H3N2-Subj1: Time-course gene expression data collected from a H3N2...

In Thakar-Lab/FUNNEL-GSEA-R-Package: FUNNEL-GSEA: FUNctioNal ELastic-net Regression in time-course Gene Set Enrichment Analysis

Description

This is the processed gene expression data extracted from Huang et al (2011). PloS Comp. Genet. study, with GEO accession number GSE52428. Expressions are log2-transformed and filtered by the criterion IQR>=0.3. Also, pre-specified CP:KEGG gene sets are downloaed from the Broad Institute.

Usage

data("H3N2-Subj1")

Format

The data set contains the following:

X

A 11189x16 pre-processed gene expression matrix taken from a H3N2 human influenza challenge study (Subject1). Genes are ordered as rows and each column represent a time point. Row names must be gene names used in genesets. Columns must be ordered by tt.

tt

A vector of ordered time points.

genesets

A list of 186 CP:KEGG gene sets. Each gene set is an element of the list. Gene set names are as element names in the list. Genes in genesets should be annotated in the same way rownames of the X matrix does.

References

Huang Y, Zaas AK, Rao A, Dobigeon N, Woolf PJ, Veldman T, et al. (2011) Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection. PLoS Genet 7(8): e1002234. doi:10.1371/journal.pgen.1002234

Examples

data(H3N2-Subj1)

Thakar-Lab/FUNNEL-GSEA-R-Package documentation built on May 8, 2019, 9:57 p.m.