Validating the genomic signature of pediatric septic shock

We assayed peripheral blood leucocyte global gene expression for a prospective discovery cohort of 265 adult patients admitted to UK intensive care units with sepsis due to community-acquired pneumonia and evidence of organ dysfunction.We then validated our findings in a replication cohort consisting of a further 106 patients.

We discovered that following admission to intensive care, transcriptomic analysis of peripheral blood leucocytes defines two distinct sepsis response signatures (SRS1 and SRS2).

We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data.

Database URL: Bgee (a data Base for Gene Expression Evolution) (1) is a resource to perform high-throughput and automated comparisons of gene expression patterns between species.

To this end, it integrates expression data of different types (ESTs, hybridization, Affymetrix and RNA-Seq data, as of Bgee release 12), from different species (fruit fly, human, mouse, Xenopus and zebrafish, as of Bgee release 12).

Each data type is analysed using dedicated statistical tests, to generate present/absent expression calls, and differential expression calls (overexpression and underexpression).

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In contrast, genome-wide expression varied significantly among different subjects and leukocyte subpopulations.

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