Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of human adrenocortical tumors to identify molecular predictors of diagnosis and prognosis

ABSTRACT: A ""Cartes d'Identite des Tumeurs"" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). 92 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 92 patients with Adrenocortical Tumors (ACT). 4 normal adrenal samples from the same batch are also included. 10 ACTH-independant Macronodular Adrenal Hyperplasia (AIMAH) from the same batch are also included.

ORGANISM(S): Homo sapiens

SUBMITTER: Aurelien de Reynies

PROVIDER: E-TABM-311 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma.

Caramuta Stefano S Lee Linkiat L Ozata Deniz M DM Akçakaya Pinar P Xie Hong H Höög Anders A Zedenius Jan J Bäckdahl Martin M Larsson Catharina C Lui Weng-Onn WO

Endocrine-related cancer 20130704 4

Deregulation of microRNA (miRNA) expression in adrenocortical carcinomas (ACCs) has been documented to have diagnostic, prognostic, as well as functional implications. Here, we evaluated the mRNA expression of DROSHA, DGCR8, DICER (DICER1), TARBP2, and PRKRA, the core components in the miRNA biogenesis pathway, in a cohort of 73 adrenocortical tumors (including 43 adenomas and 30 carcinomas) and nine normal adrenal cortices using a RT-qPCR approach. Our results show a significant over-expression ...[more]

PMID: 23671264

Similar Datasets

Transcription profiling of human head and neck squamous cell carcinomas to identify metastasis predictors and descriptors, and differentiation classifiers

Project description:A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). 81 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 81 patients with primary Head and Neck Squamous Cell Carcinoma (HNSCC; oral cavity, tongue, oro- or hypopharynx); metastases as first recurrent event in a 36-month follow up; histologically tumor-free margins (?3 mm); patients had undergone surgical resection as the first treatment and had no clinically evident distant metastases.

2007-08-23 | E-TABM-302 | biostudies-arrayexpress

Genome and transcriptome integrative study to identify a likely driver of cell proliferation in lung adenocarcinoma (CIT - Homo sapiens - APUP)

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French National League Against Cancer (http://cit.ligue-cancer.net ) : 165 lung adenocarcinomas without prior chemotherapy, hybridized on Illumina SNP HumanCNV370 and Affymetrix HGU133Plus2 arrays. Project leader : Prof. Pierre FOURET (pierre.fouret@igr.fr). Note: Bronchiolo-alveolarComponent : a non invasive tumor component shown in well differentiated tumor cells. EGFR Gene Mutation Status: Gene mutation status of epidermal growth factor receptor (erythroblastic leukemia viral (v; -erb-b) ; oncogene homolog, avian) ; HGNC:3236 ; Approved Symbol:EGFR; Chromosome:7p12 ; UniProt ; ID:P00533 ; OMIMID:131550 ; EntrezGeneID:1956 ; ; RefSeq:NM_201283 ; M=mutated ; WT=non mutated=wild type. KRAS Gene Mutation Status: Gene mutation status of v-Ki-ras2 Kirsten rat ; sarcoma viral oncogene homolog ; HGNC:6407 ; Approved Symbol:KRAS ; Chromosome:12p12.1 ; UniProtID:P01116; OMIM ID:190070 ; EntrezGeneID:3845 ; ;RefSeq:NM_033360 ; M=yes=mutated ; WT=non mutated.

2012-10-19 | E-MTAB-923 | biostudies-arrayexpress

Transcription profiling by array of human non anaplastic T-cell lymphoma biopsies and cell lines

