Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of 13 squamous cell carcinomas arising in the vulva

ABSTRACT: The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38228 | GEO | 2013/01/16

SECONDARY ACCESSION(S): PRJNA167467

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Expression analysis of 13 squamous cell carcinomas arising in the vulva

Project description:The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated. The whole-gene expression profile of 14 SCC of the vulva was compared to 5 normal vulvar samples to identify genes that were deregulated in the tumors genome. Vulvar hyperplasia 03-48 not further analyzed and not included in the normalized data but included in the non-normalized data

2013-01-16 | E-GEOD-38228 | biostudies-arrayexpress

aCGH was used to identify the overall genomic imbalances of SCC of the vulva in 14 patients

Project description:The imbalances scored by arrayCGH mapped to different chromosomes with losses being more common than gains. Frequent losses of large chromosomal segments were scored from 3p and 8p whereas same-sized gains were frequent from 3q and 8q. This is the first study of vulvar tumors using arrayCGH, and some frequent imbalances could be defined precisely.

2013-01-16 | GSE38229 | GEO

aCGH was used to identify the overall genomic imbalances of SCC of the vulva in 14 patients

2013-01-16 | E-GEOD-38229 | biostudies-arrayexpress

Genomic imbalances of lung cancer

Project description:The array comparative genomic hybridization (aCGH) was perform to identify regions with genomic imbalance in lung cancer.The aCGH analysis detected a total of 325 regions with genomic imbalance in all 8 lung cancer samples, ranging from focal rearrangements (70 kb–5 Mb) to chromosome-arm alterations with chromosomal segments amplification or deletion. Among these mutations, a total of 115 genomic imbalances were discovered occurring at high frequency varying from 25% to 50%.

2016-11-17 | GSE89927 | GEO

Human SCC-13 Cells: Control vs. Resitant populations to photodynamic therapy (PDT)

Project description:aCGH of control cells not subjected to PDT (Parental) and cells subjected to 5 or 10 sequential PDT treatments (5M-BM-:G and 10M-BM-:G, respectively). Three-condition experiment, cultures of SCC-13 cells not subjected to PDT (Parental) vs 5M-BM-:G and 10M-BM-:G generations of resistant cells.

2013-09-06 | E-GEOD-50602 | biostudies-arrayexpress

Bioinformatic evaluation and comparison of parallel aSNP and aCGH analyses of myelodysplastic syndromes patients with normal karyotype

Project description:Parallel aSNP and aCGH analyses were performed on 22 samples from MDS patients with a normal karyotype. 55 overlapping alterations, most of these corresponding to CNVs were identified with both methods. Putative tumour specific imbalances were found with both methods in three cases, a deletion of TET2, a larger deletion containing DNMT3A and one complex molecular karyotype. In two cases putative tumour specific imbalances were only seen with aCGH: a 16p deletion in a low number of cells and a small homozygous deletion in WWOX. Telomeric UPDs were only detected with aSNP in two cases: one affecting chromosome 3q and in the other, two UPD regions were present on 4q and 5p. In total, putative relevant tumour specific genomic alterations were found in seven cases (32%). Three small aberrations only detected by aCGH were present in T-cells, suggestive of germ line alterations which may confer a risk for MDS development. This part contains the aCGH analyses, for aSNP see GSE49004.

2017-01-01 | GSE50897 | GEO

Spatial transcriptome analysis for squamous cell carcinoma arising from mature teratoma

Project description:Squamous cell carcinoma arising from mature teratoma (SCC-MT) is one of the rare ovarian malignancies. Therefore, the molecular background of SCC-MT remains largely unelucidated. In this study, we performed the spatial transcriptomics for SCC-MT.

2025-03-21 | GSE272833 | GEO

Homo sapiens

Project description:aCGH was used to identify the overall genomic imbalances of SCC of the vulva in 14 patients

| PRJNA167468 | ENA

Array-Comparative Genomic Hybridization Reveals Loss of SOCS6 is Associated with Poor Prognosis in Primary Lung Squamous Cell Carcinoma

Project description:Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients. Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set.

2011-12-25 | GSE32058 | GEO

Low- and High-Grade Mucoepidermoid Carcinomas have different genomic profiles and CRTC1-MAML2 Fusion Gene Status

Project description:Using high-resolution oligonucleotide arrayCGH, FISH, and RT-PCR we have performed a comprehensive analysis of genomic imbalances, and CRTC1-MAML2 gene fusion status in a series of 28 well characterized mucoepidermoid carcinomas (MECs) with the aims to identify distinct differences in genomic profiles and CRTC1-MAML2 gene fusion status between low- and high-grade MECs. High-resolution aCGH (44K/244K) on fresh frozen and paraffin embedded tissue from 28 well-characterized MECs.

2012-12-31 | E-GEOD-36282 | 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