NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE40586 Query DataSets for GSE40586
Status Public on Sep 05, 2012
Title Peripheral blood RNA gene expression profiling in patients with bacterial meningitis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The aim of present study was to describe the genetic pathways activated during the community acquired bacterial meningitis (BM) by using genome-wide RNA expression profiling combined with functional annotation of transcriptional changes. We included 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed with GeneChip Human Gene 1.0 ST Arrays enabling the analysis of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define changed genetic networks. We also analyzed if the gene expression profile depends on the clinical course and outcome. In order to verify the genechip results, we chose ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, IL7R) and performed quantitative real-time (qRT) PCR.We identified the significant differences at p values of <0.05 in 8569 genes and after False Discovery Rate (FDR) correction, total of 5500 genes remained significant at p value of <0.01. Quantitative RT-PCR confirmed differential expression for selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in adults and in children with BM compared to the healthy controls. Gene expression profile didn’t depend on the clinical outcome, but there was very strong influence by the type of the pathogen. This study demonstrates a strong functional genomic evidence of the over-active immune response during bacterial meningitis. This hyperactive response possibly explains the complicated clinical course of this disease.
 
Overall design 22 bacterial meningitis patients and 18 healthy controls
 
Contributor(s) Lill M, Kõks S, Soomets U, Schalkwyk LC, Fernandes C, Lutsar I, Taba P
Citation(s) 23515576
Submission date Sep 04, 2012
Last update date Jul 26, 2018
Contact name Sulev Koks
E-mail(s) sulev.koks@murdoch.edu.au
Phone +61864570313
Organization name Murdoch University
Department Centre for Molecular Medicine and Innovative Therapeutics
Street address 90 South Street
City Perth
State/province Western Australia
ZIP/Postal code 6150
Country Australia
 
Platforms (1)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Samples (39)
GSM997332 US_BM_01_M038
GSM997333 US_BM_02_K003
GSM997334 US_BM_03_K027
Relations
BioProject PRJNA174349

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40586_RAW.tar 162.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap