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  • COMPLEX  (12)
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  • 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
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  • 2
    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
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  • 3
    Keywords: CELLS ; human ; DISTINCT ; GENE ; GENES ; PROTEIN ; PROTEINS ; COMPLEX ; DOMAIN ; SEQUENCE ; SEQUENCES ; VARIANTS ; MOUSE ; IDENTIFICATION ; PATTERNS ; PROMOTERS ; HUMAN GENOME ; LOCALIZATION ; KAPPA-B ; DOMAINS ; SUBCELLULAR-LOCALIZATION ; RE ; VARIANT ; LOCUS ; EVENTS ; OPEN READING FRAMES ; function ; SPLICING VARIANTS ; transcriptome ; MAMMALIAN GENOMES ; PRE-MESSENGER-RNA
    Abstract: We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants
    Type of Publication: Journal article published
    PubMed ID: 16914452
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  • 4
    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
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  • 5
    Keywords: RECEPTOR ; CELLS ; IN-VITRO ; Germany ; IN-VIVO ; VITRO ; PROTEIN ; RELEASE ; COMPLEX ; COMPLEXES ; AP-1 ; DOMAIN ; ASSOCIATION ; MEMBRANE ; LIVING CELLS ; OVEREXPRESSION ; DOMAIN-CONTAINING PROTEIN ; SUBCELLULAR-LOCALIZATION ; FRACTION ; secretion ; STRUCTURAL BASIS ; interaction ; CATHEPSIN-D ; PROFILES ; ADP-RIBOSYLATION FACTOR ; ADAPTIN EAR DOMAIN ; APPENDAGE DOMAIN ; CLATHRIN-COATED VESICLES ; gamma-adaptin ; MANNOSE 6-PHOSPHATE RECEPTORS ; mannose-6-phosphate receptor ; post-Golgi transport ; SORTING SIGNALS ; TGN ; TRANS-GOLGI
    Abstract: A novel peripheral membrane protein (2c18) that interacts directly with the gamma 'ear' domain of the adaptor protein complex 1 (AP-1) in vitro and in vivo is described. Ultrastructural analysis demonstrates a colocalization of 2c18 and gamma 1-adaptin at the trans-Golgi network (TGN) and on vesicular profiles. Overexpression of 2c18 increases the fraction of membrane-bound gamma 1-adaptin and inhibits its release from membranes in response to brefeldin A. Knockdown of 2c18 reduces the steady-state levels of gamma 1-adaptin on membranes. Overexpression or downregulation of 2c18 leads to an increased secretion of the lysosomal hydrolase cathepsin D, which is sorted by the mannose-6-phosphate receptor at the TGN, which itself involves AP-1 function for trafficking between the TGN and endosomes. This suggests that the direct interaction of 2c18 and gamma 1-adaptin is crucial for membrane association and thus the function of the AP-1 complex in living cells. We propose to name this protein gamma-BAR
    Type of Publication: Journal article published
    PubMed ID: 15775984
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  • 6
    Keywords: EXPRESSION ; COMBINATION ; SYSTEM ; SYSTEMS ; GENE ; GENE-EXPRESSION ; GENOME ; microarray ; COMPLEX ; MEMBERS ; EXPERIENCE ; gene expression ; MICROARRAY DATA ; ASSAY ; genetics ; DATABASE ; OUTCOMES ; heredity ; PROTEOMICS ; MANAGEMENT ; genomics ; TECHNOLOGY ; USA ; microbiology ; ENGLAND ; biotechnology ; CONSORTIUM ; UK ; DATA STANDARDS ; MINIMUM INFORMATION
    Abstract: This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)
    Type of Publication: Journal article published
    PubMed ID: 18447634
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  • 7
    Keywords: ONCOLOGY ; breast cancer ; BREAST-CANCER ; BREAST ; CANCER ; COMPLEX ; COMPLEXES
    Type of Publication: Meeting abstract published
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  • 8
    Keywords: CELLS ; CELL ; Germany ; screening ; SYSTEM ; PROTEIN ; PROTEINS ; SAMPLE ; COMPLEX ; COMPLEXES ; TRANSPORT ; ACQUISITION ; ASSAY ; TRAFFICKING ; LOCALIZATION ; ER ; green fluorescent protein,proteomics,functional analysis,high-content screening microscopy,membrane ; MANAGEMENT
    Abstract: A modular microscope-based screening platform, with applications in large-scale analysis of protein function in intact cells is described. It includes automated sample preparation, image acquisition, data management and analysis, and the genome-wide automated retrieval of bioinformatic information. The modular nature of the system ensures that it is rapidly adaptable to new biological questions or sets of proteins. Two automated functional assays addressing protein secretion and the integrity of the Golgi complex were developed and tested. This shows the potential of the system in large-scale, cell-based functional proteomic projects. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 14623100
