orthologs: Example ortholog data set

In disco: Discordance and Concordance of Transcriptomic Responses

Description

Example object of class matchedOrtholog containing mouse and human data sets

Details

The matchedOrtholog object orthologs contains matched orthologous genes from mouse and human samples, and the results of differential expression analysis as log_2 fold changes and p-values.

The human data set contains blood transcriptional profiles of 46 TB patients and 62 healthy individuals and is available on the Gene Expression Omnibus database under the accession number GSE28623 (Maertzdorf et al., 2011).

The mouse data set was derived from 129S2 mice infected with TB for 24h (5 mice) and before infection (5 mice) and is available under the accession number GSE89392. The data sets have been analyzed with limma R package for differential expression analysis (Ritchie et al., 2015). The data sets were background corrected using the normexp method and quantile normalized between arrays. Limma lmFit function was used to fit linear models which included the factors: stimulus type and time point. The p-values were calculated based on the moderated t-statistic and most differentially regulated genes were retrieved with topTable function. Orthologous genes were assigned to each other between corresponding human and mouse data sets used in each comparison. Probe names specific to the microarray used were assigned an ENSEMBL identifier with use of mapIds function from the biomaRt package (version 2.24.1, Durinck et al., 2005; Durinck, Spellman, Birney, & Huber, 2009).

Multiple repeating probes were averaged by applying limma avereps function. Then, orthologous human and mouse genes were identified with biomaRt getLDS function based on homology mapping between different species interlinked in Ensembl data base (with attributes and filters defined as ensembl_gene_id. Only the putative orthologs with a 1:1 mapping (no potential in-paralogs) were included in the further analysis.

The gene names in the object correspond to the human gene names.

Examples

data(orthologs)
# view the object as a data frame
head(as(orthologs, "data.frame"))
# calculate the disco score
ds <- disco.score(orthologs)

disco documentation built on May 2, 2019, 9:40 a.m.