GEO DataSets

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

(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

(Submitter supplied) Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH). Keywords: Repeat sample.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2920

68 Samples

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(Submitter supplied) Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.

Organism:

Homo sapiens

1 Series

68 Samples

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(Submitter supplied) Recently it was shown that gene expression signatures generated from DNA microarray analyses have promise as biomarkers of clinical outcome and that the molecular characteristics of tumors could be elucidated. Through this study, we have determined a high-risk signature for recurrence as a prognostic biomarker using formalin-fixed HNSCC tumors and tested the results to an independent data set obtained from fresh frozen tumors as a comparison. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1352

40 Samples

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(Submitter supplied) Oncogene expressing human papillomavirus type 16 (HPV16) is found in a subset of head and neck squamous cell carcinomas (HNSCC). HPV16 drives carcinogenesis by inactivating p53 and pRb with the viral oncoproteins E6 and E7, reflected by a low level of mutations in TP53 and allelic loss at 3p, 9p and 17p, genetic changes frequently found in HNSCCs of non-viral etiology. We hypothesize that two pathways to HNSCC exist: one determined by HPV16 and one by environmental carcinogens. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL3441

24 Samples

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(Submitter supplied) The success of targeted therapies creates a need to discriminate tumors accurately by their histological and genetic characteristics. Here, we used cDNA microarray analysis to identify gene expression profiles and single markers that recapitulate the pathological and genetic background (i.e., BRAF, EGFR, KRAS, LKB1, PIK3CA, and TP53 gene alterations) of non-small cell lung cancer (NSCLC). Gene expression profiles were determined for 6 normal lung tissues and 69 lung tumors from patients diagnosed with NSCLC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5645

75 Samples

Download data: GPR

(Submitter supplied) We compared the prognostic significance of ectodomain isoforms of the epidermal growth factor receptor (EGFR), which lack the tyrosine kinase (TK) domain, with that of the full length receptor and its autophosphorylation status in cervical cancers treated with conventional chemoradiotherapy. We further explored signaling pathways that were correlated with high expression of ectodomain isoforms by gene expression analysis of 110 of the tumors, and validated the results in an independent cohort of 41 tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

151 Samples

Download data: TXT

(Submitter supplied) Forty-four paired (from the same patient) samples of head and neck squamous cell carcinoma (HNSCC) and normal tissue were studied with Affymetrix U95A chips. A stringent multi-test approach, combining 7 traditional and microarray-specific statistical tests, was used to analyze the resultant data. Candidate genes were assigned to tiers of significance based on the number of statistical tests that each gene satisfied. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2520

Platform:

GPL8300

44 Samples

Download data: CEL

Analysis of paired normal tissues and tumor samples from patients with head and neck squamous cell carcinoma (HNSCC). Results used to assess the effectiveness of using a combinatorial approach to analyze microarray data in identifying differentially expressed genes.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 22 individual sets

Platform:

GPL8300

Series:

GSE6631

44 Samples

Download data: CEL

(Submitter supplied) Chromosomal comparative genomic hybridization (CGH) and oligonucleotide microarrays were used to examine 8 HNSCC cell lines and a plot of gene expression levels relative to their position on the chromosome was produced. Three highly up-regulated genes, NT5C3, ANLN and INHBA, were identified on chromosome 7p14. These genes were subjected to quantitative real-time RT-PCR on cDNA and genomic DNA derived from 8 HNSCC cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1291

8 Samples

Download data: TXT

(Submitter supplied) Laryngeal squamous cell carcinoma is a very common in head and neck cancer, accounting for 25% of all cases, with high mortality rates and poor prognosis. In this study, we compared expression profiles of clinical samples from15 larynx tumors and 10 non-neoplastic larynx tissue using a custom-built cDNA microarray containing 332 probes for 285 genes previously identified as up- or down-regulated in head and neck tumors by the Head and Neck Annotation Consortium (Reis et al., Cancer Res 65:1693-99, 2005). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6426

46 Samples

Download data: TXT

(Submitter supplied) In order to identify putative targets in squamous cell carcinoma (SCC), a survey of parallel chromosomal alterations and gene expression studies in 10 SCC cell lines were performed using array-CGH and microarray techniques. The most frequent changes were gains of 11q13.1-13.3 and losses of 18q12.1-23 in SCC. Furthermore, the expression levels of the sets of genes at both these loci in SCC were measured using microarray analysis. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

10 Samples

Download data: TXT

(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

(Submitter supplied) Gene expression profiles of human HNSCC lines were compared with human normal keratinocytes by 24K cDNA microarray. The ten HNSCC analyzed are derived by the University of Michigan (UM-SCC), representing late stage SCC of different anatomic sites. Principle component analysis and hierarchical gene clustering classified ten cancer cell lines into two subsets, and associated each of the subsets with a distinctive p53 status. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6569

14 Samples

Download data: GPR

(Submitter supplied) A growing proportion of head and neck squamous cell carcinomas (HNSCC) is associated with the human papilloma virus (HPV), particularly HPV16. We compare tumors with different HPV16 DNA and RNA (E6*I) status from 290 consecutively recruited HNSCC patients by gene expression profiling and targeted sequencing of 50 genes. We confirm that the HPV16 DNA+ RNA+ tumors are molecularly distinct from the HPV-negative (DNA-) HNSCC and have elevated expression of cell cycle genes and rare TP53 mutations (3.6%, 1/28). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

270 Samples

Download data: TXT

(Submitter supplied) Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

23 Samples

Download data: TXT

(Submitter supplied) The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9115

6 Samples

Download data: WIG

(Submitter supplied) Current classification of head and neck squamous cell carcinomas (HNSCC) based on anatomic site and clinical stage fails to capture biologic heterogeneity or adequately inform treatment. Here we use consensus clustering on 371 HNSCC in three cohorts, including a new cohort of 134 patients with locoregionally advanced HNSCC and 43% HPV(+) tumors to identify five HNSCC subtypes. Subtypes closely correlate with biologic processes (hypoxia, cytotoxic T-cell infiltration, copy number changes, EGFR/HER-ligand phenotype), survival, and HPV-status. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

134 Samples

Download data: TXT

(Submitter supplied) Array-based comparative genomic hybridization (aCGH) was used to evaluate DNA copy number alterations related and non related to HPV infection status aiming to identify potential molecular markers in penile cancer (PC).

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL8841

38 Samples

Download data: TXT