Sepsis Multi-Cohort Analysis Papers
Sepsis vs. Non-Infectious Inflammation Manuscript (Sci Transl Med, 2015)
Full-text link to the manuscript (gets behind paywall): Sweeney TE, Shidham A, Wong HR, Khatri P. "A Comprehensive Time-Course-Based Multi-Cohort Analysis of Sepsis and Sterile Inflammation Reveals a Robust Diagnostic Gene Set". Science Translational Medicine, 7, 287ra71 (May 13, 2015).
A BBC interview discussing the impact of these results (sepsis discussion begins @ 13:53):
The R scripts for running the multi-cohort analysis (data not included):
Bacterial - Viral Classification Manuscript (Sci Transl Med, 2016)
The R scripts for running the multi-cohort analysis (same as above, data not included):
sepsis_mc_analysis.zip
COCONUT is available on CRAN for R: COCONUT R package
Link to COCONUT-conormalized data objects used in manuscript
Benchmarking sepsis gene expression diagnostics using public data
Full-text link: Sweeney TE & Khatri P, "Benchmarking sepsis gene expression diagnostics using public data". Critical Care Medicine, 2016
Benchmarking scripts described in the manuscript
Link to data objects
Neonatal Sepsis Analysis
Data for: Sweeney, TE et al., "Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis", J Ped Inf Dis Soc, 2017
COCONUT-normalized, unique patients from GSE25504 (Smith et al., 2015)
Sepsis Mortality Analysis
The preprint linked below will be updated with the final, peer-reviewed version once published.
Sweeney, TE et al., "Mortality prediction in sepsis via gene expression analysis: a community approach". BioArxiv, 2016
COCONUT-normalized data from Herberg et al, JAMA 2016: GSE72829
The dataset GSE72829 described in Herberg et al, JAMA 2016 is composed of 4 smaller datasets spread across three microarray platforms. We used COCONUT to pool these data into a single dataset. Notably, since GSE80412 has no healthy controls, these were initially co-normalized using Limma with GSE72809, and then healthy controls between all three remaining datasets were used to make the final COCONUT-conormalized object. The pooled data are available as a .RDS (R object) here.
Glue Grant Data Access
Some of the data used in the manuscript (the Inflammation and Host Response to Injury Glue Grant data) require IRB access. This can be obtained by following the instructions here: https://www.gluegrant.org/
Briefly, you will need to first register as a Consortium Member: Glue Grant Consortium Registration
You will then be able to access the consortium page, which explains exact instructions for obtaining data access at the bottom section, titled “Our Policies for Access to Data, Methodologies, and Protocols”.
When access to the Glue Grant database has been issued by the Glue Grant team, please email (1) IRB approval and (2) the letter of approval from the Glue Grant consortium to: tes17 [at] stanford [dot] edu to request access to the data object.