Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human ovarian tumors and normal ovaries

ABSTRACT: 99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples, each assayed on an Affymetrix HG_U133A array Experiment Overall Design: 99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples. RNA expression was analyzed using one Affymetrix HG_U133A array per sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Rork Kuick

PROVIDER: E-GEOD-6008 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Fibroblast growth factor 9 has oncogenic activity and is a downstream target of Wnt signaling in ovarian endometrioid adenocarcinomas.

Hendrix Neali D ND Wu Rong R Kuick Rork R Schwartz Donald R DR Fearon Eric R ER Cho Kathleen R KR

Cancer research 20060201 3

Wnt signaling plays a key role in development and adult tissues via effects on cell proliferation, motility, and differentiation. The cellular response to Wnt ligands largely depends on their ability to stabilize beta-catenin and the ability of beta-catenin to bind and activate T-cell factor (TCF) transcription factors. Roughly 40% of ovarian endometrioid adenocarcinomas (OEA) have constitutive activation of Wnt signaling as a result of oncogenic mutations in the beta-catenin protein or inactiva ...[more]

PMID: 16452189

Similar Datasets

Human ovarian tumors and normal ovaries

Project description:99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples, each assayed on an Affymetrix HG_U133A array Keywords: Individual tumor comparisons

2007-04-09 | GSE6008 | GEO

DNA methylation analysis of ovarian cancers and normal peripheral blood lymphocyte DNA by Illumina Infinium platform

2012-01-01 | GSE26989 | GEO

DNA methylation analysis of ovarian cancers and normal peripheral blood lymphocyte DNA by Illumina Infinium platform

Project description:We performed a genome-scale DNA methylation analysis of 41 ovarian tumors and 10 normal lymphocytic samples. We used the Illumina Infinium HumanMethylation27 Beadchip platform that interrogates the DNA methylation profiles of approximately 27,000 CpGs to identify sensitive markers for ovarian cancer detection. The 41 tumor samples included one mixed (clear cell and endometrioid) tumor, three clear cell carcinomas, four mucinous, four endometrioid, and 32 serous epithelial ovarian carcinomas. The lymphocytic DNA samples were obtained from 10 healthy older women. DNA obtained from 41 ovarian cancer tissue samples and 10 peripheral blood leukocyte (PBL) samples was bisulfite converted and then hybridized to the Illumina Infinium 27k Human Methylation Beadchip v.1.2 biological replicate: sample WBC6, WBC11 biological replicate: sample WBC8, WBC12

2012-01-01 | E-GEOD-26989 | biostudies-arrayexpress

Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors.

2014-01-17 | GSE49888 | GEO

Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors.

Project description:Transcriptional profiling of 19 ovarian tumors of 5 distinct histologic types (serous, endometrioid, clear cell, mucinous and small cell), to investigate similar and distinct biology associated with each histologic type. RNA from fresh-frozen ovarian tumor samples were individually hybridized to a pooled RNA from all 19 tumor cases

2014-01-17 | E-GEOD-49888 | biostudies-arrayexpress

Down-regulation of PAX2 affects ovarian cancer cell growth and migration

Project description:PAX2 is one of nine PAX genes that regulate tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell lineage specification, migration, and survival. In our previous study, we found that PAX2 is highly expressed in low-grade ovarian serous carcinoma, but its expression in clear cell, endometrioid, and mucinous cell ovarian carcinomas have not been studied. More importantly, the functional role of PAX2 in ovarian cancer is not known. Downregulation of PAX2 in PAX2-expressing ovarian cancer cells inhibits cell proliferation and migration. This growth inhibition is due to the upregulation of the tumor suppressor gene G0S2 and subsequent induction of apoptosis. The PAX2 pathway thus represents a potential therapeutic target for PAX2-expressing ovarian carcinomas.

2011-12-05 | GSE30501 | GEO

Univariate and classification analysis reveals potential diagnostic biomarkers for early-stage ovarian cancer type 1 and type 2

Project description:Biomarkers for early detection of ovarian tumors are urgently needed. Tumors of the ovary grow within cysts and most are benign.Surgical sampling is the only way to ensure accurate diagnosis, but often leads to morbidity and loss of female hormones. The present study explored the deep proteome in well-defined sets of ovarian tumors, FIGO stage I, Type 1 (low-grade serous, mucinous, endometrioid; n=9), Type 2 (high-grade serous; n=9), and benign serous (n=9) using TMT-LC-MS/MS. We evaluated new bioinformatics tools in the discovery phase. This innovative selection process involved different normalizations, a combination of univariate statistics, and logistic model tree and naïve Bayes tree classifiers. We identified 142 proteins by this combined approach. One biomarker panel and nine individual proteins were validated in cyst fluid and serum: transaldolase-1, fructose-bisphosphate aldolase A (ALDOA), transketolase, ceruloplasmin, mesothelin, clusterin, tenascin- XB, laminin subunit gamma-1, and mucin-16. Six of the proteins were found significant (p<0.05) in cyst fluid while ALDOA was the only protein significant in serum. The biomarker panel achieved ROC AUC 0.96 and 0.57 respectively. We conclude that classification algorithms complement traditional statistical methods by selecting combinations that may be missed by standard univariate tests.

2019-02-02 | PXD010939 | Pride

Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions [H3K4me3]

Project description:In the current study we performed characterization of 18 different in vitro models of high-grade serous (HGSOC), low-grade serous (LGSOC), mucinous (MOC), endometrioid (ENOC) and clear cell (CCOC) carcinoma. This study seeks to fill in this gap by generating an integrative Ovarian Cancer Regulatory Atlas (OCRA) of 18 ovarian normal and cancer cells profiled for epigenomic, transcriptomic, chromatin state and chromatin looping signatures.

2024-03-18 | GSE261637 | GEO

Down-regulation of PAX2 affects ovarian cancer cell growth and migration

2011-12-05 | E-GEOD-30501 | biostudies-arrayexpress

The histotype-specific copy-number landscape of ovarian cancer (expression Japan)

Project description:Ovarian cancer is characterized by multiple structural aberrations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and till date, the histotype-specific copy number landscape has been difficult to elucidate. To dissect the heterogeneity of ovarian cancer and understand the pathogenesis of its various histotypes, we developed an in silico hypothesis-driven workflow to identify histotype-specific copy number aberrations across multiple datasets of epithelial ovarian cancer. In concordance with previous studies on global copy number changes, our study showed similar alterations. However, when the landscape was de-convoluted into histotypes, distinct alterations were observed. We report here a comprehensive histotype-specific copy number landscape of ovarian cancer and showed that there is genomic diversity between the histotypes; some involving well known cancer genes and some novel potential driver genes. Besides preferential occurrence of alterations in some histotypes, opposite trends of alteration were observed; such as ERBB2 amplification in mucinous but deletion in serous tumors. The landscape highlights the need for identifying histotype-specific aberrations in ovarian cancer and present potential to tailor management of ovarian cancer based on molecular signature of histotypes. 56 samples containing the 4 histotypes were used for this study. It contained 12 clear cell carcinoma, 6 endometrioid adenocarcinoma, 2 mucinous adenocarcinoma, 5 mucinous-borderline tumors, 26 serous adenocarcinoma, and 5 serous-borderline tumors.

2012-10-25 | E-GEOD-30274 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data