• Title/Summary/Keyword: DNA microarray techniques

Search Result 29, Processing Time 0.025 seconds

Proteomic Application in Cell Biology (세포생물학과 Proteomics 응용)

  • 김동욱
    • Korean Journal of Microbiology
    • /
    • v.37 no.2
    • /
    • pp.109-113
    • /
    • 2001
  • As the complete genomic sequences accumulate, the use of global techniques became possible. DNA microarray is a powerful technology for measuring global mRNA levels. This method, however, does not provide information on post-translational modifications of proteins. In addition, mRNA levels do not strictly correlate with protein concentrations, especially for lower-abundance proteins. Therefore, studies at the level of transcription are not sufficient to understand cellular activity. Proteomic techniques to analyze protein expression and function at the large-scale have been developed and used. This review introduces a simple explanation for proteomic analysis and examples of how proteomics is applied in cell biology.

  • PDF

Standard-based Integration of Heterogeneous Large-scale DNA Microarray Data for Improving Reusability

  • Jung, Yong;Seo, Hwa-Jeong;Park, Yu-Rang;Kim, Ji-Hun;Bien, Sang Jay;Kim, Ju-Han
    • Genomics & Informatics
    • /
    • v.9 no.1
    • /
    • pp.19-27
    • /
    • 2011
  • Gene Expression Omnibus (GEO) has kept the largest amount of gene-expression microarray data that have grown exponentially. Microarray data in GEO have been generated in many different formats and often lack standardized annotation and documentation. It is hard to know if preprocessing has been applied to a dataset or not and in what way. Standard-based integration of heterogeneous data formats and metadata is necessary for comprehensive data query, analysis and mining. We attempted to integrate the heterogeneous microarray data in GEO based on Minimum Information About a Microarray Experiment (MIAME) standard. We unified the data fields of GEO Data table and mapped the attributes of GEO metadata into MIAME elements. We also discriminated non-preprocessed raw datasets from others and processed ones by using a two-step classification method. Most of the procedures were developed as semi-automated algorithms with some degree of text mining techniques. We localized 2,967 Platforms, 4,867 Series and 103,590 Samples with covering 279 organisms, integrated them into a standard-based relational schema and developed a comprehensive query interface to extract. Our tool, GEOQuest is available at http://www.snubi.org/software/GEOQuest/.

A Bayesian Validation Method for Classification of Microarray Expression Data (마이크로어레이 발현 데이터 분류를 위한 베이지안 검증 기법)

  • Park, Su-Young;Jung, Jong-Pil;Jung, Chai-Yeoung
    • Journal of the Korea Institute of Information and Communication Engineering
    • /
    • v.10 no.11
    • /
    • pp.2039-2044
    • /
    • 2006
  • Since the bio-information now even exceeds the capability of human brain, the techniques of data mining and artificial intelligent are needed to deal with the information in this field. There are many researches about using DNA microarray technique which can obtain information from thousands of genes at once, for developing new methods of analyzing and predicting of diseases. Discovering the mechanisms of unknown genes by using these new method is expecting to develop the new drugs and new curing methods. In this Paper, We tested accuracy on classification of microarray in Bayesian method to compare normalization method's Performance after dividing data in two class that is a feature abstraction method through a normalization process which reduce or remove noise generating in microarray experiment by various factors. And We represented that it improve classification performance in 95.89% after Lowess normalization.

High Throughput Genotyping for Genomic Cohort Study (유전체 코호트 연구를 위한 대용량 염기서열 분석)

  • Park, Woong-Yang
    • Journal of Preventive Medicine and Public Health
    • /
    • v.40 no.2
    • /
    • pp.102-107
    • /
    • 2007
  • Human Genome Project (HGP) could unveil the secrets of human being by a long script of genetic codes, which enabled us to get access to mine the cause of diseases more efficiently. Two wheels for HGP, bioinformatics and high throughput technology are essential techniques for the genomic medicine. While microarray platforms are still evolving, we can screen more than 500,000 genotypes at once. Even we can sequence the whole genome of an organism within a day. Because the future medicne will focus on the genetic susceptibility of individuals, we need to find genetic variations of each person by efficient genotyping methods.

