Human Gene Set: LI_ESTROGENE_EARLY_E2_RESPONSE_UP


Standard name LI_ESTROGENE_EARLY_E2_RESPONSE_UP
Systematic name M48213
Brief description High confident estrogen up-regulated genes in early treatment duration (≤6 hours) in breast cancer cells merged from 58 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.
Related gene sets (show 14 additional gene sets from the source publication)

(show 39 gene sets from any of these 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 88 genes
Gene families ? Categorize these 88 genes by gene family
Show members (show 88 source identifiers mapped to 88 genes)
Version history 2024.1.Hs: First Introduced.

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