RESUMO
Serial Analysis of Gene Expression (SAGE) is an important means of obtaining quantitative information about expression of genes in different samples. Short SAGE tags are 10 nucleotides long and often contain enough information to uniquely identify the gene(s) corresponding to the tag. We have observed, however, that the currently available resources are not adequate for accurate mapping of all SAGE tags to genes. Here, we describe development of a web-based tool called TAGmapper (http://tagmapper.ibioinformatics.org), which provides a comprehensive and accurate mapping of SAGE tags to genes. We were able to map SAGE tags accurately in several instances where two other popular resources, SAGEmap (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and SAGE Genie (http://cgap.nci.nih.gov/SAGE), provided incorrect or no assignment of tags to genes. Finally, we experimentally determined the expression of a subset of genes assigned by TAGmapper using DNA microarrays and/or quantitative PCR to confirm the reliability of the gene mappings. We anticipate that TAGmapper will be a useful tool in functional genomic approaches by providing accurate identification of genes in SAGE experiments.
Assuntos
Mapeamento Cromossômico/métodos , Expressão Gênica , Internet , Interface Usuário-Computador , Sequência de Bases , Etiquetas de Sequências Expressas , Modelos GenéticosRESUMO
Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778 distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein-coding regions were mapped onto the protein sequences. We found a number of examples of isoform-specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org.
Assuntos
Proteínas Sanguíneas/química , Proteínas Sanguíneas/genética , Bases de Dados de Proteínas , Proteômica/métodos , Motivos de Aminoácidos , Biologia Computacional/métodos , Genoma Humano , Humanos , Espectrometria de Massas , Peptídeos/química , Polimorfismo de Nucleotídeo Único , Isoformas de Proteínas , Estrutura Terciária de Proteína , Fatores de TempoAssuntos
Cromossomos Humanos X/genética , Processamento Alternativo , Sequência de Aminoácidos , Sequência de Bases , Mapeamento Cromossômico , Biologia Computacional , DNA Complementar/genética , Bases de Dados Genéticas , Bases de Dados de Proteínas , Éxons , Humanos , Dados de Sequência Molecular , Fases de Leitura Aberta/fisiologia , Alinhamento de SequênciaRESUMO
BACKGROUND: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. RESULTS: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. CONCLUSIONS: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.
Assuntos
Sistemas de Gerenciamento de Base de Dados , Bases de Dados de Proteínas , Proteínas/fisiologia , Software , Biologia Computacional/métodos , Biologia Computacional/normas , Bases de Dados de Proteínas/normas , Humanos , Internet , Proteínas/normas , Software/normas , Design de SoftwareRESUMO
The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.
