NovelFam3000 – Uncharacterized human protein domains conserved across model organisms View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-12

AUTHORS

Danielle Kemmer, Raf M Podowski, David Arenillas, Jonathan Lim, Emily Hodges, Peggy Roth, Erik LL Sonnhammer, Christer Höög, Wyeth W Wasserman

ABSTRACT

BACKGROUND: Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in one protein, the presence of a similar sequence in an uncharacterized protein serves as a basis for inference of function. Thus knowledge of a domain's function, or the protein within which it arises, can facilitate the analysis of an entire set of proteins. DESCRIPTION: From the Pfam domain database, we extracted uncharacterized protein domains represented in proteins from humans, worms, and flies. A data centre was created to facilitate the analysis of the uncharacterized domain-containing proteins. The centre both provides researchers with links to dispersed internet resources containing gene-specific experimental data and enables them to post relevant experimental results or comments. For each human gene in the system, a characterization score is posted, allowing users to track the progress of characterization over time or to identify for study uncharacterized domains in well-characterized genes. As a test of the system, a subset of 39 domains was selected for analysis and the experimental results posted to the NovelFam3000 system. For 25 human protein members of these 39 domain families, detailed sub-cellular localizations were determined. Specific observations are presented based on the analysis of the integrated information provided through the online NovelFam3000 system. CONCLUSION: Consistent experimental results between multiple members of a domain family allow for inferences of the domain's functional role. We unite bioinformatics resources and experimental data in order to accelerate the functional characterization of scarcely annotated domain families. More... »

PAGES

48

References to SciGraph publications

  • 2003-12. PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine in BMC BIOINFORMATICS
  • 2005-12. Ulysses - an application for the projection of molecular interactions across species in GENOME BIOLOGY
  • 2006. ProDom in ENCYCLOPEDIC REFERENCE OF GENOMICS AND PROTEOMICS IN MOLECULAR MEDICINE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-7-48

    DOI

    http://dx.doi.org/10.1186/1471-2164-7-48

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1027148749

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16533400


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    HOW TO GET THIS DATA PROGRAMMATICALLY:

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    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-7-48'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-7-48'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-7-48'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-7-48'


     

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