• Title, Summary, Keyword: differentially expressed genes

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Screening of Differentially Expressed Genes Related to Bladder Cancer and Functional Analysis with DNA Microarray

  • Huang, Yi-Dong;Shan, Wei;Zeng, Li;Wu, Yang
    • 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.

Regulatory Network of MicroRNAs, Target Genes, Transcription Factors and Host Genes in Endometrial Cancer

  • Xue, Lu-Chen;Xu, Zhi-Wen;Wang, Kun-Hao;Wang, Ning;Zhang, Xiao-Xu;Wang, Shang
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.2
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    • pp.475-483
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    • 2015
  • Genes and microRNAs (miRNAs) have important roles in human oncology. However, most of the biological factors are reported in disperse form which makes it hard to discover the pathology. In this study, genes and miRNAs involved in human endometrial cancer(EC) were collected and formed into regulatory networks following their interactive relations, including miRNAs targeting genes, transcription factors (TFs) regulating miRNAs and miRNAs included in their host genes. Networks are constructed hierarchically at three levels: differentially expressed, related and global. Among the three, the differentially expressed network is the most important and fundamental network that contains the key genes and miRNAs in EC. The target genes, TFs and miRNAs are differentially expressed in EC so that any mutation in them may impact on EC development. Some key pathways in networks were highlighted to analyze how they interactively influence other factors and carcinogenesis. Upstream and downstream pathways of the differentially expressed genes and miRNAs were compared and analyzed. The purpose of this study was to partially reveal the deep regulatory mechanisms in EC using a new method that combines comprehensive genes and miRNAs together with their relationships. It may contribute to cancer prevention and gene therapy of EC.

Identification of Differentially Expressed Genes by Exposure of Methylmercury in Neuroblastoma Cell Line Using Suppression Subtractive Hybridization (SSH)

  • Kim, Youn-Jung;Ryu, Jae-Chun
    • 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.

Differential Gene Expression in the Pathogenic Strains of Actinobacillus pleuropneumoniae Serotypes 1 and 3

  • Xie, Fang;Zhang, Mingjun;Li, Shuqing;Du, Chongtao;Sun, Changjiang;Han, Wenyu;Zhou, Liang;Lei, Liancheng
    • Journal of Microbiology and Biotechnology
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    • v.20 no.4
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    • pp.789-797
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    • 2010
  • The limited information on differential gene expression in the different serotypes of Actinobacillus pleuropneumoniae has significantly hampered the research on the pathogenic mechanisms of this organism and the development of multivalent vaccines against A. pleuropneumoniae infection. To compare the gene expressions in the A. pleuropneumoniae strains CVCC259 (serotype 1) and CVCC261 (serotype 3), we screened the differentially expressed genes in the two strains by performing representational difference analysis (RDA). Northern blot analyses were used to confirm the results of RDA. We identified 22 differentially expressed genes in the CVCC259 strain and 20 differentially expressed genes in the CVCC261 strain, and these genes were classified into 11 groups: (1) genes encoding APX toxins; (2) genes encoding transferrin-binding protein; (3) genes involved in lipopolysaccharide (LPS) biosynthesis; (4) genes encoding autotransporter adhesin; (5) genes involved in metabolism; (6) genes involved in the ATP-binding cassette (ABC) transporter system; (7) genes encoding molecular chaperones; (8) genes involved in bacterial transcription and nucleic acid metabolism; (9) a gene encoding protease; (10) genes encoding lipoprotein/membrane protein; and (11) genes encoding various hypothetical proteins. This is the first report on the systematic application of RDA for the analysis of differential gene expression in A. pleuropneumoniae serotypes 1 and 3. The determination of these differentially expressed genes will serve as an indicator for future research on the pathogenic mechanisms of A. pleuropneumoniae and the development of a multivalent vaccine against A. pleuropneumoniae infection.

