Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

ABSTRACT: We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70462 | GEO | 2016/02/05

SECONDARY ACCESSION(S): PRJNA288722

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

Project description:We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures. RNA-Seq of DEK-dependent gene signatures in HNSCC cell lines

2016-02-05 | E-GEOD-70462 | biostudies-arrayexpress

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

Project description:The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples Analysis of the 6 methylomes, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-01 | E-GEOD-38263 | biostudies-arrayexpress

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 42 450k methylation profiles, comprising 21 HPV+ HNSCC samples and 21 HPV- HNSCC samples

2012-11-30 | E-GEOD-38266 | biostudies-arrayexpress

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

Project description:The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-01 | GSE38263 | GEO

450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 6 450k methylation profiles, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-30 | E-GEOD-38268 | biostudies-arrayexpress

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38266 | GEO

450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38268 | GEO

Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

Project description:Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-. In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

2021-12-01 | GSE181805 | GEO

p63 Directs Subtype Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma

Project description:Gene expression analysis of p63 knockdown in 2 HPV+ HNSCC cell lines using RNA-seq, Genomic profiling of p63 binding across 2 HPV+ HNSCC cell lines, Epigenomic landscape of 2 HPV+ HNSCC cell lines

2022-04-19 | GSE182133 | GEO

miRNA expression in head and neck squamous cell carcinoma (HNSCC)

Project description:The involvement of microRNAs (miRNAs) in cancer and their potential as biomarkers of diagnosis, prognosis and response to therapy is becoming increasingly appreciated. The etiology of head and neck squamous cell carcinoma (HNSCC) is predominantly associated with the synergistic effects of tobacco and alcohol use, as well as Human Papilloma Virus (HPV) infection, which embodies a distinct clinical and biological phenotype. We sought to examine whether the profile of miRNAs in HNSCC varies based on HPV status, and to identify specific miRNAs altered in head and neck carcinogenesis. Total RNA was isolated from 16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines. The miRNA profile of 662 individual miRNAs in these tissues was examined by microarray. 18 miRNAs are significantly altered in their expression between normal tissues and HNSCC tumors and 5 miRNAs are identified as significantly differentially expressed between HPV-positive (HPV+) and HPV-negative (HPV-) tumors. A striking difference in expression pattern of miRNA was also observed between primary tissues and cell lines. These data suggest that the pattern of miRNA expression may be reflective of disease etiology, and may be useful in the realm of diagnostic biomarkers defining broadly responsive prevention and treatment strategies for HNSCC. These data also suggest that cultured tumor cell lines may be inappropriate for novel miRNA biomarker identification. Keywords: miRNA; Disease-state analysis Expression of 662 individual miRNA was assessed in16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines were arrayed

2010-05-19 | E-GEOD-11163 | 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