• Title/Summary/Keyword: protein microarray

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GSnet: An Integrated Tool for Gene Set Analysis and Visualization

  • Choi, Yoon-Jeong;Woo, Hyun-Goo;Yu, Ung-Sik
    • Genomics & Informatics
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    • v.5 no.3
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    • pp.133-136
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    • 2007
  • The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

Effects of Baicalin on Gene Expression Profiles during Adipogenesis of 3T3-L1 Cells (3T3-L1 세포의 지방세포형성과정에서 Baicalin에 의한 유전자 발현 프로파일 분석)

  • Lee, Hae-Yong;Kang, Ryun-Hwa;Chung, Sang-In;Cho, Soo-Hyun;Yoon, Yoo-Sik
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.39 no.1
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    • pp.54-63
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    • 2010
  • Baicalin, a flavonoid, was shown to have diverse effects such as anti-inflammatory, anti-cancer, anti-viral, anti-bacterial and others. Recently, we found that the baicalin inhibits adipogenesis through the modulations of anti-adipogenic and pro-adipogenic factors of the adipogenesis pathway. In the present study, we further characterized the molecular mechanism of the anti-adipogenic effect of baicalin using microarray technology. Microarray analyses were conducted to analyze the gene expression profiles during the differentiation time course (0 day, 2 day, 4 day and 7 day) in 3T3-L1 cells with or without baicalin treatment. We identified a total of 3972 genes of which expressions were changed more than 2 fold. These 3972 genes were further analyzed using hierarchical clustering analysis, resulting in 20 clusters. Four clusters among 20 showed clearly up-regulated expression patterns (cluster 8 and cluster 10) or clearly down-regulated expression patterns (cluster 12 and cluster 14) by baicalin treatment for over-all differentiation period. The cluster 8 and cluster 10 included many genes which enhance cell proliferation or inhibit adipogenesis. On the other hand, the cluster 12 and cluster 14 included many genes which are related with proliferation inhibition, cell cycle arrest, cell growth suppression or adipogenesis induction. In conclusion, these data provide detailed information on the molecular mechanism of baicalin-induced inhibition of adipogenesis.

Gene Expression Profiles in Cervical Cancer with Radiation Therapy Alone and Chemo-radiation Therapy (자궁경부암의 방사선치료 및 방사선항암화학 병용치료에 따른 유전자발현 조절양상)

  • Lee Kyu Chan;Kim Meyoung-kon;Kim Jooyoung;Hwang You Jin;Choi Myung Sun;Kim Chul Yong
    • Radiation Oncology Journal
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    • v.21 no.1
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    • pp.54-65
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    • 2003
  • Purpose : To analyze the gene expression Profiles of uterine ceulcal cancer, and its variation after radiation therapy, with or without concurrent chemotherapy, using a CDNA microarray. Materials and Methods :Sixteen patients, 8 with squamous ceil carcinomas of the uterine cervix, who were treated with radiation alone, and the other 8 treated w14h concurrent chemo-radiation, were Included in the study. Before the starling of the treatment, tumor biopsies were carried out, and the second time biopsies were peformed after a radiation dose of 16.2$\~$27 Gy. Three normal cervix tissues were used as a control group. The microarray experiments were peformed with 5 groups of the total RNAs extracted individually and then admixed as control, pre-radiation therapy alone, during-radiation therapy alone, pre-chemoradiation therapy, and during-chemoradlation therapy. The 33P-iabeled CDNAS were synthesized from the total RNAs of each group, by reverse transcription, and then they were hybridized to the CDNA microarray membrane. The gene expression of each microarrays was captured by the intensity of each spot produced by the radioactive isotopes. The pixels per spot were counted with an Arrayguage, and were exported to Microsoft Excel The data were normalized by the Z transformation, and the comparisons were peformed on the Z-ratio values calculated. Results : The expressions of 15 genes, including integrin linked kinase (ILK), CDC28 protein kinase 2, Spry 2, and ERK 3, were increased with the Z-ratio values of over 2.0 for the cervix cancer tissues compared to those for the normal controls. Those genes were involved In cell growth and proliferation, cell cycle control, or signal transduction. The expressions of the other 6 genes, Including G protein coupled receptor kinase 5, were decreased with the Z-ratio values of below -2.0. After the radiation thorapy, most of the genes, with a previously Increase expressions, represented the decreased expression profiles, and the genes, with the Z-ratio values of over 2.0, were cyclic nucleotlde gated channel and 3 Expressed sequence tags (EST). In the concurrent chemo-radiation group, the genes involved in cell growth and proliferation, cell cycle control, and signal transduction were shown to have increased expressions compared to the radiation therapy alone group. The expressions of genes involved in anglogenesis (angiopoietln-2), immune reactions (formyl peptide receptor-iike 1), and DNA repair (CAMP phosphodiesterase) were increased, however, the expression of gene involved In apoptosls (death associated protein kinase) was decreased. Conclusion : The different kinds of genes involved in the development and progression of cervical cancer were identified with the CDNA microarray, and the proposed theory is that the proliferation signal stalls with ILK, and is amplified with Spry 2 and MAPK signaling, and the cellular mitoses are Increased with the increased expression oi Cdc 2 and cell division kinases. After the radiation therapy, the expression profiles demonstrated 4he evidence of the decreased cancer cell proliferation. There was no sigificant difference in the morphological findings of cell death between the radiation therapy aione and the chemo-radiation groups In the second time biopsy specimen, however, the gene expression profiles were markedly different, and the mechanism at the molecular level needs further study.

