High confident estrogen up-regulated genes in middle treatment duration (6-24 hours) in breast cancer cells merged from 44 NGS datasets-based comparisons (10% topmost up-regulated genes and consistent in at least 50% comparisons).
Full description or abstract
As one of the most successful cancer therapeutic targets, estrogen receptor-alpha (ER/ESR1) has been extensively studied over the past few decades. Sequencing technological advances have enabled genome-wide analysis of ER action. However, comparison of individual studies is limited by different experimental designs, and few meta-analyses are available. Here, by ingesting large amount of E2-related transcriptomic data sets in breast cancer cell lines, we identified gene expression changes across 66 RNA-seq and 80 microarray experiments based upon the E2-induced fold change in gene expression. Among the 146 merged transcriptomic datasets, 27 different time points were annotated spanning from 5 minutes to 600 hours of estrogen stimulation. We separated all the comparisons into three signatures of duration: EstroGene_Early (≤6 hours, n = 58), EstroGene_Mid (6-24 hours, n = 44) and EstroGene_Late (≥ 24 hours, n = 44). Upregulated and downregulated genes present in the top 10th percentile of regulated genes in each individual study, and consistently present across at least 50% of studies at each time period, were extracted from each signature (early, mid, and late) and intersected accordingly. We identified 165, 59 and 136 genes representing early, mid, and late estrogen response signatures, respectively.
Collection
C2: Curated CGP: Chemical and Genetic Perturbations
Source publication
Pubmed 37272757 Authors: Li Z,Li T,Yates ME,Wu Y,Ferber A,Chen L,Brown DD,Carroll JS,Sikora MJ,Tseng GC,Oesterreich S,Lee AV
Exact source
Supplementary Table S10: EstroGene temporal, contextual and directional signatures. Detailed GEO IDs of all the datasets used can be found in Supplementary Table S1 Inventory of EstroGene Database of the publication.
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