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E-GEOD-20436 - Expression data from Gambian children with and without the clinical signs of active trachoma: U133 Plus2.0 array

Status
Released on 3 September 2010, last updated on 10 June 2011
Organism
Homo sapiens
Samples (60)
Array (1)
Protocols (8)
Description
Conjunctival samples from 60 individuals with and without the clinical signs of active trachoma were analysed on the U133 Plus 2.0 arrays. Global transcriptional changes characteristic of disease and infection phenotypes were identified. Two analysis methods found large numbers of differentially regulated genes and the existence of networks of co-expressed genes. There were signatures characteristic of the host defence response with evidence supporting infiltration of various types of leukocytes and activation of innate responses of epithelial cells. Two separate methods could classify disease and infection phenotype based on transcription signatures with 70% accuracy. These results provide an insight into the complexity of the acute response in trachoma but are able to partly explain the biology of trachoma through the identification of pathways and gene expression sets useful to future studies on chlamydial immunopathogenesis. Conjunctival samples from 60 participants were tested on U133 plus 2.0 arrays (40 participants with clinical signs of active trachoma and 20 controls with normal conjunctivas as before). Samples were further sub-divided based on the detection and quantification of ocular Chlamydia trachomatis load by PCR tests. Gene expression was then assessed using differential expression and construction of co-expression networks. The content of the constructed gene lists which were identified as part of a network or differentially expressed were then tested for enrichment using publically available analysis tools to identify biological pathways expressed in the conjunctiva during C. trachomatis infection and disease episodes.
Experiment type
transcription profiling by array 
Contacts
Martin James Holland <Martin.Holland@lshtm.ac.uk>, Angels Natividad, David C Mabey, David Jeffries, Martin J Holland, Matthew J Burton, Robin L Bailey, Tom C Freeman
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20436.idf.txt
Sample and data relationshipE-GEOD-20436.sdrf.txt
Raw data (2)E-GEOD-20436.raw.1.zip, E-GEOD-20436.raw.2.zip
Processed data (1)E-GEOD-20436.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-20436.eSet.r
Links