siTAZdiffex_HFL1_diffexDT: Differential expression from RNAseq assay of TAZ siRNA...

In adamsardar/metaDEGth: Combining differential expression P-values in a statistically consistent fashion whilst respecting background signal/noise trends

Differential expression from RNAseq assay of TAZ siRNA knockdowns in HFL-1

Description

GSE73555 studied genes regulated by the transcription co-factor TAZ in a lung fibroblast cell line (HFL-1). The authors used siRNA to knock down the TAZ gene (aka WWTR1); two different siRNAs for TAZ and a negative control (NTC) siRNA. It serves as a perfect 'spike-in' study for us to test gene set enrichment techniques against.

Usage

data(siTAZdiffex_HFL1_diffexDT)

Format

A data.table with 14,501 rows, documenting differential gene expression (logFC and unadjusted P-values) of 14,475 ENSEMBL gene entities in two experimental conditions (siTAZ1 and siTAZ2). Addition gene symbols, entrez gene IDs and uniprot annotations also included (duplicated ENSG entries result from many-to-one mappings)

Details

Generated 6 December 2019 from the trimmed reads associated with project. These were downloaded and aligned against the human genome using Kallisto before transcript abundances were estimated using limma-voom. Finally, differential gene expression values were computed.

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73555

References

https://www.genecards.org/cgi-bin/carddisp.pl?gene=WWTR1

Noguchi S, Saito A, Mikami Y, Urushiyama H, Horie M, Matsuzaki H, et al. TAZ contributes to pulmonary fibrosis by activating profibrotic functions of lung fibroblasts. Sci Rep. 2017

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods. 2017

Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014

Examples

library(ggplot2)
library(magrittr)
data(siTAZdiffex_HFL1_diffexDT)

siTAZdiffex_HFL1_diffexDT %>% ggplot(aes(x = siTAZ1_logFC, y = -log10(siTAZ1_pValue))) + 
    geom_point(aes(colour = p.adjust(siTAZ1_pValue, "fdr") < 0.01)) +
    scale_colour_manual(values = c("darkgrey","dodgerblue")) +
    theme_bw()

adamsardar/metaDEGth documentation built on Sept. 28, 2022, 10:12 p.m.