Linked Life Data

18226600

Source:http://linkedlifedata.com/resource/pubmed/id/18226600

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2008-4-4
pubmed:abstractText
The iron absorption by duodenal enterocytes is a key step of its homeostasis. But the control of this absorption is complex and cannot be fully explicated with present knowledge. In a global transcriptome approach, we identified 60 genes over-expressed in hemin (iron) overload in Caco-2 cells, an in vitro model of duodenal enterocytes. The challenge from there was to identify the affected molecular mechanisms and achieve a biological interpretation for that cluster. In that purpose, we built up a functional annotation method combining evidence and literature. Our method identified four pathways in the Process hierarchy of the Gene Ontology (GO): lipid metabolism, amino acid and cofactor metabolism, response to stimulus and transport. The accuracy of this functional profile is supported by the identification of known pathways associated with the iron overload (response to oxidative stress, glutathione metabolism). But our method also suggests new hypotheses on the regulation of iron uptake in Caco-2 cells. It is hypothesized that plasma membrane remodeling and vesicular recycling could be a potential modulator of iron transport proteins activities. These assumptions yet require a biological validation and they will therefore direct further research. Our functional annotation method is a valuable tool designed to help the biologist understand the biological links between the genes of a cluster, elaborate working hypotheses and direct future work. This work is also a validation 'by hand' of a biomedical text-mining system.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0300-9084
pubmed:author
pubmed:issnType
Print
pubmed:volume
90
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
669-78
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Iron-related transcriptomic variations in Caco-2 cells: in silico perspectives.
pubmed:affiliation
Plateau Transcriptome OUEST-genopol Rennes, Université de Rennes 1, 35043 Rennes Cedex, France. marc.aubry@univ-rennes1.fr
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't