Profiling of Differentially Expressed Genes in Human Cervical Carcinoma

  • Lee, Seung-Hoon;Shim, Chan-Sub;Lee, Je-Ho
    • Animal cells and systems
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    • v.13 no.4
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    • pp.381-389
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    • 2009
  • Using the DDRT-PCR, a series of differentially expressed genes in human primary cervical cancer was isolated. Among the 250 PCR amplimers, 88 gene fragments were confirmed by reverse Northern hybridization. Homology searches indicated that 26 out of 88 were previously known genes including calmodulin, human BBC1, histone H3.3, a series of ribosomal proteins (RPL19, RPS19, and RPS12), translation initiation factor (eIF-4AI), lactoferrin, integrin ${\alpha}6$, cell-surface antigens (CD9 and CD59), transcription factor (mbp-1), and mitochondrial proteins. Several unknown clones showed sequence homology with known genes. Furthermore, six of the unknown genes showed identical sequence with expressed sequence tags (EST) of unknown function. Differential expression patterns of identified genes were further examined and confirmed with multiple pairs of cervical cancer samples using Northern hybridization. Our profiling of differentially expressed genes may provide useful information about the underlying genetic alterations in human cervical carcinoma and diagnostic markers for this disease. The precise roles of these genes in cancer development remain to be elucidated.

Detection of Differentially Expressed Genes by Clustering Genes Using Class-Wise Averaged Data in Microarray Data

  • Kim, Seung-Gu
    • 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.

Identification of differentially expressed genes using an annealing control primer system in periodontitis

  • Na, Hee-Sam;Kim, Ji-S.;Chung, Jin
    • 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.

Cloning and Identification of Differentially Expressed Genes Induced by Fungal Infection from Silkworm, Bombyx mori (누에에서 곰팡이(Aspergillus niger) 감염에 의해 유도 발현되는 유전자의 클로닝과 동정)

  • Lee, Jin-Sung;Hong, Su-Young;Lee, Ki-Hwa
    • Journal of Life Science
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    • v.20 no.6
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    • pp.929-933
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    • 2010
  • We tried to identify differentially expressed genes (DEGs) from a silkworm, Bombyx mori, involved in fungal (Aspergillus niger) infection. A total RNA purified from fungal-induced and normal B. mori ($5^{th}$ instar larvae) was used for the cDNA synthesis. Differentially expressed genes were screened by annealing control primer (ACP)-based PCR technique. Comparing the gene expression profiles between fungal infection and control silkworm, we detected 10 genes that were differentially expressed in fungal induction and performed molecular cloning and nucleotide sequencing of the 10 genes. We confirmed the expression patterns of 3 DEGs by RT-PCR. The 3 DEGs over-expressed in fungal infection were identified as lysozyme, enbocin and an unknown gene. They were first identified to be genes induced by fungal infection. Although the detailed functions of 3 genes and their products remain to be determined, the genes will provide insight into the molecular mechanisms of insect-immune systems induced by fungal infection.

Identification of Differentially Expressed Genes in Human Mesenchymal Stem Cell-Derived Neurons

  • Heo, Ji-Hye;Cho, Kyung-Jin;Choi, Dal-Woong;Kim, Suhng-Wook
    • Toxicological Research
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    • v.26 no.1
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    • pp.15-19
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    • 2010
  • Mesenchymal stem cells (MSCs) have greater potential for immediate clinical and toxicological applications, due to their ability to self-renew, proliferate, and differentiate into a variety of cell types. To identify novel candidate genes that were specifically expressed during transdifferentiation of human MSCs to neuronal cells, we performed a differential expression analysis with random priming approach using annealing control primer-based differential display reverse transcription-polymerase chain reaction approach. We identified genes for acyl-CoA thioesterase, tissue inhibitor of metalloproteinases-1, brain glycogen phosphorylase, ubiquitin C-terminal hydrolase and aldehyde reductase were up-regualted, whereas genes for transgelin and heparan sulfate proteoglycan were down-regulated in MSC-derived neurons. These differentially expressed genes may have potential role in regulation of neurogenesis. This study could be applied to environmental toxicology in the field of testing the toxicity of a chemical or a physical agent.

Identification of Differentially Expressed Genes Between Preadipocytes and Adipocytes Using Affymetrix Bovine Genome Array

  • Yu, Seong-Lan;Lee, Sang-Mi;Kang, Man-Jong;Jeong, Hang-Jin;Sang, Byung-Chan;Jeon, Jin-Tae;Lee, Jun-Heon
    • 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.