Polyhydroxyalkanoate Chip for the Specific Immobilization of Recombinant Proteins and Its Applications in Immunodiagnostics

  • Park, Tae-Jung;Park, Jong-Pil;Lee, Seok-Jae;Hong, Hyo-Jeong;Lee, Sang-Yup
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.11 no.2
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    • pp.173-177
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    • 2006
  • In this study, a novel strategy was developed for the highly selective immobilization of proteins, using the polyhydroxyalkanoate (PHA) depolymerase substrate binding domain (SBD) as an active binding domain. In order to determine the appropriacy of this method for immunodiagnostic assays, the single-chain antibody (ScFv) against the hepatitis B virus (HBV) preS2 surface protein and the severe acute respiratory syndrome coronavirus (SARS-CoV) envelope protein (SCVe) were fused to the SBD, then directly immobilized on PH A-coated slides via microspotting. The fluorescence-labeled HBV antigen and the antibody against SCVe were then utilized to examine specific interactions on the PHA-coated surfaces. Fluorescence signals were detected only at the spotted positions, thereby indicating a high degree of affinity and selectivity for their corresponding antigens/antibodies. Furthermore, we detected small amounts of ScFv-SBD (2.7 ng/mL) and SCVe-SBD fusion proteins (0.6ng/mL). Therefore, this microarray platform technology, using PHA and SBD, appears generally appropriate for immunodiagnosis, with no special requirements with regard to synthetic or chemical modification of the biomolecules or the solid surface.

Identification of prognosis-specific network and prediction for estrogen receptor-negative breast cancer using microarray data and PPI data (마이크로어레이 데이터와 PPI 데이터를 이용한 에스트로겐 수용체 음성 유방암 환자의 예후 특이 네트워크 식별 및 예후 예측)

  • Hwang, Youhyeon;Oh, Min;Yoon, Youngmi
    • Journal of the Korea Society of Computer and Information
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    • v.20 no.2
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    • pp.137-147
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    • 2015
  • This study proposes an algorithm for predicting breast cancer prognosis based on genetic network. We identify prognosis-specific network using gene expression data and PPI(protein-protein interaction) data. To acquire the network, we calculate Pearson's correlation coefficient(PCC) between genes in all PPI pairs using gene expression data. We develop a prediction model for breast cancer patients with estrogen-receptor-negative using the network as a classifier. We compare classification performance of our algorithm with existing algorithms on independent data and shows our algorithm is improved. In addition, we make an functionality analysis on the genes in the prognosis-specific network using GO(Gene Ontology) enrichment validation.

Evaluation of c-erbB2/neu Oncogene Status in Canine Mammary Tumors on Tissue Microarray

  • Kang, Jong-il;Cho, Ho-seong;A.W.M. Effendy;Park, Nam-yong
    • Proceedings of the Korean Society of Veterinary Pathology Conference
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    • 2003.10a
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    • pp.40-40
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    • 2003
  • The c-erbB2/neu oncogene (alias HER2, NEU) encoding a tyrosine kinase receptor protein, the overexpression of which correlates with a more rapid progression and a worse prognosis in human breast cancer [1]. Otherwise, this gene is still poorly investigated in veterinary oncology [2,3]. To gain insight into the patterns of c-erbB2/neu status in canine mammary tumor, we constructed one such mammary tumor tissue microarray (TMA) from 60 tumors from our lab. This enabled the amplification of c-erbB2/neu oncogene of all 60 tumors to be simultaneously analyzed by chromogenic in situ hybridization (CISH). The aim of this study was to evaluate status of c-erbB2/neu oncogene in canine mammary tumors and to correlate this status with the differentiation grade of neoplasm. (omitted)

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Proteomics-Driven Identification of SCO4677-Dependent Proteins in Streptomyces lividans and Streptomyces coelicolor

  • Choi, Si-Sun;Kim, Seon-Hye;Kim, Eung-Soo
    • Journal of Microbiology and Biotechnology
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    • v.20 no.3
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    • pp.480-484
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    • 2010
  • AfsR2 is a global regulatory protein that stimulates antibiotic biosynthesis in both Streptomyces lividans and S. coelicolor. Previously, various afsR2-dependent genes including a putative abaA-like regulatory gene, SCO4677, were identified through comparative DNA microarray analysis. To further identify the putative SCO4677-dependent proteins, the comparative proteomics-driven approach was applied to the SCO4677-overexpressing strains of S. lividans and S. coelicolor along with the wild-type strains. The 2D gel electrophoresis gave approximately 277 protein spots for S. lividans and 207 protein spots for S. coelicolor, showing different protein expression patterns between the SCO4677-overexpressing strains and the wild-type strains. Further MALDI-TOF analysis revealed that only 18 proteins exhibited similar expression patterns in both S. lividans and S. coelicolor, suggesting that the SCO4677 could encode an abaA-like regulator that controls a few cross-species common proteins as well as many species-specific proteins in Streptomyces species.

