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  1. AU="Bansemer, Sven"
  2. AU="Kochetov, O"
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  1. Article: Automatic construction of gene relation networks using text mining and gene expression data.

    Karopka, Thomas / Scheel, Thomas / Bansemer, Sven / Glass, Anne

    Medical informatics and the Internet in medicine

    2004  Volume 29, Issue 2, Page(s) 169–183

    Abstract: Microarray gene expression analysis is a powerful high-throughput technique that enables researchers to monitor the expression of thousands of genes simultaneously. Using this methodology huge amounts of data are produced which have to be analysed. ... ...

    Abstract Microarray gene expression analysis is a powerful high-throughput technique that enables researchers to monitor the expression of thousands of genes simultaneously. Using this methodology huge amounts of data are produced which have to be analysed. Clustering algorithms are used to group genes together based on a predefined distance measure. However, clustering algorithms do not necessarily group the genes in a biological meaningful way. Additional information is needed to improve the identification of disease relevant genes. The primary objective of our project is to support the analysis of microarray gene expression data by construction of gene relation networks (GRNs). Required information can not be found in a structured representation like a database. In contrast, a large number of relations are described in biomedical literature. The main outcome of this project is the implementation of a software system that provides clinicians and researchers with a tool that supports the analysis of microarray gene expression data by mapping known relationships from the biomedical literature to local gene expression experiments.
    MeSH term(s) Abbreviations as Topic ; Abstracting and Indexing as Topic ; Algorithms ; Cluster Analysis ; Databases, Genetic/standards ; Gene Expression Profiling/methods ; Gene Expression Profiling/standards ; Humans ; Information Systems/organization & administration ; Leukemia, Myeloid, Acute/classification ; Leukemia, Myeloid, Acute/genetics ; MEDLINE ; Natural Language Processing ; Neural Networks (Computer) ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Array Sequence Analysis/standards ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/classification ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; User-Computer Interface
    Language English
    Publishing date 2004-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
    ZDB-ID 1470814-0
    ISSN 1464-5238 ; 1463-9238
    ISSN (online) 1464-5238
    ISSN 1463-9238
    DOI 10.1080/14639230412331280422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1252: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  2. Article: Representation of Individual Gene Expression in Completely Pooled mRNA Samples

    GLASS, Änne / HENNING, Jeannette / KAROPKA, Thomas / SCHEEL, Thomas / BANSEMER, Sven / KOCZAN, Dirk / GIERL, Lothar / ROLFS, Arndt / GIMSA, Ulrike

    Bioscience, biotechnology, and biochemistry. 2005 Jan. 1, v. 69, no. 6

    2005  

    Abstract: Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be ... ...

    Abstract Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be considered part of sub-pooling designs, gene expression data from three complete pooling experiments were analyzed. Data from complete pooled versus individual mRNA samples of rat brain tissue were compared to answer the question whether the pooled sample represents individual samples in small-sized experiments. Our analytic approach provided clear results concerning the Affymetrix® MAS 5.0 signal and detection call parameters. Despite a strong similarity of arrays within experimental groups, the individual signals were evidently not appropriately represented in the pooled sample, with slightly more than half of all the genes considered. Our analysis reveals problems in cases of small complete pooling designs with less than six subjects pooled.
    Keywords biotechnology ; brain ; gene expression ; microarray technology ; rats
    Language English
    Dates of publication 2005-0101
    Size p. 1098-1103.
    Publishing place Japan Society for Bioscience, Biotechnology, and Agrochemistry
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1106450-x
    ISSN 1347-6947 ; 0916-8451
    ISSN (online) 1347-6947
    ISSN 0916-8451
    DOI 10.1271/bbb.69.1098
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Representation of individual gene expression in completely pooled mRNA samples.

    Glass, Anne / Henning, Jeannette / Karopka, Thomas / Scheel, Thomas / Bansemer, Sven / Koczan, Dirk / Gierl, Lothar / Rolfs, Arndt / Gimsa, Ulrike

    Bioscience, biotechnology, and biochemistry

    2005  Volume 69, Issue 6, Page(s) 1098–1103

    Abstract: Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be ... ...