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 7 NKTCL biopsies, 2 NKTCL cell lines (SNK6, SNT8), 16 PTCL NOS biopsies, 2 NK cells samples | Biopsies and cell lines of NK/T-cell lymphoma, nasal-type (NKTCL) were subject to combined gene expression profiling and array-based comparative genomic hybridization analyses. Compared to PTCL, NOS, NKTCL had higher transcript levels for NK-cell markers and cytotoxic molecules, especially granzyme H, a novel sensitive biomarker of NKTCL. Compared to normal NK cells, tumors were closer to activated than resting cells and overexpressed several genes related to vascular biology, EBV-induced genes and PDGFRA. Notably, PDGFR? and its phosphorylated form were confirmed at the protein level, and in vitro the MEC04 NKTCL-cell line was sensitive to imatinib. Deregulation of the AKT, JAKSTAT and NF-?B pathways suggested by bioinformatical analysis, was corroborated by nuclear expression of phosphorylated AKT, STAT3 and RelA in NKTCL, and several deregulated genes in these pathways mapped to regions of recurrent copy number aberrations (AKT3 (1q44), IL6R (1q21.3), CCL2 (17q12), TNFRSF21 (6p12.3)). Several features of NKTCL uncovered by this analysis (overexpression of VEGFA and its receptor KDR by the tumor cells, overexpression of MET-HGF) suggest deregulation of angiogenic pathways. Integrative analysis also identified a novel putative tumor suppressor HACE1 in the frequently deleted 6q21 region. This study highlights emerging oncogenic pathways in NKTCL and identifies novel diagnostic and therapeutic targets. | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr>

2009-12-31 | E-TABM-702 | biostudies-arrayexpress

Genome and transcriptome study of the response to irinotecan and bevacizumab in recurrent glioblastomas (CIT - Homo sapiens - BEVA)

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French National League Against Cancer (http://cit.ligue-cancer.net ) 25 glioblastoma multiforme tumors hybridized on Illumina SNP and Affymetrix gene expression arrays. Project leader : François DUCRAY (francois.ducray@chu-lyon.fr). CIT Analysis : Julien LAFFAIRE (laffairej@ligue-cancer.net). Note: PFS : progression-free survival, OS: Overall Survival,BCNU : Carmustine (chemotherapy agent). RESPONDER: if the patient has shown or not shown a response to the treatment (Bevacizumab (Avastin) plus Irinotecan). Progression during : If the disease has progressed (cancer relapse or patient's death); otherwise (patient is alive without relapse).

2013-01-15 | E-MTAB-951 | biostudies-arrayexpress

Transcription profiling of pheochromocytomas and paragangliomas (188 tumor samples)

Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 188 tumor samples |Pheochromocytomas and paragangliomas are neuroendocrine tumors occuring in the context of inherited cancer syndromes in approximately 30% of cases, linked to germline mutations in VHL, RET, NF1, SDHA, SDHB, SDHC, SDHD, SDHAF2 or TMEM127 genes. Although progress has been made with regard to tumorigenesis mechanisms in pheochromocytoma/paraganglioma thanks to genome-wide expression studies, the question of a putative molecular distinction between VHL- and SDHx- on one hand, and RET- and NF1-related tumors on the other hand, remained to be addressed as well as the characterization of genetic events in sporadic tumors. With this purpose, 202 pheochromocytomas/paragangliomas, including 75 hereditary tumors, were investigated by expression profiling, array CGH and somatic mutation screening. The systematic characterization of somatic genetic events associated with tumor suppressor gene germline mutations in tumor tissues reveals a majority of loss of heterozygosity (LOH) but also point mutations and copy neutral LOH. Gene-expression signature defined the hereditary tumors according to their genotype. Especially, a complete sub-separation between SDHx- and VHL-related tumors was observed. Moreover, guided by the transcriptome classification and the LOH profile, somatic mutations in VHL or RET genes were identified in 14% of sporadic pheochromocytomas/paragangliomas. A genetic cause was found in 45.5% (92/202) of the large series of pheochromocytomas/paragangliomas analyzed. Regarding mutated genes, specific molecular pathways involved in tumorigenesis mechanisms are showed. Altogether, these new findings suggest that somatic mutation analysis would give important clues for personalized molecular target therapies.

2011-07-07 | E-MTAB-733 | biostudies-arrayexpress

MESO-JD

Project description:A Cartes dM-^RIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net/) | Affymetrix HG-U133 Plus 2.0 : 43 samples. Characteristics[OS.event] means the survival status (0: dead/1:alive). Characteristics[OS_delay] means the survival delay form diagnosis to the last follow up. Characteristics[Asbestos.Exposure] : exposure history to the asbestos (E: Exposed, PE: probably exposed, NE: not exposed). BAP1.Gene.mutation: (M: mutated, WT: wild type). Characteristics[CDKN2B.Gene.mutation]: (M: mutated, WT: wild type) . Characteristics[CTNNB1.Gene.mutation]: (M: mutated, WT: wild type). Characteristics[NF2.Gene.mutation]: (M: mutated, WT: wild type). Characteristics[P14ARF.Gene.mutation]: (M: mutated, WT: wild type). Characteristics[P16INKa.Gene.mutation]: (M: mutated, WT: wild type). Characteristics[TP53.Gene.mutation]: (M: mutated, WT: wild type). Characteristics[molecular.subgroup]: the clusters identified by the unsupervised analyses of gene expression. NOTE: This experiment was updated on 10th April 2014. The following changes were made: 5 samples (MPM39, MPM40, MPM41, MPM42, MPM430) and their associated data files were removed. Histology values were updated and the column headings regarding gene mutations were modified.

