Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Breast cancer relapse free survival

ABSTRACT: This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis. Please see attached patient clinical parameters sheet for more information (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSE2034&id=40089&db=GeoDb_blob26). Keywords: other

ORGANISM(S): Homo sapiens

SUBMITTER: Tim Jatkoe

PROVIDER: E-GEOD-2034 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide analysis of estrogen receptor binding sites.

Carroll Jason S JS Meyer Clifford A CA Song Jun J Li Wei W Geistlinger Timothy R TR Eeckhoute Jérôme J Brodsky Alexander S AS Keeton Erika Krasnickas EK Fertuck Kirsten C KC Hall Giles F GF Wang Qianben Q Bekiranov Stefan S Sementchenko Victor V Fox Edward A EA Silver Pamela A PA Gingeras Thomas R TR Liu X Shirley XS Brown Myles M

Nature genetics 20061001 11

The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation, particularly in the case of estrogen-suppre ...[more]

PMID: 17013392

Publication: 1/2

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Project description:Lymph node involvement is the most important prognostic factor in breast cancer, but little is known about the underlying molecular changes. First, to identify a molecular signature associated with nodal metastasis, gene expression analysis was performed on a homogeneous group of 96 primary breast tumors, balanced for lymph node involvement. Each tumor was diagnosed as a poorly differentiated, estrogen positive, her2-neu negative invasive ductal cancer. (Affymetrix Human U133 Plus 2.0 microarray chips). A model, including 241 genes was built and validated on an internal and external dataset performed with Affymetrix technology. All samples used for validation had the same characteristics as the initial tumors. The area under the ROC curve (AUC) for the internal dataset was 0.646 and 0.651 for the external datasets. Thus, the molecular profile of a breast tumor reveals information about lymph node involvement, even in a homogeneous group of tumors. However, an AUC of 0.65 indicates only a weak correlation. Our model includes multiple kinases, apoptosis related and zinc ion binding genes. Pathway analysis using the Molecular Signatures Database revealed relevant gene sets (BAF57, Van 't Veer). Next, miRNA profiling was performed on 82/96 tumors using Human MiRNA microarray chips (Illumina). Eight miRNAs were significantly differentially expressed according to lymph node status at a significance level of 0.05, without correcting for multiple testing. The analysis of the inverse correlation between a miRNA and its computationally predicted targets point to general deregulation of the miRNA machinery potentially responsible for lymph node invasion. In conclusion, our results provide evidence that lymph node involvement in breast cancer is not a random process. Gene expression profiling: A training set of 96 patients and an independent internal dataset of 20 patients balanced for lymph node involvement was selected from the multidisciplinary breast centre database miRNA profiling not provided in this Series.

Project description:We used high density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes resistant congenic strains and two nondiabetic control strains. Owing to the importance of T cells in the development of T1D we decided to target two organs, the spleen and thymus. We profiled gene expression in thymi from four week old female mice and spleens from three month old female mice. For each of the 14 strain-tissue combinations (7 strains x 2 tissues) we performed two independent replicate experiments, making the total number of hybridizations performed 28. In each case, an RNA population from a pool of two or three organs was generated to minimize the chances of within strain variation masking genuine variation between the strains. To minimize any variation introduced during target preparation, all samples within a given replicate group were processed in parallel. Three samples from group two (spleen: B10.H2g7_S2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm594 (GSM594); thymus: B10.H2g7_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm608 (GSM608), B10.H2g7 Idd3_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm609 (GSM609)) and one from group one (spleen B10.H2g7_S1 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm587 (GSM587) failed a preliminary quality control check. Consequently, the steps involved in preparing labelled cRNA from the initial starting material had to be repeated for these four samples at a later date. A subsequent comparison of the variation seen between samples within the same replicate group (samples processed in parallel) versus samples in distinct replicate groups (samples processed at different times) revealed that the variation between the two groups (i.e. owing to independent sample preparation) was higher than the small amount of variation between the closely matched strains. Ignoring the variability introduced during sample preparation was therefore likely to result in spurious changes being detected and genuine strain-specific differences in gene expression being masked. Consequently, we decided to exclude the four samples that had had to be prepared independently owing to failing initial quality control. Keywords = NOD, diabetes, congenic Keywords: other

Dataset Information

Breast cancer relapse free survival

Publications

Genome-wide analysis of estrogen receptor binding sites.

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