Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Germany  (16)
Collection
Keywords
  • 1
    Keywords: EXPRESSION ; Germany ; human ; MODEL ; THERAPY ; DIAGNOSIS ; INFORMATION ; NETWORK ; TOOL ; DISEASE ; GENE ; GENES ; GENOME ; PROTEIN ; PROTEINS ; COMPLEX ; COMPLEXES ; BIOLOGY ; SEQUENCE ; FORM ; IDENTIFICATION ; HEALTH ; DATABASE ; PRODUCT ; bioinformatics ; LOCALIZATION ; WEB ; HUMAN GENES ; FUNCTIONAL GENOMICS ; PROTEOMICS ; PRODUCTS ; databases ; ANNOTATION ; RESOURCE ; PROTEIN-ANALYSIS ; FULL-LENGTH HUMAN ; HUMAN CDNAS
    Abstract: As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a human ORFeome resource and established a functional genomics and proteomics analysis pipeline to address the major topics in the post-genome-sequencing era: the identification of human genes and splice forms, and the determination of protein localization, activity, and interaction. Combined with the understanding of when and where gene products are expressed in normal and diseased conditions, we create information that is essential for understanding the interplay of genes and proteins in the complex biological network. We have implemented bioinformatics tools and databases that are suitable to store, analyze, and integrate the different types of data from high-throughput experiments and to include further annotation that is based on external information. All information is presented in a Web database (http://www.dkfz.de/LIFEdb). It is exploited for the identification of disease-relevant genes and proteins for diagnosis and therapy
    Type of Publication: Journal article published
    PubMed ID: 15489336
    Signatur Availability
    BibTip Others were also interested in ...
  • 2
    facet.materialart.
    facet.materialart.
    Genome Biology 7 (7), Art.Nr.R66- 
    Keywords: Germany ; PATHWAY ; PATHWAYS ; screening ; GENOME ; RNA ; COMPONENTS ; IDENTIFICATION ; MICROARRAY DATA ; CAENORHABDITIS-ELEGANS ; STATISTICAL-ANALYSIS ; PHENOTYPE ; DOUBLE-STRANDED-RNA ; INTEGRATION ; RE ; INTERFERENCE ; RNA INTERFERENCE ; STANDARDS ; GENETIC INTERFERENCE ; FUNCTIONAL-CHARACTERIZATION ; TECHNOLOGY ; technique ; BIOCONDUCTOR
    Abstract: RNA interference (RNAi) screening is a powerful technology for functional characterization of biological pathways. Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data. It is implemented in an open-source Bioconductor/R package, cellHTS (http://www.dkfz.de/signaling/cellHTS). The method is useful for the analysis and documentation of individual RNAi screens. Moreover, it is a prerequisite for the integration of multiple experiments
    Type of Publication: Journal article published
    PubMed ID: 16869968
    Signatur Availability
    BibTip Others were also interested in ...
  • 3
    Keywords: EXPRESSION ; proliferation ; CELL-PROLIFERATION ; Germany ; INFORMATION ; screening ; GENE ; GENE-EXPRESSION ; GENES ; GENOME ; PROTEIN ; PROTEINS ; gene expression ; ASSAY ; DATABASE ; bioinformatics ; INTERFACE ; PROJECT ; INTEGRATION ; FEATURES ; RE ; cell proliferation ; FULL-LENGTH HUMAN ; HUMAN CDNAS ; ASSAYS ; genomic ; NORTHERN
    Abstract: LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an updated user interface with enhanced query capabilities, (ii) a configurable output table and the option to download search results in XML, (iii) the integration of data from cell-based screening assays addressing the influence of protein-overexpression on cell proliferation and (iv) the display of the relative expression ('Electronic Northern') of the genes under investigation using curated gene expression ontology information. LIFEdb enables researchers to systematically select and characterize genes and proteins of interest, and presents data and information via its user-friendly web-based interface
    Type of Publication: Journal article published
    PubMed ID: 16381901
    Signatur Availability
    BibTip Others were also interested in ...
  • 4
    Keywords: Germany ; GENOME ; microarray ; SEQUENCE ; SEQUENCES ; ELEMENT ; ELEMENTS ; STRATEGIES ; PROJECT ; IMPLEMENTATION ; NUCLEOTIDE-SEQUENCE ; NUCLEOTIDE-SEQUENCES
    Abstract: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation of data packages for curating, distributing and working with probe sequence data in a uniform, across-types-of-microarrays manner. While the implementation is specific to the Bioconductor project, the ideas and general strategies are more general and could be easily adopted by other projects
    Type of Publication: Journal article published
    PubMed ID: 14988118
    Signatur Availability
    BibTip Others were also interested in ...
