WZ4002_adrH1975_diffexDT: Microarray assay studying aberrant MAPK1/ERK signaling,...

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

Microarray assay studying aberrant MAPK1/ERK signaling, causing resistance to EGFR kinase inhibitors

Description

GSE37699: WZ4002 is a second generation TKI, effective at treating cells with the most common T790M mutation of aquired drug resistance. This study inspects cell lines which have evolved resitance to WZ4002 by repeated exposure, concluding that it is a result of upregulated MAPK1 and/or ERK pathway activity. Expression captured using Illumina HumanHT-12 V3.0 expression beadchip.

Usage

data(WZ4002_adrH1975_diffexDT)

Format

A data.table with 22,277 rows, documenting probe-level differential expression between unchallenged and immune (evolved resistance) NCI-H1975 cell lines. Addition gene symbols and entrez gene IDs are also included.

Details

Generated 10 December 2019 from raw expression values dowloaded from GEO. Values were normalised using limma::neqc and processed with further limma functions.

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37699

References

Ercan D, Xu C, Yanagita M, Monast CS, Pratilas CA, Montero J, et al. Reactivation of ERK signaling causes resistance to EGFR kinase inhibitors. Cancer Discov. 2012

Examples

library(ggplot2)
library(magrittr)

data(WZ4002_adrH1975_diffexDT)

WZ4002_adrH1975_diffexDT %>%
ggplot(aes(x = H1975_logFC, y = -log10(H1975_pValue))) +
    geom_point(aes(colour = p.adjust(H1975_pValue) < 0.01 )) +
    scale_colour_manual(values = c("darkgrey","dodgerblue")) +
    theme_bw() 

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