Similar studies for GEO DataSets (Select 200038263) - GEO DataSets

(Submitter supplied) Background. Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers, for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described and the evidence of a functional impact on gene expression is still limited. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
11 Samples

Download data: IDAT

Series

Accession:: GSE95036

ID:: 200095036

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000240916.

Expression and methylation analyses of HPV(-) and HPV(+) squamous cell carcinoma cell lines

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Methylation profiling by array; Expression profiling by array; Methylation profiling by genome tiling array

9 related Platforms
36 Samples

Download data: CEL

Series

Accession:: GSE24091

ID:: 200024091

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000240907.

Genome-wide methylation analysis in HPV(-) and HPV(+) squamous cell carcinoma cell lines

(Submitter supplied) HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. HPV(+) tumors have overall higher DNA methylation in genic and LINE1 regions than HPV(-) tumors, and polycomb repressive complex 2 (PRC2) targets tend to be much more highly methylated in HPV(+) cells.

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

7 related Platforms
28 Samples

Download data: BED, CEL, TXT

Series

Accession:: GSE24090

ID:: 200024090

PubMed Full text in PMC Similar studies

Select item 2000240898.

Expression data from HPV(-) and HPV(+) squamous cell carcinoma cell lines

(Submitter supplied) Oncogenic human papillomaviruses (HPVs) are associated with nearly all carcinomas of the uterine cervix and have also become an increasingly important factor in the etiology of a subset of oropharyngeal tumors. HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. We analyzed the genome-wide expression patterns in two HPV(+) and two HPV(-) squamous cell carcinoma (SCC) cell lines.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
4 Samples

Download data: CEL

Series

Accession:: GSE24089

ID:: 200024089

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000240879.

Epigenome analysis in HPV(-) and HPV(+) squamous cell carcinoma cell lines

(Submitter supplied) Human papillomavirus (HPV)-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. Promoter hypermethylation has been widely recognized as an important mechanism in the progression of HNSCC, but the extent to which this mechanism is consistent between HPV(+) and HPV(-) tumors is unknown. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
4 Samples

Download data: TXT

Series

Accession:: GSE24087

ID:: 200024087

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000329210.

Gene expression signature of HPV in head and neck squamous cell carcinoma

(Submitter supplied) Introduction: Human Papilloma Virus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC), between 15% and 35% of HNSCC harboring HPV, almost exclusively of subtype 16. Demographic and exposure differences between HPV-positive (+) and negative (-) HNSCCs suggest that HPV(+) tumors may constitute a subclass with different biology, while clinical differences have also been observed. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Dataset:: GDS1667
Platform:: GPL570
36 Samples

Download data: CEL

Series

Accession:: GSE3292

ID:: 200003292

Select item 166711.

Head and neck squamous cell carcinoma tumors harboring human papillomavirus

Analysis of 8 head and neck squamous cell carcinoma (HNSCC) tumors positive for human papilloma virus (HPV). 28 HNSCC HPV negative tumors examined. Between 15% and 35% of HNSCCs harbor HPV DNA. Results provide insight into the effect of HPV infection in HNSCC.

Organism:: Homo sapiens

Type:: Expression profiling by array, transformed count, 2 infection sets

Platform:: GPL570
Series:: GSE3292
36 Samples

Download data: CEL

DataSet

Accession:: GDS1667

ID:: 1667

Select item 20011202112.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (ChIP-Seq)

(Submitter supplied) Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16791
26 Samples

Download data: NARROWPEAK

Series

Accession:: GSE112021

ID:: 200112021

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012435713.

Transcriptome of human keratinocytes with or without HPV16 oncogene expression

(Submitter supplied) We used freshly established immortalized human keratinocytes with a well-defined HPV16 E6 E7 expression cassette to get a more complete and less biased overview about global changes induced by HPV16 using RNA-seq. We identified novel factors regulated by HPV oncogenes that could serve an essential role in cancer development.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: TXT, XLSX

Series

Accession:: GSE124357

ID:: 200124357

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20004002014.

Gene expression characterization of HPV positive head and neck cancer to predict response to Chemoradiation

(Submitter supplied) Background: Human papillomavirus has been shown to have a causal role in the development of head and neck squamous cell carcinoma and represents a distinct and well-defined pathology. While HPV-positive HNSCC is associated with a better response to treatment and prognosis, a subset of patients do not respond favorably to current standard of care thus suffering unnecessary morbidity and delay to receive effective therapy. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL5175
19 Samples

Download data: CEL

Series

Accession:: GSE40020

ID:: 200040020

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004115215.

(Submitter supplied) Using MCIp, we enriched highly methylated DNA from a normal mucosa control and from three OPSCC patient subgroups regarding the HPV status: group A, DNA-RNA- (Tu1-Tu5); group B, DNA+RNA- (Tu6-Tu10); group C, DNA+RNA+ (Tu11-Tu15).

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL16108
15 Samples

Download data: TXT

Series

Accession:: GSE41152

ID:: 200041152

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20008705316.

Genome wide DNA methylation in oral squamous cell carcinoma (OSCC) disease and adjacent normal tissue samples

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
21 Samples

Download data: IDAT

Series

Accession:: GSE87053

ID:: 200087053

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003827017.

450k Analysis of 24 HNSCC cell lines

(Submitter supplied) The methylation analysis of HPV+ HNSCC cell lines and HPV- HNSCC cell lines as well as clones from an infected HPV- cell line by Infinium HumanMethylation450 BeadChip

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
24 Samples

Download data: CSV

Series

Accession:: GSE38270

ID:: 200038270

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005863018.

MeDIP-chip from head and neck squamous cell carcinoma tissues and normal subjects

(Submitter supplied) Profiling the genome-wide methylation status of head and neck squamous cell carcinoma and normal subjects

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL16062
6 Samples

Download data: PAIR

Series

Accession:: GSE58630

ID:: 200058630

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20016064519.

Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Methylation profiling by array; Expression profiling by array

Platforms:: GPL23126 GPL13534
31 Samples

Download data: CEL, IDAT

Series

Accession:: GSE160645

ID:: 200160645

Select item 20015687720.

Gene expression data from formalin-fixed paraffin-embedded (FFPE) human uveal melanoma tumors; subset early metastasis vs subset no metastasis

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation correlated to gene expression in relation to survival data.We sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL23126
8 Samples

Download data: CEL

Series

Accession:: GSE156877

ID:: 200156877

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