Human Gene Set: LI_ESTROGENE_NON_MCF7_T47D_E2_RESPONSE_DN

Standard name

LI_ESTROGENE_NON_MCF7_T47D_E2_RESPONSE_DN

Systematic name

M48224

Brief description

High confident estrogen up-regulated genes in non-MCF7/T47D breast cancer cell lines merged from 44 NGS datasets-based comparisons (10% topmost up-regulated genes and consistent in at least 40% 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. MCF7 and T47D cell lines have been used extensively as ER+ breast cancer models. However, extrapolation of this data to breast cancer is complicated by the known heterogeneity of breast cancer and potential biases arising from cell line-specific results. Importantly, while EstroGene contains transcriptomic data from 19 different breast cancer cell lines, data from MCF7 and T47D account for ~50% and ~20%, respectively, of all experiments . To characterize and describe contextual cell-line specific responses, we identified the top 10th percentile of upregulated and downregulated genes in an individual study and consistent among 50% of comparisons within MCF7 or T47D experiments. For non-MCF7/T47D experiments we lowered the threshold to 40% across studies due to the larger heterogeneity in this subset. Intersection of the three subsets yielded 89 and 96 uniquely regulated genes in MCF7 and T47D, we also identified 26 genes that were not regulated in MCF7 and T47D but showed E2-induction in some other cell lines.

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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