  • 5
    Keywords: CANCER ; GROWTH ; INHIBITOR ; proliferation ; SURVIVAL ; tumor ; CELL-PROLIFERATION ; Germany ; KINASE ; INFORMATION ; TOOL ; DISEASE ; GENE ; GENES ; GENOME ; microarray ; PROTEIN ; PROTEINS ; transcription ; TUMORS ; RESOLUTION ; ACTIVATION ; DNA ; BIOLOGY ; cell cycle ; CELL-CYCLE ; CYCLE ; ASSOCIATION ; MOUSE ; IDENTIFICATION ; PROGRESSION ; ASSAY ; microarrays ; PROSTATE-CANCER ; STRATEGIES ; DNA-REPLICATION ; REPLICATION ; signaling ; RE ; TUMORIGENICITY ; genomics ; TRANSITION ; DNA replication ; C-ELEGANS ; cell proliferation ; PROTEIN-ANALYSIS ; development ; ASSAYS ; DIFFERENTIALLY EXPRESSED GENES ; high throughput ; HIGH-THROUGHPUT ; LONG ; PRIME ; PRINCIPLES ; REPRESSOR ; ROLES
    Abstract: Cancer transcription microarray studies commonly deliver long lists of "candidate" genes that are putatively associated with the respective disease. For many of these genes, no functional information, even less their relevance in pathologic conditions, is established as they were identified in large-scale genomics approaches. Strategies and tools are thus needed to distinguish genes and proteins with mere tumor association from those causally related to cancer. Here, we describe a functional profiling approach, where we analyzed 103 previously uncharacterized genes in cancer relevant assays that probed their effects on DNA replication (cell proliferation). The genes had previously been identified as differentially expressed in genome-wide microarray studies of tumors. Using an automated high-throughput assay with single-cell resolution, we discovered seven activators and nine repressors of DNA replication. These were further characterized for effects on extracellular signal-regulated kinase 1/2 (ERK1/2) signaling (G(1)-S transition) and anchorage-independent growth (tumorigenicity). One activator and one inhibitor protein of ERK1/2 activation and three repressors of anchorage-independent growth were identified. Data from tumor and functional profiling make these proteins novel prime candidates for further in-depth study of their roles in cancer development and progression. We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies
    Type of Publication: Journal article published
    PubMed ID: 16140941
    Signatur Availability
    BibTip Others were also interested in ...
  • 6
    Keywords: COMBINATION ; Germany ; GENERATION ; GENOME ; microarray ; PROTEIN ; PROTEINS ; MONOCLONAL-ANTIBODY ; BIOLOGY ; MOLECULAR-BIOLOGY ; antibodies ; antibody ; microarrays ; ARRAYS ; NUMBER ; REPRODUCIBILITY ; FUSION ; FUSION PROTEINS ; SURFACE ; MONOCLONAL-ANTIBODIES ; IMMOBILIZATION ; PROTEOMICS ; protein microarray ; PROTEIN MICROARRAYS ; FUSION PROTEIN ; SERUM ; molecular biology ; molecular ; RECOMBINANT ; ARRAY ; RESOURCE ; ANTIBODY MICROARRAYS ; CHIP ; 3D ; monoclonal antibodies ; monoclonal antibody ; ALLERGEN-SPECIFIC IGE ; DYES ; FLUORESCENT DYES
    Abstract: To process large numbers of samples in parallel is one potential of protein microarrays for research and diagnostics. However, the application of protein arrays is currently hampered by the lack of comprehensive technological knowledge about the suitability of 2-D and 3-D slide surface coatings. We have performed a systematic study to analyze how both surface types perform in combination with different fluorescent dyes to generate significant and reproducible data. In total, we analyzed more than 100 slides containing 1152 spots each. Slides were probed against different monoclonal antibodies (mAbs) and recombinant fusion proteins. We found two surface coatings to be most suitable for protein and antibody (Ab) immobilization. These were further subjected to quantitative analyses by evaluating intraslide and slide-to-slide reproducibilities, and the linear range of target detection. in summary, we demonstrate that only suitable combinations of surface and fluorescent dyes allow the generation of highly reproducible data
    Type of Publication: Journal article published
    PubMed ID: 16267812
    Signatur Availability
    BibTip Others were also interested in ...