Comparative Analysis of Gene Expression in the Female Reproductive Organs

  • Kim, Min-Goo;Seo, Hee-Won;Choi, Yo-Han;Lee, Chang-Kyu;Ka, Hak-Hyun
    • Journal of Embryo Transfer
    • /
    • v.24 no.2
    • /
    • pp.77-87
    • /
    • 2009
  • To understand molecular and cellular mechanisms of many gene products in the female reproductive organs including the ovary and uterine endometrium as well as during embryo development, researchers have developed and utilized many effective methodologies to analyze gene expression in cells, tissues and animals over the last several decades. For example, blotting techniques have helped to understand molecular functions at DNA, RNA and protein levels, and the reverse transcription-polymerase chain reaction (RT-PCR) method has been widely used in gene expression analysis. However, some conventional methods are not sufficient to understand regulation and function of genes expressed in very complex patterns in many organs. Thus, it is required to adopt more high-throughput and reliable techniques. Here, we describe several techniques used widely recently to analyze gene expression, including annealing control based-PCR, differential display-PCR, expressed sequence tag, suppression subtractive hybridization and microarray techniques. Use of these techniques will help to analyze expression pattern of many genes from small scale to large scale and to compare expression patterns of genes in one sample to another. In this review, we described principles of these methodologies and summarized examples of comparative analysis of gene expression in female reproductive organs with help of those methodologies.

Oral Metagenomic Analysis Techniques

  • Chung, Sung-Kyun
    • Journal of dental hygiene science
    • /
    • v.19 no.2
    • /
    • pp.86-95
    • /
    • 2019
  • The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.

GENE EXPRESSION PATTERNS INDUCED BY $TAXOL^{(R)}$ AND CYCLOSPORIN A IN ORAL SQUAMOUS CELL CARCINOMA CELL LINE USING CDNA MICROARRAY (cDNA Microarray를 이용한 구강편평세포암종 세포주에서 $Taxol^{(R)}$과 Cyclosporin A로 유도된 유전자 발현양상)

  • Kim, Yong-Kwan;Lee, Jae-Hoon;Kim, Chul-Hwan
    • Maxillofacial Plastic and Reconstructive Surgery
    • /
    • v.28 no.3
    • /
    • pp.202-212
    • /
    • 2006
  • It is well-known that paclitaxel($Taxol^{(R)}$), which is extracted from the pacific and English yew, has been used as a chemotherapeutic agent for ovarian carcinoma and advanced breast carcinoma and Cyclosporin A, which is highly lipophilic cyclic peptide and isolated from a fungus, has been also used as an useful immunosuppressive drug after transplantation and is associated with cellular apoptosis. Since 1953, in which James Watson, Rosalind Franklin and Francis Crick discovered the double helical structure of DNA, a few kinds of techniques for identifying gene expression have been developed. In postgenomic period, many of researchers have used the DNA microarray which is high throughput screening technique to screen large numbers of gene expression simultaneously. In this study, we searched and screened the gene expression in the oral squamous cell carcinoma cell lines treated with $Taxol^{(R)}$, cyclosporin or cyclosporin combined with $Taxol^{(R)}$ using cDNA microarray. The results were as following; 1. It was useful that the appropriate concentration of Cyclosporin A and $Taxol^{(R)}$ used in oral squamous cell carcinoma cell line was under 1${\mu}g/ml$ and 3${\mu}g/ml$. 2. In the experimental group in which $Taxol^{(R)}$ and $Taxol^{(R)}$ + Cyclosporin A were used, the cell growth was extremely decreased. 3. In the group in which Cyclosporin A was used, the MTT assay was rarely decreased which means the activity of succinyl dehydrogenase is remained in mitochondria but in the group in which the mixture of Cyclosporin A and $Taxol^{(R)}$ were used, the MTT assay was extremely decreased. 4. In the each group in which Cyclosporin A(3 ${\mu}g/ml$) and $Taxol^{(R)}$(1 ${\mu}g/ml$) were used, the cell arrest was appeared in $G_2/M$ phase and in the group in which $Taxol^{(R)}$(3 ${\mu}g/ml$) was used, the cell arrest was appeared in both S phase and $G_2/M$ phase. 5. In the oral squamous cell carcinoma cell line treated with $Taxol^{(R)}$, several genes including ANGPTL4, RALBP1 and TXNRD1, associated with apoptosis, SUI1, MAC30, RRAGA and CTGF, related with cell growth, HUS1 and DUSP5, related with cell cycle and proliferation, ATF4 and CEBPG, associated with transcription factor, BTG1 and VEGF, associated with angiogenesis, FDPS, FCER1G, GPA33 and EPHA4 associated with signal transduction and receptor activity and AKR1C2 and UGTA10 related with carcinogenesis were detected in increased levels. The genes that showed increaced expression in the oral squamous cell carcinoma cell line treated with Cyclosporin A were CYR61, SERPINB2, SSR3 and UPA3A which are known as genes associated with cell growth, carcinogenesis, receptor activity and transcription factor. The genes expressed in the HN22 cell line treated with cyclosporin combined with $taxol^{(R)}$ were ALCAM and GTSE1 associated with cancer invasiveness and cell cycle regulation.