Gene Expression Analysis of Anticancer Drug Induced Hepatotoxicity Using cDNA Microarray

  • Lee, Gyoung-Jae;Kim, Yang-Suk;Jung, Jin-Wook;Hwang, Seung-Yong;Park, Joon-Suk;Kang, Kyung-Sun;Lee, Yong-Soon;Chon, Man-Suk;Chon, Kum-Jin;Kang, Jong-Soo;Kim, Dong-Hyean;Park, Young-Keun
    • Molecular & Cellular Toxicology
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    • v.2 no.2
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    • pp.141-149
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    • 2006
  • Tamoxifen (TAM), a non-steroidal anti estrogen anticancer drug and chemopreventive agent for breast cancer, have caused cholestasis in liver. The potent hepatocarcinogenicity of this drug has been reported. Methotrexate (MTX) is dihydrofolate reductase inhibitor which interfaces with the synthesis for urine nucleotide and dTMP. And it may cause atrophy, necrosis and steatosis in liver. These two anticancer drug have well-known hepatotoxicity. So, in this study we compare the gene expression pattern of antitumor agent TAM and MTX, using the cDNA microarray. We have used 4.8 K cDNA microarray to identify hepatotoxicity-related genes in 5-week-old male Sprague-Dawley (SD) rats. Confirm the pattern of gene expression, we have used Real time PCR for targeted gene. In the case of MTX, Protease related gene (Ctse, Ctsk) and Protein kinase (Pctk 1) have shown specific expression pattern. And in the case of TAM, apoptosis related gene (Pdcd 8) and signal transduction related gene (kdr) have significantly up regulated during treatment time. Gene related with growth factor, lipid synthesis, chemokins were significantly changed. From the result of this study, the information about influence of TAM and MTX to hepatoxicity will provide.

Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq

  • Chae, Songhwa;Kim, Joung Sug;Jun, Kyong Mi;Lee, Sang-Bok;Kim, Myung Soon;Nahm, Baek Hie;Kim, Yeon-Ki
    • Molecules and Cells
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    • v.40 no.10
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    • pp.714-730
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    • 2017
  • Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

The effect on gene expression profile of rat hippocampus caused by administration of memory enhancing herbal extract (육미지황탕가미방(六味地黃湯加味方)이 흰쥐의 기억능력과 중추신경계 유전자 발현에 미치는 영향)

  • Choi, Bo-Eop
    • Korean Journal of Oriental Medicine
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    • v.8 no.1
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    • pp.109-126
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    • 2002
  • The herbal extract (YMT_02) is a modified herbal extracts from Yukmijihwangtang (YMJ) to promote memory-enhancing. The YMJ extracts has been widely used as an anti-aging herbal medicine for hundred years in Asian countries. The purpose of this study is to; 1) quantitatively evaluate the memory-enhancing effect of YMT_02 by hehavior task, 2) identify candidate genes responsible for enhancing memory by cDNA microarray and 3) assess the anti-oxidant effect of YMT_02 on PC12 cell. Memory retention abilities are addressed by passive avoidance task with Sprague-Dawley (SD) male rat. Before the training session, the rats are subdivided into four groups and administrated with YMT_02, Ginkgo biloba, Soya lecithin and normal saline for 10 days. The retention test was performed. 24 hours after the training session. The retention time of the YMT_02 group was significantly (p<0.05) delayed $({\sim}100%)$, whereas Ginkgo biloba and Soya lecithin treatment delayed 20% and 10% respectively. The hippocampi of YMT_02 and control group were dissected and mRNA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied and mRNA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied to Incyte rat GEMTM 2 cDNA microarray. The microarray results show that prealbumin(transthyretin), phosphotidy lethanolamine N-methyltransferase, and PEP-19 are expressed abundantly in the YMT_02 treated group. Especially, PEP-19 is a neuron-specific protein, which inhibits apoptotic processes in neuronal cell. On the other hand, transcripts of RAB15, glutamate receptor subunit 2 and CDK 108 are abundant in control group. Besides, neuronal genes involved in neuronal death or neurodegeneration such as neuronal-pentraxin and spectrin are abundantly expressed in control group. Additionally, the YMT_02 shows an anti oxidative effect in the PC12 cell. The list of differentially expressed genes may implicate further insight on the action and mechanism behind the memory-enhancing effect of herbal extracts YMT_02, for example, anti-apoptotic, anti-oxidative, and neuroprotective effects.

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