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Series GSE54479 Query DataSets for GSE54479
Status Public on Dec 01, 2014
Title Molecular diversity of breast cancers at the time of endocrine resistance [mRNA]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Dataset containing whole-genome expression profiles of breast cancers at the time of endocrine resistance. It has been used to identify five distinctive phenotypes with different expression of gene clusters associated with ER-signalling, stromal rearrangement and cytokine-signalling. Pathway-focused analysis suggested individual tumours with active ER-signalling (24/55, 44%), PIK3CA-signalling (18/55, 32%), RAS (12/55, 22%) and MYC-signalling (11/55, 20%). 3 or 4 of the above pathways were simultaneously active in 6/55 (11%) cases. Results provide important information about prevalence of different mechanisms of endocrine resistance in clinical samples of breast cancer.

Please note that the tumor samples are clinically quite homogeneous: all are post-menopausal ER+ve breast cancers, endocrine treated and growing on treatment. The main purpose of collecting these data was not to compare transcriptional profiles with clinical parameters, but rather to use the transcriptional profiles of these clinically homogeneous tumours for identifying intrinsic subgroups within endocrine resistance. However, the relevant clinical data was also provided as Series supplementary file (ClinicalData_AL28Jan2014.xlsx).
 
Overall design Total RNA extracted from 60 fresh-frozen clinical biopsies of breast cancer at the time of endocrine resistance has been profiled with Illumina HT-12 whole-genome expression micro-arrays. The profiles have been analysied using un-supervised and pathway-focused bioinformatics techniques to study diversity between tumours and potential mechanisms of resistance for individual tumours.
 
Contributor(s) Larionov AA
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Submission date Jan 28, 2014
Last update date Aug 16, 2018
Contact name Alexey A Larionov
E-mail(s) alexey_larionov@hotmail.com
Organization name The University of Cambridge
Department School of Clinical Medicine
Lab Academic Laboratory of Medical Genetics
Street address Box 238, Lv 6 Addenbrooke's Treatment Centre, Cambridge BioMedical Campus
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platforms (1)
GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
Samples (60)
GSM1316407 BreastCancer_EndocrineResistant_Biopsy_R56_mRNA
GSM1316408 BreastCancer_EndocrineResistant_Biopsy_R01_mRNA
GSM1316409 BreastCancer_EndocrineResistant_Biopsy_R62_mRNA
This SubSeries is part of SuperSeries:
GSE54497 Molecular diversity of breast cancers at the time of endocrine resistance
Relations
BioProject PRJNA236605

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
GSE54479_ClinicalData_AL28Jan2014.xlsx.gz 23.5 Kb (ftp)(http) XLSX
GSE54479_RAW.tar 6.2 Mb (http)(custom) TAR
GSE54479_non_normalized.txt.gz 19.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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