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Series GSE4888 Query DataSets for GSE4888
Status Public on May 24, 2006
Title Molecular phenotyping of human endometrium
Organism Homo sapiens
Experiment type Expression profiling by array
Summary To examine the possibility that biochemical or molecular signatures of endometrium may prove to be more useful, we have investigated whole genome molecular phenotyping (54,600 genes/ESTs) of this tissue sampled across the cycle in 28 normo-ovulatory women, using high-density oligonucleotide microarrays. The results demonstrate that endometrial samples obtained by two different sampling techniques (biopsy and curetting hysterectomy specimens) from subjects who are as normal as possible in a human study and 4 including those with unknown histology, can be classified by their molecular signatures and correspond to known phases of the menstrual cycle with identical results using two independent analytical methods. Also, the results enable global identification of biological processes and molecular mechanisms that occur dynamically in the endometrium in the changing steroid hormone milieu across the menstrual cycle in normo-ovulatory women. The results underscore the potential of gene expression profiling for developing molecular diagnostics of endometrial normalcy and abnormalities and identifying molecular targets for therapeutic purposes in endometrial disorders.
Keywords: Gene expression arrays human endometrium
 
Overall design Unsupervised principal component analysis (PCA) of all samples revealed that samples selfcluster into four groups consistent with histologic phenotypes of proliferative (PE), early secretory (ESE), mid-secretory (MSE), and late secretory (LSE) endometrium. Independent hierarchical clustering analysis revealed equivalent results, with 2 major dendrogram branches corresponding to PE/ESE and MSE/LSE and sub-branching into the 4 respective phases with heterogeneity among samples within each sub-branch. K-means clustering of genes revealed 4 major patterns of gene expression (high in PE, high in ESE, high in MSE, and high in LSE), and gene ontology analysis of these clusters demonstrated cycle-phase specific biological processes and molecular functions. Six samples with ambiguous histology were identically assignable to a cycle phase by both PCA and hierarchical clustering. Additionally, pair-wise comparisons of relative gene expression across the cycle revealed genes/families that clearly distinguish the transitions of PE to ESE, ESE to MSE, and MSE to LSE, including receptomes and signaling pathways. Select genes were validated by quantitative RT-PCR.
 
Contributor(s) Talbi S, Hamilton AE, Vo KC, TulaC S, Overgaard MT, Dosiou C, Le Shay N, Le Shay N, Kimpson R, Lessey BA, Nayak NR, Giudice LC
Citation(s) 16306079
Submission date May 22, 2006
Last update date Mar 25, 2019
Contact name Said Talbi
E-mail(s) talbis@obgyn.ucsf.edu
Phone 415-514-2846
Organization name UCSF
Street address 500 Parnassus
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (27)
GSM109814 endometrium 598
GSM109815 endometrium M165
GSM109816 endometrium M169
Relations
BioProject PRJNA156795

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4888_RAW.tar 223.8 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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