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  • human  (13)
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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: 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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  • 3
    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
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  • 4
    Keywords: RECEPTOR ; human ; MODEL ; MODELS ; EXPOSURE ; RISK ; GENE ; TIME ; PATIENT ; ASSOCIATION ; FREQUENCY ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; PATTERNS ; STRESS-RESPONSE ; DNA-BINDING ; ethanol ; INDIVIDUALS ; ALCOHOL ; CHILDREN ; PREVALENCE ; ALCOHOL-CONSUMPTION ; CONSUMPTION ; ENHANCER ; DISORDERS ; ADULTS ; DEPENDENCE ; MICE LACKING ; haplotype-tagging ; alcohol consumption ; animal model ; HORMONE-RECEPTOR ; TRANSCRIPTION FACTOR SP1 ; ADOLESCENTS ; AFFECTIVE-DISORDERS ; CORTICOTROPIN-RELEASING-FACTOR ; EARLY ADULTHOOD ; HPA-axis
    Abstract: To investigate the role of the corticotropin releasing hormone receptor 1 (CRHR1) in patterns of human alcohol drinking and its potential contribution to alcohol dependence, we analysed two independent samples: a sample of adolescents, which consisted of individuals from the 'Mannheim Study of Risk Children' (MARC), who had little previous exposure to alcohol, and a sample of alcohol-dependent adults, who met DSM-IV criteria of alcohol dependence. Following determination of allelic frequencies of 14 polymorphisms of the CRHR1 gene, two haplotype tagging (ht)SNPs discriminating between haplotypes with a frequency of 〉= 0.7% were identified. Both samples were genotyped and systematically examined for association with the htSNPs of CRHR1. In the adolescent sample, significant group differences between genotypes were observed in binge drinking, lifetime prevalence of alcohol intake and lifetime prevalence of drunkenness. The sample of adult alcohol-dependent patients showed association of CRHR1 with high amount of drinking. This is the first time that an association of CRHR1 with specific patterns of alcohol consumption has been reported. Our findings support results from animal models, suggesting an importance of CRHR1 in integrating gene environment effects in alcohol use disorders
    Type of Publication: Journal article published
    PubMed ID: 16550213
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  • 5
    Keywords: Germany ; human ; SYSTEM ; CDNA ; GENOME ; PROTEIN ; PROTEINS ; SAMPLE ; SEQUENCES ; DATABASE ; INTERFACE ; WEB ; TRACKING ; HUMAN GENES ; FUNCTIONAL GENOMICS ; PROTEOMICS ; CDNAS ; SUBCELLULAR-LOCALIZATION
    Abstract: We have implemented LIFEdb (http://www.dkfz.de/ LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions
    Type of Publication: Journal article published
    PubMed ID: 14681468
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  • 6
    Keywords: EXPRESSION ; Germany ; human ; DISEASE ; GENE ; GENE-EXPRESSION ; GENES ; TISSUE ; TISSUES ; LINKAGE ; MOUSE ; IDENTIFICATION ; IN-SITU ; gene expression ; NUMBER ; DATABASE ; REGION ; REGIONS ; LOCALIZATION ; ORGANIZATION ; RE ; EXPRESSION PATTERNS ; MAP ; MENTAL-RETARDATION ; SUBUNIT PROTEIN ; CPG-BINDING PROTEIN-2
    Abstract: Background: Well known for its gene density and the large number of mapped diseases, the human sub-chromosomal region Xq28 has long been a focus of genome research. Over 40 of approximately 300 X-linked diseases map to this region, and systematic mapping, transcript identification, and mutation analysis has led to the identification of causative genes for 26 of these diseases, leaving another 17 diseases mapped to Xq28, where the causative gene is still unknown. To expedite disease gene identification, we have initiated the functional characterisation of all known Xq28 genes. Results: By using a systematic approach, we describe the Xq28 genes by RNA in situ hybridisation and Northern blotting of the mouse orthologs, as well as subcellular localisation and data mining of the human genes. We have developed a relational web-accessible database with comprehensive query options integrating all experimental data. Using this database, we matched gene expression patterns with affected tissues for 16 of the 17 remaining Xq28 linked diseases, where the causative gene is unknown. Conclusion: By using this systematic approach, we have prioritised genes in linkage regions of Xq28-mapped diseases to an amenable number for mutational screens. Our database can be queried by any researcher performing highly specified searches including diseases not listed in OMIM or diseases that might be linked to Xq28 in the future
    Type of Publication: Journal article published
    PubMed ID: 16503986
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  • 7
    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
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  • 8
    Keywords: human ; GENE ; GENES ; PROTEINS ; SEQUENCE ; ACID ; ACIDS ; NUCLEIC-ACID ; NUCLEIC-ACIDS ; DATABASE ; PREDICTION ; HUMAN GENES ; RE ; ANNOTATION ; RESOURCE ; GENOMIC DNA
    Abstract: Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, proteinprotein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
    Type of Publication: Journal article published
    PubMed ID: 18089548
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  • 9
    Keywords: ENVIRONMENT ; CANCER ; Germany ; human ; MODEL ; MODELS ; PATHWAY ; PATHWAYS ; NETWORKS ; TOOL ; GENE ; GENES ; GENOME ; BIOLOGY ; bioinformatics ; pancreatic cancer ; DISSECTION ; MAPS ; PANCREATIC-CANCER ; SOFTWARE ; biotechnology ; GENOMES ; WELL ; BETWEENNESS ; CENTRALITY
    Abstract: Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory. Results: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway
    Type of Publication: Journal article published
    PubMed ID: 19307239
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  • 10
    Keywords: Germany ; human ; KINASE ; TYROSINE KINASE ; COHORT ; NEW-YORK ; RISK ; GENE ; PROTEIN ; PATIENT ; TOLERANCE ; ASSOCIATION ; polymorphism ; single nucleotide polymorphism ; HUMANS ; NUMBER ; SNP ; REGION ; RELIABILITY ; PHENOTYPE ; SELECTION ; ALCOHOL ; INTERVIEW ; alcohol dependence,protein tyrosine kinase,fyn,early onset,withdrawal,alcohol intake,association,lin ; ETHANOL SENSITIVITY
    Abstract: Background: Decreased sensitivity to and increased tolerance for the effects of alcohol is a phenotype, which was shown to be associated with an increased risk for alcoholism in humans and was observed in protein tyrosine kinase (PTK) fyn knockout mice.Methods: We performed an association study of genetic variations of PTK fyn in 430 alcohol-dependent patients and 365 unrelated control subjects from two independent samples.Results: In a combined analysis, we found an association of alcohol dependence with the single nucleotide polymorphism (SNP) T137346C in the 5' untranslated region (UTR) of the gene. A relevant association could be excluded for the remaining two informative SNPs. Selection by phenotype showed that a high number of withdrawal symptoms, high amount of alcohol intake, and high maximum number of drinks compared with unrelated control subjects was associated with the SNP in the 5'-UTR region but not with the remaining SNPs.Conclusions: Our results indicate a possible association of alcohol dependence with a genotype of the SNP T137346C of the PTK fyn, with C being the risk allele
    Type of Publication: Journal article published
    PubMed ID: 14675807
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