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Series GSE9692 Query DataSets for GSE9692
Status Public on Dec 01, 2007
Title Validation of Genome-wide Expression patterns in Pediatric Septic Shock
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Rationale: We previously generated genome-wide expression data in children with septic shock, based on whole blood-derive RNA, having the potential to lead the field into novel areas of investigation.
Objective: Herein we seek to validate our data through a bioinformatic approach centered on a validation patient cohort.
Methods: Microarray- and bioinformatics-centered analyses involving our previous data as a training data set (n = 42) and a new, validation cohort (n = 30) as the test data set.
Measurements and Main Results: Class prediction modeling using the training data set and the previously reported genome-wide expression signature of pediatric septic shock correctly identified 93 to 100% of septic shock patients in the test data set, depending on the class prediction algorithm and the gene selection method. Subjecting the test data set to an identical filtering strategy as that used for the training data set, demonstrated 72% concordance between the two gene lists. Subjecting the test data set to a purely statistical filtering strategy, with highly stringent correction for multiple comparisons, demonstrated less than 50% concordance with the previous gene filtering strategy. However, functional analysis of this statistics-based gene list demonstrated similar functional annotations and signaling pathways as that seen in the learning data set. In particular, we validated that pediatric septic shock is characterized by large scale repression of genes related to zinc homeostasis and lymphocyte function.
Conclusions: These data demonstrate that the previously reported genome-wide expression signature of pediatric septic shock is applicable to a validation cohort of patients.
Keywords: Inflammation; sepsis; innate immunity; T cells; MHC antigen; zinc
 
Overall design Table 1: Clinical and demographic data for all subjects in test data set.

Controls Septic Shock
No. of individual subjects 15 30
Mean age (years) ± S.D. 3.1 ± 3.5 3.2 ± 2.9
Mean PRISM Score ± S.D. n/a 18.9 ± 12.3
Gender (Male/Female) 8/7 16/14
Race (no.) A.A./Black (6) A.A./Black (2)
Asian (4) White (26) White (5) Unreported (2)
 
Contributor(s) Cvijanovich N, Stanley TP, Lin R, Allen GL, Thoams NJ, Checcia P, Anas N, Freishtat RJ, Monaco M, Odoms K, Sakthivel B, Wong HR
Citation(s) 18460642
Submission date Nov 26, 2007
Last update date Mar 25, 2019
Contact name Hector R Wong
E-mail(s) hector.wong@cchmc.org
Phone 513-636-4259
Fax 513-636-4267
Organization name CIncinnati Children's Hospital Medical Center
Department Division of Critical Care Medicine
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229-3039
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (45)
GSM244467 01-0007A_Day1_0
GSM244468 01-0036A_Day1_1
GSM244469 01-0043A_Day1_2
Relations
BioProject PRJNA103591

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
GSE9692_RAW.tar 207.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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