2014-04-04 | E-MTAB-1719 | biostudies-arrayexpress

Bladder-RI

Project description:A Cartes dM-^RIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net/). Seven transcriptome datasets corresponding to a new series of 85 MIBC (Muscle-invasive bladder cancer) and six publicly-available series (298 MIBC) were analyzed. Tumors were classified by consensus clustering. Overall survival was determined from Kaplan-Meier curves. The role of the EGFR pathway was investigated by pathway bioinformatics analysis, determination of the expression levels of its components (by microarray, RT-qPCR and western blot) and of EGFR copy number by CGH arrays. A 40-gene transcriptomic classifier was used to identify basal-like cell lines and a basal-like mouse model. Please note M-^QMIBC molecular subtype': tumors classification using consensus clustering.

2014-06-01 | E-MTAB-1803 | biostudies-arrayexpress

Expression and CGHarray profiling of Hepatosplenic T-cell Lymphomas (10 tumor samples)

Project description:A Cartes dIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 10 HSTL samples including biopsies (n=6), sorted tumor cells (n=3), cell line (n=1) | Agilent SurePrint G3 Human CGH Microarray 4x180K Arrays : 7 HSTL samples including biopsies (n=5), sorted tumor cells (n=1), cell line (n=1) | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr> The E-MTAB-638.additional.1.zip archive contains the CGH processed data file with additional chromosome coordiantes.

2011-09-30 | E-MTAB-638 | biostudies-arrayexpress

Expression and CGH array profiling of ductal carcinoma (135 tumor samples)

Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 46 samples| Agilent SurePrint G3 Human CGH Microarray 4x180K Arrays : 135 samples| To explore the prognostic value of genomic alterations present in primary tumours we perfom a comparative genomic hybridization study on BAC arrays for a panel of breast carcinoma from 45 patients with metastatic relapse and 95 others one, matched for age and axillary node involvement, without any recurrence after 11 years of follow up. Array CGH data was used in establishing a two parameters index representative first of the global level of aneusomy by chromosomal arm and second of the number of breackpoints throughout the genome. Submitter : Nabila Elarouci <elaroucin@ligue-cancer.fr> | Project leader : Michel Longy <longy@bergonie.org>

2012-02-01 | E-MTAB-748 | biostudies-arrayexpress

Transcription profiling of human ductal and lobular breast cancers with familial or Cowden disease history.

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | 74 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 74 patients. 5 samples on CGH CIT v7 | Breast carcinoma is the main malignant tumor occurring in patients with Cowden disease, a cancer prone syndrome caused by germline mutation of the tumor suppressor gene PTEN. To better understand this disease, we have performed a transcriptomic study of three Cowden disease breast carcinomas included in a panel of 74 familial breast cancers. Unsupervised clustering of these 74 tumors followed the intrinsic gene classification of breast cancer except for a group of five tumors that included the three Cowden tumors. The gene expression profile of the Cowden tumors shows considerable overlap with that of a breast cancer subgroup known as molecular apocrine breast carcinoma, which is suspected to have increased androgenic signaling and shows frequent ERBB2 amplification. A histological and immunohistochemical study performed on 13 additional cases of Cowden disease breast carcinomas, for which RNA was not available, showed that they have apocrine histological features and express GGT1, a marker of molecular apocrine breast carcinoma. These data suggest that activation of the ERBB2-PI3K-AKT pathway by loss of PTEN at early stages of tumorigenesis promotes the formation of breast tumors with apocrine features. | Submitter : Renaud Schiappa schiappar@ligue-cancer.net | Project leader : Michel Longy longy@bergonie.org

2010-07-29 | E-TABM-854 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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