    Abstract Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be considered part of sub-pooling designs, gene expression data from three complete pooling experiments were analyzed. Data from complete pooled versus individual mRNA samples of rat brain tissue were compared to answer the question whether the pooled sample represents individual samples in small-sized experiments. Our analytic approach provided clear results concerning the Affymetrix MAS 5.0 signal and detection call parameters. Despite a strong similarity of arrays within experimental groups, the individual signals were evidently not appropriately represented in the pooled sample, with slightly more than half of all the genes considered. Our analysis reveals problems in cases of small complete pooling designs with less than six subjects pooled.
    MeSH term(s) Animals ; Gene Expression ; Male ; Oligonucleotide Array Sequence Analysis/methods ; RNA, Messenger/chemistry ; Rats ; Rats, Wistar ; Reproducibility of Results ; Research Design
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2005-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106450-x
    ISSN 1347-6947 ; 0916-8451
    ISSN (online) 1347-6947
    ISSN 0916-8451
    DOI 10.1271/bbb.69.1098
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4647: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  4. Article: 3-Hydroxy-3-methylglutaryl coenzyme A reductase inhibitor Atorvastatin mediated effects depend on the activation status of target cells in PLP-EAE.

    Mix, Eilhard / Ibrahim, Saleh M / Pahnke, Jens / Glass, Anne / Mazón-Peláez, Ignacio / Lemcke, Susanne / Koczan, Dirk / Gimsa, Ulrike / Bansemer, Sven / Scheel, Thomas / Karopka, Thomas / Böttcher, Tobias / Müller, Jana / Dazert, Eike / Antipova, Veronica / Hoffrogge, Raimund / Wree, Andreas / Zschiesche, Marlies / Strauss, Ulf /
    Kundt, Günther / Warzok, Rolf / Gierl, Lothar / Rolfs, Arndt

    Journal of autoimmunity

    2006  Volume 27, Issue 4, Page(s) 251–265

    Abstract: The effect of Atorvastatin on transcriptional activity in murine experimental autoimmune encephalomyelitis (EAE) induced by PLP peptide 139-151 was analyzed by DNA microarray technique in lymph nodes and spinal cord at onset (10 days), height (20 days) ... ...

    Abstract The effect of Atorvastatin on transcriptional activity in murine experimental autoimmune encephalomyelitis (EAE) induced by PLP peptide 139-151 was analyzed by DNA microarray technique in lymph nodes and spinal cord at onset (10 days), height (20 days) and first remission (30 days) of disease. Fourteen genes were selectively influenced by Atorvastatin in EAE mice. They are mainly related to immune cell functions and regulation of cell-to-cell interaction. Interestingly, seven genes were also differentially regulated in CFA-injected control mice. But qualitative and quantitative differences to EAE mice argue for a dependency of statin effects on the activation status of target cells. Differential regulation of the newly detected candidate genes of statin effects COX-1 and HSP-105 and the previously known statin-responsive genes ICAM-1 and CD86 was confirmed by Western blot and immunohistochemistry. Flow cytometric analysis of lymph node cells revealed that the effect of Atorvastatin treatment in non-immunized healthy animals resembled the effect of immunization with PLP peptide regarding changes of T helper cells, activated B cells and macrophages. In EAE mice, these effects were partially reversed by Atorvastatin treatment. Monitoring of expression of the newly identified candidate genes and patterns of lymphocyte subpopulations might predict the responsiveness of multiple sclerosis patients to statin treatment.
    MeSH term(s) Animals ; Atorvastatin Calcium ; Encephalomyelitis, Autoimmune, Experimental/drug therapy ; Encephalomyelitis, Autoimmune, Experimental/enzymology ; Encephalomyelitis, Autoimmune, Experimental/genetics ; Encephalomyelitis, Autoimmune, Experimental/immunology ; Flow Cytometry ; Gene Expression ; Heptanoic Acids/pharmacology ; Hydroxymethylglutaryl CoA Reductases/metabolism ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/metabolism ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; Leukocytes/immunology ; Lymph Nodes/immunology ; Male ; Mice ; Multiple Sclerosis/drug therapy ; Multiple Sclerosis/enzymology ; Multiple Sclerosis/genetics ; Multiple Sclerosis/immunology ; Myelin Proteolipid Protein ; Oligonucleotide Array Sequence Analysis/methods ; Peptide Fragments ; Pyrroles/pharmacology ; Spinal Cord/immunology
    Chemical Substances Heptanoic Acids ; Hydroxymethylglutaryl-CoA Reductase Inhibitors ; Myelin Proteolipid Protein ; Peptide Fragments ; Pyrroles ; myelin proteolipid protein (139-151) ; Atorvastatin Calcium (48A5M73Z4Q) ; Hydroxymethylglutaryl CoA Reductases (EC 1.1.1.-)
    Language English
    Publishing date 2006-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639452-8
    ISSN 0896-8411
    ISSN 0896-8411
    DOI 10.1016/j.jaut.2006.09.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2368: Show issues Location:
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