GEO DataSets

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

43 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL5175 GPL13534 GPL14943

132 Samples

Download data: CEL, TXT

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14943

43 Samples

Download data: TXT

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

46 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL5175 GPL6801

201 Samples

Download data: CEL, CHP

(Submitter supplied) In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6801

122 Samples

Download data: CEL, CHP, TXT

(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

(Submitter supplied) Objectives: Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. Materials and Methods: We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL6480 GPL8490

60 Samples

Download data: TXT

(Submitter supplied) Genome-wide profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL22687

75 Samples

Download data: TXT

(Submitter supplied) Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention. DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9075 GPL10150

151 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. BACKGROUND: Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL18947 GPL6480

18 Samples

Download data: TXT

(Submitter supplied) Profiling of copy number mutations in commonly used non-cancerous oral cell lines

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL18947

8 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. METHODS: Six immortalized normal, one immortalized dysplasia, one self-immortalized dysplasia, and two primary normal cell lines derived from oral tissues were analyzed for DNA copy number changes and changes in both mRNA and miRNA expression using SMRT-v.2 genome-wide tiling comparative genomic hybridization arrays, Agilent Whole Genome 4x44k expression arrays, and Exiqon V2.M-RT-PCR microRNA Human panels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

10 Samples

Download data: TXT

(Submitter supplied) A comparative microarray analysis of indolent or aggressive mouse oral cancer cell lines was performed to identify gene expression signatures and specific molecules involved in aggressive tumor growth.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

24 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL23126 GPL18281

138 Samples

Download data: CEL, IDAT

(Submitter supplied) Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

87 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

18 Samples

Download data: CEL

(Submitter supplied) Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18281

33 Samples

Download data: TXT