Systematic name M10541
Brief description Genes up-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones.
Full description or abstract About 70-80% of breast cancers express estrogen receptor alpha (ER-alpha), and estrogens play important roles in the development and growth of hormone-dependent tumors. Together with lymph node metastasis, tumor size, and histological grade, ER status is considered as one of the prognostic factors in breast cancer, and an indicator for hormonal treatment. To investigate genes and pathways that are associated with ER status and epithelial cells in breast tumor, we applied laser capture microdissection (LCM) technology to capture epithelial tumor cells from 28 lymph node-negative breast tumor samples, in which 17 patients had ER-alpha+ tumors, and 11 patients have ER-alpha- tumors. Gene expression profiles were analysed on Affymetrix Hu133A GeneChip. Meanwhile, gene profiles using total RNA isolated from bulk tumors of the same 28 patients were also generated. In total, 146 genes and 112 genes with significant P-value and having significant differential expression between ER-alpha+ and ER-alpha- tumors were identified from the LCM data set and bulk tissue data set, respectively. A total of 61 genes were found to be common in both data sets, while 85 genes were unique to the LCM data set and 51 genes were present only in the bulk tumor data set. Pathway analysis with the 85 genes using Gene Ontology suggested that genes involved in endocytosis, ceramide generation, Ras/ERK/Ark cascade, and JAT-STAT pathways may play roles related to ER. The gene profiling with LCM-captured tumor cells provides a unique approach to study epithelial tumor cells and to gain an insight into signaling pathways associated with ER.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 16261164   Authors: Yang F,Foekens JA,Yu J,Sieuwerts AM,Timmermans M,Klijn JG,Atkins D,Wang Y,Jiang Y
Exact source Table 2S: Relative expression +
Related gene sets (show 5 additional gene sets from the source publication)

(show 82 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Leona Saunders (MSigDB Team)
Source platform or
identifier namespace
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 ? GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 32 genes
Gene families ? Categorize these 32 genes by gene family
Show members (show 34 source identifiers mapped to 32 genes)
Version history 3.0: First introduced

We need your help: Update on GSEA/MSigDB funding support

Last November we submitted a proposal to NCI's Information Technology for Cancer Research (ITCR) program for the continued funding of GSEA and MSigDB. Unfortunately, our proposal was not funded in this round, but we were encouraged to resubmit for the next one. This funding is critical for our continuing support and enhancement of the GSEA-MSigDB resource.

For our original submission many of you sent us emails of support, an important requirement for these grants. We now ask for your help again. We would greatly appreciate a short email message from you describing how the resource has been of value to your work and any concerns you may have about its continued availability.

Please send us your message of support to on or before Monday June 5, 2023.

Thanks in advance for your help and support.
The GSEA/MSigDB Team.

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