were compared on 2-D gels to develop diagnostic marker proteins for organic rice. The selected proteins, differentially expressed between organic and conventional rice, were compared with the differentially expressed proteins of another organic and conventional rice pairing, produced at a different location. In the first comparison among conventional, no-chemical, and organic rice grown in the same region, Korea, 13 proteins exhibiting differential expression in organic and conventionally grown plants were selected. Eight of the 13 proteins were down-regulated, and the 5 remaining proteins were up-regulated from conventional to organic rice. The second comparison pairing from Kyungju, revealed 12 differentially expressed proteins, with 8 down-regulated and 4 up-regulated proteins. Ten of the differentially expressed proteins that overlapped between the two comparison sets could not be clustered into any functional group using a functional annotation clustering tool. Further comparisons using another set of conventional and organic rice, belonging to a different variety of Oryza sativa L and produced in Sanchung, revealed 8 differentially expressed proteins, 5 of which were down-regulated and 3 of which were upregulated in the organic rice. Overall, 3 differentially expressed proteins were commonly found in all three organic rice crops. These 3 proteins, along with other overlapping differentially expressed proteins, can provide a good starting point for the development of signature proteins that can be used for the authentication of organic rice with a follow-up studies with more comparison sets.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4553-4557
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• 2013

Objective: The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. Methods: After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. Results: A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. Conclusion: We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.

• Molecular & Cellular Toxicology
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• v.2 no.1
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• pp.60-66
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• 2006

Methylmercury (MeHg), one of the heavy metal compounds, can cause severe damage to the central nervous system in humans. Many reports have shown that MeHg is poisonous to human body through contaminated foods and has released into the environment. Despite many studies on the pathogenesis of MeHg-induced central neuropathy, no useful mechanism of toxicity has been established so far. This study, using of suppression subtractive hybridization (SSH) method, was peformed to identify differentially expressed genes by MeHg in SH-SY5Y human neuroblastoma cell line. We prepared to total RNA from SH-SY5Y cells treated with solvent (DMSO) and $6.25\;{\mu}M\;(IC_{50})$ MeHg and performed forward and reverse SSH. Differentially expressed cDNA clones were screened by dot blot, sequenced and confirmed that individual clones indeed represent differentially expressed genes with real time RT-PCR. These sequences were identified by BLAST homology search to known genes or expressed sequence tags (ESTs). Analysis of these sequences may provide an insight into the biological effects of MeHg in the pathogenesis of neurodegenerative disease and a possibility to develop more efficient and exact monitoring system of heavy metals as ubiquitous environmental pollutants.

• Communications for Statistical Applications and Methods
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• v.14 no.3
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• pp.687-698
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• 2007

A normal mixture model with which dependence between classes is incorporated is proposed in order to detect differentially expressed genes. Gene clustering approaches suffer from the high dimensional column of microarray expression data matrix which leads to the over-fit problem. Various methods are proposed to solve the problem. In this paper, use of simple averaging data within each class is proposed to overcome the various problems due to high dimensionality when the normal mixture model is fitted. Some experiments through simulated data set and real data set show its availability in actuality.

• International Journal of Oral Biology
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• v.37 no.3
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• pp.109-114
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• 2012

In the gingival tissues of patients with periodontitis, inflammatory responses are mediated by a wide variety of genes. In this study, we screened for differentially expressed genes (DEGs) in periodontitis compared with normal tissue using an annealing control primer (ACP) system. By ACP RT-PCR analysis, we obtained about 160 amplicons, 8 of which were found to be differentially expressed. DEGs in patients with periodontitis were thus successfully and reliably identified by the ACP-based RT PCR technique. The DEGs identified in the screen may also enhance our understanding of the pathogenesis of periodontitis.

