Breast and ovarian carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE4268 | GEO | 2006/02/25
SECONDARY ACCESSION(S): PRJNA94959
REPOSITORIES: GEO
Similar Datasets
Project description:Schaner, M., et al.; Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 4 Clustering of breast and ovarian carcinoma cases. 68 breast and 57 ovarian cases were co-clustered to discern both similarities and disparities between the two sample sets. An ovarianspecific set of highly expressed transcripts was identified in comparison to breast across the 3363 transcripts. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation
2006-02-24 | E-GEOD-4268 | biostudies-arrayexpress
Project description:Schaner, M., et al. Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1 Ovarian Cell Lines Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2006-02-25 | GSE4197 | GEO
Project description:Schaner, M., et al. Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1 Ovarian Cell Lines Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2006-02-24 | E-GEOD-4197 | biostudies-arrayexpress
Project description:Schaner M., et al.; Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1 Unsupervised hierarchical clustering of ovarian cell lines and ovarian cancers. Cell lines were not co-clustered with the tumor specimens, because these cell lines have a very prominent proliferation cluster (Perou et al., 1999; Ross et al., 2000) that significantly influences the clustering of the tumor samples if the two sample sets are not analyzed separately. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2006-02-25 | GSE4198 | GEO
Project description:Schaner M., et al.; Mol Biol Cell. 2003 Nov;14(11):4376-86. Figure 1 Unsupervised hierarchical clustering of ovarian cell lines and ovarian cancers. Cell lines were not co-clustered with the tumor specimens, because these cell lines have a very prominent proliferation cluster (Perou et al., 1999; Ross et al., 2000) that significantly influences the clustering of the tumor samples if the two sample sets are not analyzed separately. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2006-02-24 | E-GEOD-4198 | biostudies-arrayexpress
Project description:We used microarray analysis to study the expression differences between controls and hESCs expressing RB7LP for 3 days, and controls and hESCs expressing T121 for 3 days. RB7LP is the large pocket fragment of the retinoblastoma protein (RB) fused to GFP, in which seven phosphorylation sites for Cdk have been mutated (Angus, SP et al. Mol Cell Biol 23, 8172 (Nov, 2003). T121 is a truncated form of the SV40 Large T (LT) viral oncoprotein that inactivates the function of the three members of the retinoblastoma (RB) protein family (RB, p107, p130).
2012-06-29 | GSE29783 | GEO
Project description:Stress experiments repeating Gasch et al.,2000 conditions (Mol Biol Cell. 2000 Dec;11(12):4241-57). For each set of conditions I compared a deletion mutant for a predicted transcription regulator with a congenic wt strain. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-12-15 | GSE3812 | GEO
Project description:The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types. This ROMA experiment was performed on Ovarian Tumor samples using the same platform as previously reported by Navin, N. et. al. Genome Res. 2010 Jan;20(1):68-80 (PMID: 19903760). Analysis of the array data was performed as previously reported in Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. (PMID: 18836286 ). The genomic DNA from each tumor was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. The value data repesents a log ratio. (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).
2011-10-16 | E-GEOD-28013 | biostudies-arrayexpress
Project description:Objectives: MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate gene expression primarily through post-transcriptional modification. We tested the hypothesis that miRNA expression is associated with overall survival in advanced ovarian cancer. Methods: Cases included newly diagnosed patients with stage III or IV serous ovarian cancer. RNA from a training set of 62 cases was hybridized to an miRNA microarray containing 470 mature human transcripts. Cox regression was performed to identify miRNAs associated with overall survival. External validation was performed using quantitative RT-PCR miRNA assays in an independent test set of 123 samples. MiRNA targets and associated biologic pathways were predicted in silico. Results: Of all patients, 80% had high-grade, stage IIIC tumors and 64% underwent optimal cytoreduction. The median survival for the entire cohort was 49 ± 4 months. The training set identified 3 miRNAs associated with survival - miR-337, miR-410, and miR-645. An miRNA signature containing miR-410 and miR-645 was most strongly associated with overall survival in the training set (HR=2.96, 95% CI: 1.51-5.78). This miRNA survival signature (MiSS) was validated in the test set (HR=1.71, 95% CI: 1.05-2.78). The MiSS was independent of FIGO stage and surgical debulking. Conclusions: The data suggest that an MiSS that contains miR-410 and miR-645 is negatively associated with overall survival in advanced serous ovarian cancer. This signature, when further validated, may be useful in individualizing care for the ovarian cancer patient. Pathway analyses identify biologically plausible mechanisms. Cases included newly diagnosed patients with stage III or IV serous ovarian cancer. RNA from a training set of 62 cases was hybridized to an miRNA microarray containing 470 mature human transcripts. Cox regression was performed to identify miRNAs associated with overall survival.
2011-02-15 | E-GEOD-27290 | biostudies-arrayexpress
Project description:RNAs directly interacting with EZH2 were isolated from human colorectal HCT116 cells using an in vivo crosslinking and immunoprecipitation strategy (iCLIP, König J et al, Nat Struct Mol Biol 2010) coupled to an ultrasequencing approach.
2012-04-23 | GSE36070 | GEO