Your email was sent successfully. Check your inbox.

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

Proceed reservation?

Export
Filter
  • CELL  (19)
  • PROTEOMICS  (13)
Collection
Keywords
Publisher
  • 1
    Keywords: PROTEOMICS ; genomic ; methods ; LOCALIZATION
    Type of Publication: Book chapter
    Signatur Availability
    BibTip Others were also interested in ...
  • 2
    Keywords: genomic ; PROTEOMICS
    Type of Publication: Book chapter
    Signatur Availability
    BibTip Others were also interested in ...
  • 3
    Keywords: NETWORK ; CDNA ; FUNCTIONAL GENOMICS ; PROTEOMICS ; CDNAS
    Abstract: Among the greatest challenges facing biology today is the exploitation of huge amounts of genomic data, and their conversion into functional information about the proteins encoded. For example, the large-scale cDNA sequencing project of the German cDNA Consortium is providing vast numbers of open reading frames (ORFs) encoding novel proteins of completely unknown function. As a first step towards their characterization we have tagged over 500 of these with the green fluorescent protein (GFP), and examined the subcellular localizations of these fusion proteins in living cells. These data have allowed us to classify the proteins into subcellular groups which determines the next step towards a detailed functional characterization. To make further use of these GFP-tagged constructs, a series of functional assays have been designed and implemented to assess the effect of these novel proteins on processes such as cell growth, cell death, and protein transport. Functional assays with such a large set of molecules is only possible by automation. Therefore, we have developed, and adapted, functional assays for use by robotic liquid handling stations and reading stations. A transport assay allows to identify proteins which localize to distinct organelles of the secretory pathway and have the potential to be new regulators in protein transport, a proliferation assay helps identifying proteins that stimulate or repress mitosis. Further assays to monitor the effects of the proteins in apoptosis and signal transduction pathways are in progress. Integrating the functional information that is generated in the assays with data from expression profiling and further functional genomics and proteomics approaches, will ultimately allow us to identify functional networks of proteins in a morphological context, and will greatly contribute to our understanding of cell function.
    Type of Publication: Journal article published
    PubMed ID: 14649292
    Signatur Availability
    BibTip Others were also interested in ...
  • 4
    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 ...
  • 5
    Keywords: PEPTIDE ; EXPRESSION ; Germany ; ALGORITHM ; DISTINCT ; GENOME ; PROTEIN ; ACCURACY ; COMPLEX ; COMPLEXES ; SEQUENCE ; SEQUENCES ; MOUSE ; IDENTIFICATION ; PATTERNS ; Drosophila ; NUMBER ; HUMAN GENOME ; LOCALIZATION ; PROTEOMICS ; PROGRAM ; RE ; INCREASE ; REQUIREMENT ; NUCLEOTIDE-SEQUENCES ; FULL-LENGTH HUMAN ; HUMAN CDNAS ; FIDELITY ; Internet
    Abstract: Background: The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. Results: We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-of-m pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements can be constrained by operators, and individual characters may be excluded. The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and finds ALL possible solutions in protein sequences in cases of length-ambiguous patterns instead of simply reporting the longest or shortest hits. Grouping and combined search for patterns provides a hierarchical arrangement of larger patterns sets. The algorithm is implemented as internet application and freely accessible. The application is available at http://dkfz.de/mga2/3of5/3of5.html. Conclusion: The 3of5 application offers an extended vocabulary for the definition of search patterns and thus allows the user to comprehensively specify and identify peptide patterns with variable elements. The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms
    Type of Publication: Journal article published
    PubMed ID: 16542452
    Signatur Availability
    BibTip Others were also interested in ...
  • 6
    Keywords: RECEPTOR ; EXPRESSION ; INVASION ; CELL ; Germany ; KINASE ; PATHWAY ; PATHWAYS ; TYROSINE KINASE ; SYSTEM ; SYSTEMS ; GENE ; GENES ; GENOME ; PROTEIN ; PROTEINS ; validation ; BIOLOGY ; TARGET ; REQUIRES ; PCR ; SIGNALING PATHWAY ; SIGNALING PATHWAYS ; EPITHELIAL-CELLS ; systems biology ; TARGETS ; OVEREXPRESSION ; real-time PCR ; protein expression ; CROSS-TALK ; CYTOTOXICITY ; signaling ; SINGLE ; ARRAY ; analysis ; EVENTS ; technique ; USA ; quantitative ; SIGNALING NETWORK ; protein arrays ; combinatorial protein knockdown ; reverse-phase protein arrays
    Abstract: The elucidation of cross-talk events between intersecting signaling pathways is one main challenge in biological research. The complexity of protein networks, composed of different pathways, requires novel strategies and techniques to reveal relevant interrelations. Here, we established a combinatorial RNAi strategy for systematic single, double, and triple knockdown, and we measured the residual mRNAs and proteins quantitatively by quantitative real-time PCR and reverse-phase protein arrays, respectively, as a prerequisite for data analysis. Our results show that the parallel knockdown of at least three different genes is feasible while keeping both untargeted silencing and cytotoxicity low. The technique was validated by investigating the interplay of tyrosine kinase receptor ErbB2 and its downstream targets Akt-1 and MEK1 in cell invasion. This experimental approach combines multiple gene knockdown with a subsequent quantitative validation of reduced protein expression and is a major advancement toward the analysis of signaling pathways in systems biology
