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dc.contributor.authorNaba, Alexandra
dc.contributor.authorHoersch, Sebastian
dc.contributor.authorHynes, Richard O.
dc.contributor.authorHynes, Richard O.
dc.date.accessioned2017-01-31T15:43:49Z
dc.date.available2017-01-31T15:43:49Z
dc.date.issued2012-09
dc.identifier.issn0945053X
dc.identifier.urihttp://hdl.handle.net/1721.1/106801
dc.description.abstractThose of us interested in the extracellular matrix (ECM) are faced with significant challenges of definition. ECM proteins are large, complex and assembled into crosslinked insoluble matrices. This has meant that defining the biochemical composition of ECMs has been difficult. Nonetheless, protein chemistry and molecular biology have defined many familiar ECM proteins — collagens, proteoglycans, laminins, thrombospondins, tenascins, fibronectins, etc. With the completion of many genomes it should now be possible to develop complete “parts lists” for the ECM. Such lists are needed for analyzing data from “omic” approaches such as expression arrays, latest-generation sequencing and proteomics. These approaches generate long lists and it is typically necessary to extract from those lists the genes/proteins of interest. Anyone who attempts to do this using the commonly used gene ontology (GO) categories soon discovers that they are largely useless for defining ECM proteins. Many ECM proteins are unannotated and those which are, are sorted, with little evidence of logic or consistency, into diverse categories such “extracellular matrix,” “basement membrane,” “cell surface” and many others. The human and mouse orthologs are often found in different categories and attempts to use GO categories to extract a complete list of ECM genes or proteins from a data set are unsatisfactory at best.en_US
dc.language.isoen_US
dc.publisherElsevier B.V.en_US
dc.relation.isversionofhttp://dx.doi.org/10.1016/j.matbio.2012.11.008en_US
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivs Licenseen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en_US
dc.sourceProf. Hynes via Courtney Crummetten_US
dc.titleTowards definition of an ECM parts list: An advance on GO categoriesen_US
dc.typeArticleen_US
dc.identifier.citationNaba, Alexandra, Sebastian Hoersch, and Richard O. Hynes. “Towards Definition of an ECM Parts List: An Advance on GO Categories.” Matrix Biology 31, no. 7-8 (September 2012): 371–372.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.contributor.departmentKoch Institute for Integrative Cancer Research at MITen_US
dc.contributor.approverHynes, Richard O.en_US
dc.contributor.mitauthorNaba, Alexandra
dc.contributor.mitauthorHoersch, Sebastian
dc.contributor.mitauthorHynes, Richard O.
dc.relation.journalMatrix Biologyen_US
dc.eprint.versionAuthor's final manuscripten_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsNaba, Alexandra; Hoersch, Sebastian; Hynes, Richard O.en_US
dspace.embargo.termsNen_US
dc.identifier.orcidhttps://orcid.org/0000-0001-7603-8396
dspace.mitauthor.errortrue
mit.licensePUBLISHER_CCen_US


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