reference_set_davenport: Whole blood gene expression measurements for 7 genes across...

In jknightlab/SepstratifieR: Stratification of infectious disease patients by gene expression profile

Whole blood gene expression measurements for 7 genes across 3,264 individuals

Description

A data set containing gene expression measurements from whole blood for the 7 SRS signature genes defined by Davenport et al.

Usage

reference_set_davenport

Format

A data frame with 3264 rows and 7 variables:

ENSG00000152219

ARL14EP, cosine-scaled, batch corrected gene expression level

ENSG00000100814

CCNB1IP1, cosine-scaled, batch corrected gene expression level

ENSG00000127334

DYRK2, cosine-scaled, batch corrected gene expression level

ENSG00000131355

ADGRE3, cosine-scaled, batch corrected gene expression level

ENSG00000137337

MDC1, cosine-scaled, batch corrected gene expression level

ENSG00000156414

TDRD9, cosine-scaled, batch corrected gene expression level

ENSG00000115085

ZAP70, cosine-scaled, batch corrected gene expression level

...

Details

This data set is formed of 1,609 samples from healthy individuals and 1,655 samples from sepsis patients.

Sepsis patients were recruited as a part of the Genomic Advances in Sepsis (GAinS) study in Oxford, UK. Of these, 676 were profiled using the Illumina HumanHT microarray, 864 using polyA-based RNA-sequencing, and 115 using qPCR.

Healthy individual data was collected from a number of publicly available sources. In particular, 991 OIllumina HumanHT microarray samples were obtained from the SHIP-TREND consortium, 518 Illumina HumanHT microarray samples were obatained from the DILGOM cohort (an extension of the FINRISK study), and 100 polyA-based RNA-sequencing samples were obtained from the dutch 500FG cohort

RNA-seq data was log-transformed and any relevant batch effects were removed using the combat algorithm. Finally, the 7 SRS signature genes were extracted from each cohort and the data was integrated together using the mutual nearest neighbout (mNN) algorithm.

The values reported in this data set were obtained after mNN alignment, and thus they represent Cosine-scale batch-corrected values.

The main use of this data set is to serve as a reference to which new input samples can be aligned before prediction of SRS group using random forest models.

jknightlab/SepstratifieR documentation built on March 19, 2022, 9:43 p.m.