    Type of Publication: Journal article published
    PubMed ID: 17420474
    Signatur Availability
    BibTip Others were also interested in ...
  • 7
    Keywords: RECEPTOR ; CANCER ; GROWTH-FACTOR ; CELL ; Germany ; human ; MODEL ; MODELS ; TYROSINE KINASE ; LUNG-CANCER ; SYSTEM ; SYSTEMS ; GENE ; GENOME ; PROTEIN ; FAMILY ; IMPACT ; BIOLOGY ; GROWTH-FACTOR RECEPTOR ; SEQUENCE ; breast cancer ; BREAST-CANCER ; HUMAN GENOME ; CAENORHABDITIS-ELEGANS ; NETHERLANDS ; systems biology ; QUANTITATIVE-ANALYSIS ; RECEPTORS ; PROTEOMICS ; signaling ; SINGLE ; molecular biology ; FAMILIES ; RNA INTERFERENCE ; regulation ; TECHNOLOGY ; RNAi ; CLINICAL-RESPONSE ; PROGRESS ; GROWTH-FACTOR RECEPTORS ; SIGNALING NETWORK ; QUANTITATIVE PROTEOMICS ; FEDERATION ; Vision ; PROTEIN-INTERACTION NETWORK ; DOMAIN SIGNATURES ; ERBB-signaling network ; HER2 OVEREXPRESSION ; Micro RNA
    Abstract: Substantial progress in functional genomic and proteomic technologies has opened new perspectives in biomedical research. The sequence of the human genome has been mostly determined and opened new visions on its complexity and regulation. New technologies, like RNAi and protein arrays, allow gathering knowledge beyond single gene analysis. Increasingly, biological processes are studied with systems biological approaches, where qualitative and quantitative data of the components are utilized to model the respective processes, to predict effects of perturbations, and to then refine these models after experimental testing. Here, we describe the potential of applying functional genomics and proteomics, taking the ERBB family of growth-factor receptors as an example to study the signaling network and its impact on cancer. (C) 2009 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 19303877
    Signatur Availability
    BibTip Others were also interested in ...
  • 8
    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 ...
  • 9
    Keywords: CELLS ; CELL ; Germany ; PATHWAYS ; QUANTIFICATION ; SYSTEM ; SYSTEMS ; microarray ; PROTEIN ; PROTEINS ; SAMPLES ; DRUG ; BIOLOGY ; SIGNAL ; ASSAY ; microarrays ; EFFICIENT ; ELECTROPHORESIS ; BIOPSY ; PROTEOMICS ; signaling ; RECOMBINANT ; RE ; CAPACITY ; ARRAY ; GELS ; analysis ; methods ; BIOPSIES ; signaling networks ; protein arrays ; protein quantification ; reverse phase protein microarray
    Abstract: The advancement of efficient technologies to comply with the needs of systems biology and drug discovery has so far not received adequate attention. A substantial bottleneck for the time-resolved quantitative description of signaling networks is the limited throughput and the inadequate sensitivity of currently established methods. Here, we present an improved protein microarray-based approach towards the sensitive detection of proteins in the fg-range which is based on signal detection in the near-infrared range. The high sensitivity of the assay permits the specific quantification of proteins derived from as little as only 20 000 cells with an error rate of only 5%. The capacity is limited to the analysis of up to 500 different samples per microarray. Protein abundance is determined qualitatively, and quantitatively, if recombinant protein is available. This novel approach was called IPAQ (infrared-based protein arrays with quantitative readout). IPAQ offers a highly sensitive experimental approach superior to the established standard protein quantification technologies, and is suitable for quantitative proteomics. Employing the IPAQ approach, a detailed analysis of activated signaling networks in biopsy samples and of crosstalk between signaling modules as required in drug discovery strategies can easily be performed
    Type of Publication: Journal article published
    PubMed ID: 17309101
    Signatur Availability
    BibTip Others were also interested in ...
  • 10
    Keywords: CANCER ; CANCER CELLS ; CELLS ; EXPRESSION ; INVASION ; tumor ; TUMOR-CELLS ; carcinoma ; CELL ; Germany ; CLASSIFICATION ; GENE-EXPRESSION ; GENOME ; PROTEIN ; PROTEINS ; TUMORS ; TIME ; kidney ; primary ; FLOW ; BIOLOGY ; CELL-CYCLE ; MOLECULAR-BIOLOGY ; BREAST ; breast cancer ; BREAST-CANCER ; PROGRESSION ; PATTERNS ; MEMBRANE ; METASTASIS ; genetics ; metastases ; CANCER-CELLS ; ONCOGENE ; heredity ; molecular biology ; molecular ; E-cadherin ; ONCOLOGY ; RE ; INCREASE ; LEVEL ; LOSSES ; REDUCED EXPRESSION ; ENGLAND ; INCREASES ; detachment ; cell junctions ; initial cell-cell contact
    Abstract: Vacuole membrane protein 1 (Vmp1) is described as a cancer-relevant cell cycle modulator, but the function of this protein and its mode of action in tumor progression are still unknown. In this study, we show that the VMP1 mRNA level is significantly reduced in kidney cancer metastases as compared to primary tumors. Further, VMP1 expression is also decreased in the invasive breast cancer cell lines HCC1954 and MDA-MB-231 as compared to the non-invasive cell lines MCF-12A, T-47D and MCF-7. We show for the first time that Vmp1 is a plasma membrane protein and an essential component of initial cell-cell contacts and tight junction formation. It interacts with the tight junction protein Zonula Occludens-1 and colocalizes in spots between neighboring HEK293 cells. Downregulation of VMP1 by RNAi results in loss of cell adherence, and increases the invasion capacity of the non-invasive kidney cancer cell line Caki-2. In conclusion, our findings establish Vmp1 to be a novel cell-cell adhesion protein and that its expression level determines the invasion and metastatic potential of cancer cells
    Type of Publication: Journal article published
    PubMed ID: 17724469
    Signatur Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...