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| Status |
Public on Nov 30, 2005 |
| Title |
Gene expression profiling of the 20 human early breast carcinomas by three miaroarray platforms |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
In this study, we profiled gene expressions on 20 biopsy tissues of early stage breast carcinoma using Applied Biosystem’s Human Genome Survey Microarrays. Two main previously defined clinically relevant subtypes of breast tumors, Luminal A (longest survival time) and Basal (shortest survival time) were identified. Statistical analysis identified 1210 genes as signature genes characterizing the two subtypes of breast cancer. PantherTM functional classification and biological pathway analysis on these signature genes depicts a more detailed molecular portrait of these expression-based subtypes: Genes over expressed in Luminal A subtype were over-represented by biological function/processes such as cell structure and amino acid metabolism, while genes over expressed in the Basal subtype are over-represented by kinases, oncogenesis, cell cycle regulatory genes and TGF-beta signaling pathways. Our results provided further evidence that these breast tumor subtypes represent biologically distinct disease entities. In an attempt to identify the best set of genes as potential biomarkers for sub-classifying breast cancer, parallel data were generated on the same 20 patients samples using Stanford 42K cDNA Arrays and Agilent Human Whole Genome Arrays. Same subtypes of breast cancer were identified and the results from the three microarray platforms were found to be highly correlated. Using PAM (Prediction Analysis of Microarray) analysis, a minimal numbers of genes were selected to best characterize and distinguish the Luminal A and Basal subtypes of tumors. These classifier genes were further verified by TaqMan assays. Validated by multiple gene expression platforms, the classifier genes identified in this study defined potential prognostic molecular markers for breast cancers.
Keywords: sub-classification and characterization of early breast carcinomas
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| Overall design |
We analyzed 20 early breast carcinomas on Applied Biosystem Human Whole Genome Survey Arrays ( 40 arrays, with 2 replicates per sample), on Stanford 42k cDNA microarrays (20 arrays, no replicate), and Agilent Whole Human Genome Oligo Microarrays (20 arrays, no replicate)
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| Contributor(s) |
Sorlie T, Wang Y |
| Citation(s) |
16729877 |
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| Submission date |
Aug 17, 2005 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Yulei Wang |
| E-mail(s) |
wangyy@appliedbiosystems.com
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| Organization name |
Applied Biosystems
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| Street address |
850 Lincoln Centre Dr
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| City |
Foster City |
| State/province |
CA |
| ZIP/Postal code |
94404 |
| Country |
USA |
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| Platforms (3) |
| GPL1426 |
ABI Human Genome Survey Microarray Version 1 |
| GPL1708 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) |
| GPL1843 |
SHDF |
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| Samples (80)
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| Relations |
| BioProject |
PRJNA92985 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE3155_RAW.tar |
5.8 Mb |
(http)(custom) |
TAR |
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