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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human breast tumor subtypes

ABSTRACT: Experiments that were used to make the "intrinsic" gene list from.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-2227 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Repeated observation of breast tumor subtypes in independent gene expression data sets.

Sorlie Therese T Tibshirani Robert R Parker Joel J Hastie Trevor T Marron J S JS Nobel Andrew A Deng Shibing S Johnsen Hilde H Pesich Robert R Geisler Stephanie S Demeter Janos J Perou Charles M CM Lønning Per E PE Brown Patrick O PO Børresen-Dale Anne-Lise AL Botstein David D

Proceedings of the National Academy of Sciences of the United States of America 20030626 14

Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressin ...[more]

PMID: 12829800

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Transcription profiling of human breast tumor subtypes

Project description:Experiments that were used to make the "intrinsic" gene list from.

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Project description:Additional experiments used for intrinsic gene selection. Sorlie et al. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74. This Series accompanies Series GSE4335. Experiments that were used to make the "intrinsic" gene list from. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Transcription profiling of breast cancer tumor samples to identify subtypes

Project description:Background Previous studies demonstrated breast cancer tumor tissue samples could be classified into different subtypes based upon DNA microarray profiles. The most recent study presented evidence for the existence of five different subtypes: normal breast-like, basal, luminal A, luminal B, and ERBB2+. Results Based upon the analysis of 599 microarrays (five separate cDNA microarray datasets) using a novel approach, we present evidence in support of the most consistently identifiable subtypes of breast cancer tumor tissue microarrays being: ESR1+/ERBB2-, ESR1-/ERBB2-, and ERBB2+ (collectively called the ESR1/ERBB2 subtypes). We validate all three subtypes statistically and show the subtype to which a sample belongs is a significant predictor of overall survival and distant-metastasis free probability. Conclusion As a consequence of the statistical validation procedure we have a set of centroids which can be applied to any microarray (indexed by UniGene Cluster ID) to classify it to one of the ESR1/ERBB2 subtypes. Moreover, the method used to define the ESR1/ERBB2 subtypes is not specific to the disease. The method can be used to identify subtypes in any disease for which there are at least two independent microarray datasets of disease samples.

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