A Review of Detection Methods for the Plant Viruses

  • Jeong, Joo-Jin;Ju, Ho-Jong;Noh, Jaejong
    • Research in Plant Disease
    • /
    • v.20 no.3
    • /
    • pp.173-181
    • /
    • 2014
  • The early and accurate detection of plant viruses is an essential component to control those. Because the globalization of trade by free trade agreement (FTA) and the rapid climate change promote the country-to-country transfer of viruses and their hosts and vectors, diagnosis of viral diseases is getting more important. Because symptoms of viral diseases are not distinct with great variety and are confused with those of abiotic stresses, symptomatic diagnosis may not be appropriate. From the last three decades, enzyme-linked immunosorbent assays (ELISAs), developed based on serological principle, have been widely used. However, ELISAs to detect plant viruses decrease due to some limitations such as availability of antibody for target virus, cost to produce antibody, requirement of large volume of sample, and time to complete ELISAs. Many advanced techniques allow overcoming demerits of ELISAs. Since the polymerase chain reaction (PCR) developed as a technique to amplify target DNA, PCR evolved to many variants with greater sensitivity than ELISAs. Many systems of plant virus detection are reviewed here, which includes immunological-based detection system, PCR techniques, and hybridization-based methods such as microarray. Some of techniques have been used in practical, while some are still under developing to get the level of confidence for actual use.

Aptamers as Functional Nucleic Acids: in vitro Selection and Biotechnological Applications

  • You, Kyung-Man;Lee, Sang-Hyun;Aesul Im;Lee, Sun-Bok
    • Biotechnology and Bioprocess Engineering:BBE
    • /
    • v.8 no.2
    • /
    • pp.64-75
    • /
    • 2003
  • Aptamers are functional nucleic acids that can specially bind to proteins, peptides, amino acids. nucleotides, drugs, vitamins and other organic and inorganic compounds. The aptamers are identified from random DNA or RNA libraries by a SELEX (systematic evolution of ligands by exponential amplification) process. As aptamers have the advantage, and potential ability to be released from the limitations of antibodies, they are attractive to a wide range of therapeutic and diagnostic applications. Aptamers, with a high-affinity and specificity, could fulfil molecular the recognition needs of various fields in biotechnology. In this work, we reviewed some aptamer Selection techniques, properties, medical applications of their molecules and their biotechnological applications, such as ELONA (enzyme linked oligonucleotide assay), flow cytometry, biosensors, electrophoresis, chromatography and microarrays.

Genomic Applications of Biochip Informatics (유전체 발현의 정보학적 분석과 응용)

  • Kim, Ju-Han
    • KOGO NEWS
    • /
    • v.5 no.4
    • /
    • pp.9-16
    • /
    • 2005
  • Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic expression data transforms the challenges m biomedical research into ones in bioinformatics. Clinical informatics has long developed technologies to imp개ve biomedical research by integrating experimental and clinical information systems. Biomedical informatics, powered by high throughput techniques, genomic-scale databases and advanced clinical information system, is likely to transform our biomedical understanding forever much the same way that biochemistry did to biology a generation ago. The emergence of healthcare and biomedical informatics revolutionizing both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics and prognostics.

  • PDF