Your email was sent successfully. Check your inbox.

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

Proceed reservation?

Export
Filter
  • Germany  (37)
  • EXPRESSION  (29)
  • GENOME  (25)
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
    Keywords: brain ; CELLS ; EXPRESSION ; Germany ; GENE ; GENES ; GENOME ; PROTEIN ; PROTEINS ; transcription ; TISSUE ; MECHANISM ; mechanisms ; PROMOTER ; NUMBER ; DATABASE ; LOCALIZATION ; B-CELLS ; INVOLVEMENT ; TESTIS ; representational difference analysis ; RE ; VARIANT ; genomics ; regulation ; TRANSLATION ; GENE-REGULATION ; gene regulation ; NUCLEAR-PORE COMPLEX ; OVERLAPPING READING FRAMES ; SIGNAL PEPTIDES
    Abstract: Background: Given the complexity of higher organisms, the number of genes encoded by their genomes is surprisingly small. Tissue specific regulation of expression and splicing are major factors enhancing the number of the encoded products. Commonly these mechanisms are intragenic and affect only one gene. Results: Here we provide evidence that the IL4I1 gene is specifically transcribed from the apparent promoter of the upstream NUP62 gene, and that the first two exons of NUP62 are also contained in the novel IL4I1_2 variant. While expression of IL4I1 driven from its previously described promoter is found mostly in B cells, the expression driven by the NUP62 promoter is restricted to cells in testis (Sertoli cells) and in the brain (e.g., Purkinje cells). Since NUP62 is itself ubiquitously expressed, the IL4I1_2 variant likely derives from cell type specific alternative pre-mRNA processing. Conclusion: Comparative genomics suggest that the promoter upstream of the NUP62 gene originally belonged to the IL4I1 gene and was later acquired by NUP62 via insertion of a retroposon. Since both genes are apparently essential, the promoter had to serve two genes afterwards. Expression of the IL4I1 gene from the "NUP62" promoter and the tissue specific involvement of the pre-mRNA processing machinery to regulate expression of two unrelated proteins indicate a novel mechanism of gene regulation
    Type of Publication: Journal article published
    PubMed ID: 16029492
    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: 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 ...
  • 5
    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 ...
  • 6
    Keywords: EXPRESSION ; Germany ; PATHWAY ; CLASSIFICATION ; GENE ; GENE-EXPRESSION ; GENES ; GENOME ; ACCURACY ; BIOLOGY ; TARGET ; gene expression ; MICROARRAY DATA ; DATABASE ; RE ; databases ; analysis ; methods ; HIGH-THROUGHPUT ; technique ; CANDIDATE ; microbiology ; ENGLAND ; biotechnology ; ONTOLOGIES
    Abstract: Background: High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and well established technique to test for the statistically significant over-representation of particular pathways. A shortcoming of this method is however, that most genes that are investigated in the experiments have very sparse functional or pathway annotation and therefore cannot be the target of such an analysis. The approach presented here aims to assign lists of genes with limited annotation to previously described functional gene collections or pathways. This works by comparing InterPro domain signatures of the candidate gene lists with domain signatures of gene sets derived from known classifications, e. g. KEGG pathways. Results: In order to validate our approach, we designed a simulation study. Based on all pathways available in the KEGG database, we create test gene lists by randomly selecting pathway genes, removing these genes from the known pathways and adding variable amounts of noise in the form of genes not annotated to the pathway. We show that we can recover pathway memberships based on the simulated gene lists with high accuracy. We further demonstrate the applicability of our approach on a biological example. Conclusion: Results based on simulation and data analysis show that domain based pathway enrichment analysis is a very sensitive method to test for enrichment of pathways in sparsely annotated lists of genes. An R based software package domainsignatures, to routinely perform this analysis on the results of high-throughput screening, is available via Bioconductor
    Type of Publication: Journal article published
    PubMed ID: 18177498
    Signatur Availability
    BibTip Others were also interested in ...
  • 7
    Keywords: COMBINATION ; Germany ; SUPPORT ; GENE ; GENES ; COMPLEX ; MECHANISM ; mechanisms ; ASSOCIATION ; polymorphism ; SUSCEPTIBILITY ; NO ; NUMBER ; ADULT ; ADULTS ; CANDIDATE GENES ; TRANSPORTER ; HAPLOTYPE ; HAPLOTYPE RECONSTRUCTION ; genetic association ; interactive ; NO EVIDENCE ; COMT ; ADHD ; ALPHA-2A ADRENERGIC-RECEPTOR ; DEFICIT-HYPERACTIVITY DISORDER ; RATING-SCALE ; SHORT-VERSION ; SLC6A2