• Journal of Animal Science and Technology
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• v.51 no.6
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• pp.443-452
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• 2009

Adipocytes are differentiated from preadipocytes and have large capacity for storing fats inside cells. In cattle, intramuscular fat (IMF) content is one of the major determinants for meat quality and also highly affects market prices, especially in Japan and Korea. In order to profiling differentially expressed genes between intramuscular fibroblast-like cells (preadipocytes) and their differentiated adipocytes, we have established intramuscular fibroblast-like cells from M. longissimus thoracis in Korean cattle (Hanwoo). The differentially expressed genes were selected by comparing these two types of cells ug thecommercially available 23kese two types of cells ug theco. The results indan ced that 206 arecomelements were differentially expressed. Of these, 67 and 94 ks wn genes were up and d wn regulaced, respectively, in adipocytes ug ng both 2-fold difference and Welch's t-test as the cut-off points. The differentially expressed genes identified in this study can be used as good markers for improving meat quality traits with further verification of their biological functions, especially IMF contents in cattle.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7645-7652
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• 2014

Neuroblastoma (NB), the most common extracranial solid tumor, accounts for 10% of childhood cancer. To date, scientists have gained quite a lot of knowledge about microRNAs (miRNAs) and their genes in NB. Discovering inner regulation networks, however, still presents problems. Our study was focused on determining differentially-expressed miRNAs, their target genes and transcription factors (TFs) which exert profound influence on the pathogenesis of NB. Here we constructed three regulatory networks: differentially-expressed, related and global. We compared and analyzed the differences between the three networks to distinguish key pathways and significant nodes. Certain pathways demonstrated specific features. The differentially-expressed network consists of already identified differentially-expressed genes, miRNAs and their host genes. With this network, we can clearly see how pathways of differentially expressed genes, differentially expressed miRNAs and TFs affect on the progression of NB. MYCN, for example, which is a mutated gene of NB, is targeted by hsa-miR-29a and hsa-miR-34a, and regulates another eight differentially-expressed miRNAs that target genes VEGFA, BCL2, REL2 and so on. Further related genes and miRNAs were obtained to construct the related network and it was observed that a miRNA and its target gene exhibit special features. Hsa-miR-34a, for example, targets gene MYC, which regulates hsa-miR-34a in turn. This forms a self-adaption association. TFs like MYC and PTEN having six types of adjacent nodes and other classes of TFs investigated really can help to demonstrate that TFs affect pathways through expressions of significant miRNAs involved in the pathogenesis of NB. The present study providing comprehensive data partially reveals the mechanism of NB and should facilitate future studies to gain more significant and related data results for NB.

• BMB Reports
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• v.48 no.1
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• pp.19-24
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• 2015

A mouse homozygous for the spontaneous mutation uncovered (Uncv) has a hairless phenotype. A 309-bp non-frameshift deletion mutation in the N-terminal cytoplasmic domain of iRhom2 was identified in Uncv mice ($iRhom2^{Uncv}$) using target region sequencing. The detailed molecular basis for how the iRhom2 mutation causes the hairless phenotype observed in the homozygous $iRhom2^{Uncv}$ mouse remains unknown. To identify differentially expressed proteins in the skin of wild-type and homozygous $iRhom2^{Uncv}$ littermates at postnatal day 5, proteomic approaches, including two-dimensional gel electrophoresis and mass spectrometry were used. Twelve proteins were differentially expressed in the skin in a comparison between wild-type and homozygous $iRhom2^{Uncv}$ mice. A selection of the proteomic results were tested and verified using qRT-PCR, western blot and immunohistochemistry. These data indicate that differentially expressed proteins, especially KRT73, MEMO1 and Coro-1, might participate in the mechanism by which iRhom2 regulates the development of murine skin.

• Genomics & Informatics
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• v.3 no.1
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• pp.30-34
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• 2005

Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-stap-analysis with suitable statistical significances. We present a supervised model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are trying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful structure from microarray datasets.

• The Plant Pathology Journal
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• v.25 no.2
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• pp.184-188
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• 2009

Identification of differently expressed genes under specific tissues and/or environments provides insights into the nature and underlying mechanisms of cellular processes. Although cDNA-AFLP (Amplified Fragment Length Polymorphism) is a powerful method for analyzing differentially expressed genes, its use has been limited to the requirement of radioactive isotope use and the difficulty of isolating the bands of interest from a gel. Here, we describe a modified method for cDNA-AFLP that uses a fluorescence dye for detection and isolation of bands directly from a small size polyacrylamide gel. This method involves three steps: (i) preparation of cDNA templates, (ii) PCR amplification and differential display, and (iii) identification of differentially expressed genes. To demonstrate its utility and efficiency, differentially expressed genes during vegetative growth and appressorial development of Magnaporthe oryzae were analyzed. This method could be applied to compare gene expression profiles in a diverse array of organisms.