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dc.contributor.author
Thomsen, Martin
dc.contributor.author
Lundegaard, Claus
dc.contributor.author
Buus, Søren
dc.contributor.author
Lund, Ole
dc.contributor.author
Nielsen, Morten
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dc.date.available
2016-02-29T18:59:18Z
dc.date.issued
2013-09
dc.identifier.citation
Thomsen, Martin; Lundegaard, Claus; Buus, Søren; Lund, Ole; Nielsen, Morten; MHCcluster, a method for functional clustering of MHC molecules; Springer; Immunogenetics; 65; 9; 9-2013; 655-665
dc.identifier.issn
0093-7711
dc.identifier.issn
http://dx.doi.org/10.1007/s00251-013-0714-9
dc.identifier.uri
http://hdl.handle.net/11336/4529
dc.description.abstract
The identification of peptides binding to major histocompatibility complexes (MHC) is a critical step in the understanding of T cell immune responses. The human MHC genomic region (HLA) is extremely polymorphic comprising several thousand alleles, many encoding a distinct molecule. The potentially unique specificities remain experimentally uncharacterized for the vast majority of HLA molecules. Likewise, for nonhuman species, only a minor fraction of the known MHC molecules have been characterized. Here, we describe a tool, MHCcluster, to functionally cluster MHC molecules based on their predicted binding specificity. The method has a flexible web interface that allows the user to include any MHC of interest in the analysis. The output consists of a static heat map and graphical tree-based visualizations of the functional relationship between MHC variants and a dynamic TreeViewer interface where both the functional relationship and the individual binding specificities of MHC molecules are visualized. We demonstrate that conventional sequence-based clustering will fail to identify the functional relationship between molecules, when applied to MHC system, and only through the use of the predicted binding specificity can a correct clustering be found. Clustering of prevalent HLA-A and HLA-B alleles using MHCcluster confirms the presence of 12 major specificity groups (supertypes) some however with highly divergent specificities. Importantly, some HLA molecules are shown not to fit any supertype classification. Also, we use MHCcluster to show that chimpanzee MHC class I molecules have a reduced functional diversity compared to that of HLA class I molecules. MHCcluster is available at www.cbs.dtu.dk/services/MHCcluster-2.0.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Springer
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Mhc
dc.subject
Specificity
dc.subject
Functional Clustering
dc.subject.classification
Bioquímica y Biología Molecular
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
MHCcluster, a method for functional clustering of MHC molecules
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2016-03-30 10:35:44.97925-03
dc.journal.volume
65
dc.journal.number
9
dc.journal.pagination
655-665
dc.journal.pais
Alemania
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dc.journal.ciudad
Berlin
dc.description.fil
Fil: Thomsen, Martin. Technical University of Denmark. Department of Systems Biology. Center for Biological Sequence Analysis; Dinamarca
dc.description.fil
Fil: Lundegaard, Claus. Technical University of Denmark. Department of Systems Biology. Center for Biological Sequence Analysis; Dinamarca
dc.description.fil
Fil: Buus, Søren. University of Copenhagen. Laboratory of Experimental Immunology; Dinamarca
dc.description.fil
Fil: Lund, Ole. Technical University of Denmark. Department of Systems Biology. Center for Biological Sequence Analysis; Dinamarca
dc.description.fil
Fil: Nielsen, Morten. Universidad Nacional de San Martín; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Fisicoquímica Biológicas; Argentina. Technical University of Denmark. Department of Systems Biology. Center for Biological Sequence Analysis; Dinamarca
dc.journal.title
Immunogenetics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://dx.doi.org/10.1007/s00251-013-0714-9
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/issn/0093-7711
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://link.springer.com/article/10.1007%2Fs00251-013-0714-9
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750724/
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