    Abstract: Attention deficit/hyperactivity disorder (ADHD) is a complex, highly heritable psychiatric condition. Neuropsychological and pharmacological studies suggest a dysregulation of central noradrenergic neurotransmission in addition to dopaminergic and serotonergic mechanisms. Only a few studies have focused on the association of noradrenergic susceptibility genes with ADHD. In this study, we investigated the association of several ADHD symptom scores (German short form of the Wender Utah Rating Scale, WURS-k; ADHD self report, ADHD-SB, and the German validated version of the WRAADDS, WRI) with haplotypes of the catechol-O-methyltransferase (COMT) and the norepinephrine transporter (SLC6A2) genes. Subjects were genotyped for three SLC6A2 (rs5569, rs998424, rs2242447) and two COMT single nucleotide polymorphisms (rs4680, rs4818). In addition, psychosocial adversity in childhood was assessed in order to evaluate putative gene-environment interactions. We did not find main effects of the COMT and SLC6A2 NET1 gene haplotypes on any ADHD symptom severity score. Childhood psychosocial adversity was strongly associated with number of ADHD symptoms. No gene-environment interaction was found. A specific combination of two COMT and SLC6A2 gene haplotypes, containing the low functioning COMT variant was nominally associated with low ADHD scores in all scales. Results do not support the hypothesis that common variants in the SLC6A2 and COMT genes in particular are associated with ADHD, but might give some evidence for interactive effects between these gene variants on ADHD severity
    Type of Publication: Journal article published
    PubMed ID: 17994190
    Signatur Availability
    BibTip Others were also interested in ...
  • 8
    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 ...
  • 9
    Keywords: EXPRESSION ; proliferation ; MODULATION ; POTENT ; TYROSINE KINASES ; PHOSPHATIDYLINOSITOL 3-KINASE/MAMMALIAN TARGET ; RAPAMYCIN INHIBITOR ; MAMMARY-TUMOR ; DEPENDENCY ; NVP-BEZ235
    Abstract: ABSTRACT: INTRODUCTION: Targeting receptor tyrosine kinases (RTKs) with kinase inhibitors is a clinically validated anti-cancer approach. However, blocking one signaling pathway is often not sufficient to cause tumor regression and the effectiveness of individual inhibitors is often short-lived. As alterations in fibroblast growth factor receptor (FGFR) activity have been implicated in breast cancer, we examined in breast cancer models with autocrine FGFR activity the impact of targeting FGFRs in vivo with a selective kinase inhibitor in combination with an inhibitor of PI3K/mTOR or with a pan-ErbB inhibitor. METHODS: Using 4T1 or 67NR models of basal-like breast cancer, tumor growth was measured in mice treated with an FGFR inhibitor (dovitinib/TKI258), a PI3K/mTOR inhibitor (NVP-BEZ235) or a pan-ErbB inhibitor (AEE788) individually or in combination. To uncover mechanisms underlying inhibitor action, signaling pathway activity was examined in tumor lysates and transcriptome analysis carried out to identify pathways upregulated by FGFR inhibition. Anti-phosphotyrosine receptor antibody arrays (P-Tyr RTK) were also used to screen 4T1 tumors. RESULTS: The combination of dovitinib + NVP-BEZ235 causes tumor stasis and strong down-regulation of the FRS2/Erk and PI3K/Akt/mTOR signaling pathways. P-Tyr RTK arrays identified high levels of P-EGFR and P-ErbB2 in 4T1 tumors. Testing AEE788 in the tumor models revealed that the combination of dovitinib + AEE788 resulted in blockade of the PI3K/Akt/mTOR pathway, prolonged tumor stasis and in the 4T1 model, a significant decrease in lung metastasis. The results show that in vivo these breast cancer models become dependent upon co-activation of FGFR and ErbB receptors for PI3K pathway activity. CONCLUSIONS: The work presented here shows that in the breast cancer models examined, the combination of dovitinib + NVP-BEZ235 or dovitinib + AEE788 results in strong inhibition of tumor growth and a block in metastatic spread. Only these combinations strongly down-regulate the FGFR/FRS2/Erk and PI3K/Akt/mTOR signaling pathways. The resultant decrease in mitosis and increase in apoptosis was consistently stronger in the dovitinib + AEE788 treatment-group, suggesting that targeting ErbB receptors has broader downstream effects compared to targeting only PI3K/mTOR. Considering that sub-classes of human breast tumors co-express ErbB receptors and FGFRs, these results have implications for targeted therapy.
    Type of Publication: Journal article published
    PubMed ID: 23343422
    Signatur Availability
    BibTip Others were also interested in ...
  • 10
    Keywords: CANCER ; GENE ; GENOME ; MUTATIONS ; STEM-CELLS ; ZINC-FINGER PROTEIN ; T-CELL LYMPHOMAGENESIS ; MYC ; SUPER-ENHANCERS ; SUBGROUP
    Abstract: Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate 'enhancer hijacking' as an efficient mechanism driving oncogene activation in a childhood cancer.
    Type of Publication: Journal article published
    PubMed ID: 25043047
    Signatur Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...