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  • 9
    Keywords: RECEPTOR ; CANCER ; CELLS ; EXPRESSION ; IN-VITRO ; tumor ; SUPPORT ; SYSTEM ; GENE ; PROTEIN ; PROTEINS ; DIFFERENTIATION ; TUMORS ; LINES ; COMPLEX ; COMPLEXES ; DOMAIN ; INDUCTION ; mechanisms ; SKIN ; MUTATION ; HETEROZYGOSITY ; MELANOMA ; CARCINOMA-CELLS ; EXCHANGE ; EPITHELIAL-CELLS ; squamous cell carcinoma ; epidermis ; TERMINAL DIFFERENTIATION ; DMBT1 ; SALIVARY AGGLUTININ ; basal cell carcinoma ; galectin-3 ; MALIGNANT BRAIN-TUMORS
    Abstract: DMBT1 and galectin-3 are potential interacting proteins with presumably complex roles in tumorigenesis. While at present a variety of mechanisms are discussed for DMBT1 and its participation in cancer, galectin-3 is commonly known to exert tumor-promoting effects. However, in vitro studies in a rodent system have suggested that DMBT1/galectin-3 interaction in the ECM triggers epithelial differentiation, which would point to tumor-suppressive properties. To improve the understanding of DMBT1/galectin-3 action in cancer, we carried out studies in skin cancer of different origins. Mutational analyses of DMBT1 identified a missense mutation in 1 of 13 melanoma cell lines. It led to an exchange of an evolutionary conserved proline residue for serine and located within the second CUB domain of DMBT1. Immunohistochemical analyses demonstrated absence of DMBT1/galectin-3 expression from melanocytes but induction of DMBT1 expression in 1 of 8 nevi and 1 of 11 melanomas and of galectin-3 expression in 3 of 8 nevi and 4 of 8 melanomas. These data suggest that DMBT1 and galectin-3 are unlikely to act as classical tumor suppressors in melanomas. DMBT1 and galectin-3 appear to be secreted to the ECM by epithelial cells within the epidermis and the hair follicle. Compared to the flanking normal epidermis, skin tumors of epithelial origin frequently displayed downregulation of DMBT1 (18 of 19 cases) and galectin-3 (12 of 12 cases). Thus, loss of DMBT1/ galectin- 3 expression may play a role in the genesis of epithelial skin cancer. This would support the view that galectin-3 can exert tumor-suppressive effects in certain scenarios, and DMBT1/galectin-3-mediated differentiation represents a candidate mechanism for this effect. (C) 2003 Wiley-Liss, Inc
    Type of Publication: Journal article published
    PubMed ID: 12673672
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  • 10
    Keywords: CELLS ; CELL ; Germany ; human ; MICROSCOPY ; PATHWAY ; screening ; PROTEIN ; PROTEINS ; COMPLEX ; COMPLEXES ; DOMAIN ; TRANSPORT ; YEAST ; ASSAY ; MEMBRANE ; HUMAN GENOME ; GOLGI-APPARATUS ; MORPHOLOGY ; FUTURE ; ESTABLISHMENT ; REGULATOR ; REGULATORS ; DOMAINS ; ENDOPLASMIC-RETICULUM ; ER ; SUBCELLULAR-LOCALIZATION ; coiled coil ; COILED-COIL ; COPII ; MATRIX PROTEINS
    Abstract: Here we describe the establishment of microscope-based functional screening assays in intact cells that allow LIS to systematically identify new proteins involved in secretory membrane traffic, and proteins that can influence the integrity of the Golgi complex. We were able to identify 20 new proteins that affected either secretory transport, Golgi morphology, or both, when overexpressed in cells. Control experiments with human orthologs to yeast proteins with a role in membrane traffic, or already well characterized mammalian regulators of the secretory pathway, confirmed the specificity and significance of our results. Proteins localized to the Golgi complex or endoplasmic reticulum (ER) showed preferential interference in Our assays. Bioinformatic analysis of the new proteins interfering with membrane traffic and/or Golgi integrity revealed broad functional variety, but demonstrated a bias towards proteins with predicted coiled-coil domains and repeat structures. Extending our approach to a much larger set of novel proteins in the future will be an important step toward a more comprehensive understanding of the molecular basis of the secretory pathway. It will also serve as an example for similar microscope-based screens addressing different biological questions
    Type of Publication: Journal article published
    PubMed ID: 15466293
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