  • 7
    Keywords: SURVIVAL ; CELL ; Germany ; MICROSCOPY ; screening ; GENE ; GENES ; GENOME ; RNA ; IDENTIFICATION ; ARRAYS ; HUMAN GENOME ; MIGRATION ; PHENOTYPE ; ORGANIZATION ; INTERFERENCE ; RNA INTERFERENCE ; RESOURCE ; SCIENCE ; LIFE ; TISSUE-CULTURE CELLS
    Abstract: Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the similar to 21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community
    Type of Publication: Journal article published
    PubMed ID: 20360735
    Signatur Availability
    BibTip Others were also interested in ...
  • 8
    Keywords: EXPRESSION ; IN-VITRO ; SURVIVAL ; Germany ; MODEL ; VITRO ; CLASSIFICATION ; CDNA ; GENOME ; microarray ; RNA ; SAMPLE ; SAMPLES ; MESSENGER-RNA ; BREAST-CANCER ; NO ; AMPLIFICATION ; microarrays ; REQUIRES ; PARAMETERS ; STATISTICAL-ANALYSIS ; DIFFERENTIAL EXPRESSION ; QUANTITIES ; LACKING ; REQUIREMENT ; bias ; PNEUMOPERITONEUM
    Abstract: Background: The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10-100 mug of RNA. However, due to their small size, most biopsies do not yield this amount. Several different approaches for RNA amplification in vitro have been described and applied for microarray studies. In most of these, systematic analyses of the potential bias introduced by the enzymatic modifications are lacking. Results: We examined the sources of error introduced by the T7 RNA polymerase based RNA amplification method through hybridisation studies on microarrays and performed statistical analysis of the parameters that need to be evaluated prior to routine laboratory use. The results demonstrate that amplification of the RNA has no systematic influence on the outcome of the microarray experiment. Although variations in differential expression between amplified and total RNA hybridisations can be observed, RNA amplification is reproducible, and there is no evidence that it introduces a large systematic bias. Conclusions: Our results underline the utility of the T7 based RNA amplification for use in microarray experiments provided that all samples under study are equally treated
    Type of Publication: Journal article published
    PubMed ID: 15119961
    Signatur Availability
    BibTip Others were also interested in ...
  • 9
    Keywords: Germany ; FOLLOW-UP ; CDNA ; microarray ; MICROARRAY DATA ; REPRODUCIBILITY ; CDNA MICROARRAY ; RE ; normalization
    Abstract: : arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and preprocessed microarray data to high-level follow-up analysis
    Type of Publication: Journal article published
    PubMed ID: 15454413
    Signatur Availability
    BibTip Others were also interested in ...
  • 10
    Keywords: APOPTOSIS ; CELLS ; EXPRESSION ; CELL ; Germany ; human ; SYSTEM ; DISEASE ; GENES ; GENOME ; PROTEIN ; PROTEINS ; ACTIVATION ; FLOW ; antibodies ; antibody ; IDENTIFICATION ; ASSAY ; CELL-DEATH ; fragmentation ; HUMAN GENOME ; FLUORESCENCE ; INHIBITORS ; CHEMISTRY ; RE ; flow cytometry ; genomics ; MEDIATED APOPTOSIS ; methods ; NUCLEAR ; USA ; function ; CANDIDATE ; microbiology ; caspase-3 ; cell-based assay ; PERMEABILITY TRANSITION PORE ; VIRUS CORE PROTEIN
    Abstract: After sequencing the human genome, the challenge ahead is to systematically analyze the functions and disease relation of the proteins encoded. Here the authors describe the application of a flow cytometry-based high-throughput assay to screen for apoptosis-activating proteins in transiently transfected cells. The assay is based on the detection of activated caspase-3 with a specific antibody, in cells overexpressing proteins tagged C- or N-terminally with yellow fluorescent protein. Fluorescence intensities are measured using a flow cytometer integrated with a high-throughput autosampler. The applicability of this screen has been tested in a pilot screen with 200 proteins. The candidate proteins were all verified in an independent microscopy-based nuclear fragmentation assay, finally resulting in the identification of 6 apoptosis inducers
    Type of Publication: Journal article published
    PubMed ID: 17478479
    Signatur Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...