Human Gene Set: LI_ESTROGENE_MCF7_E2_RESPONSE_DN


Standard name LI_ESTROGENE_MCF7_E2_RESPONSE_DN
Systematic name M48220
Brief description High confident estrogen down-regulated genes exclusively in MCF7 cells merged from 74 NGS datasets-based comparisons (10% topmost down-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. 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.
Related gene sets (show 14 additional gene sets from the source publication)

(show 38 gene sets from the same authors)
External links https://estrogene.org/
Filtered by similarity ?
Source species Homo sapiens
Contributed by Zheqi Li (University of Pittsburgh)
Source platform or
identifier namespace		 HUMAN_GENE_SYMBOL
Dataset references  
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 38 genes
Gene families ? Categorize these 38 genes by gene family
Show members (show 38 source identifiers mapped to 38 genes)
Version history 2024.1.Hs: First Introduced.

See MSigDB license terms here. Please note that certain gene sets have special access terms.