Project description:Oral squamous cell carcinoma (OSCC) accounts for the high mortality rate and morbidity in head and neck cancer. Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues.We used the affy package under the R environment to preprocess and normalize the original gene chip data.
Project description:The present study is aimed at profiling the miRNA expression pattern in oral squamous cell carcinoma (OSCC) and adjacent oral mucosa to develop a new miRNA signature for oral cancer. Agilent Human miRNA Microarray v2.0 (G4470B, Agilent Technologies) was used to identify miRNAs differentially expressed in OSCC. MicroRNA processing was carried out according to the manufacturer’s instructions. Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings. Data pre-processing and differential expression analysis were done in R Studio using the Bioconductor AgiMicroRna package.12 The Total Gene Signal provided by the AFE image analysis software was used for data analysis. Data were normalized between arrays using the quantile method. Microarray profiling identified a set of 105 miRNAs to be differentially expressed in OSCC, out of which a subset of 19 most dysregulated miRNAs were considered to formulate the miRNA signature for oral cancer.
Project description:Oral squamous cell carcinoma (OSCC) accounts for the high mortality rate and morbidity in head and neck cancer. Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues.We used the affy package under the R environment to preprocess and normalize the original gene chip data.
Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. Oral carcinogenesis is a multifactorial process involving numerous genetic changes that affect the activity of oncogenes, tumor suppressor genes and other classes of disease-related genes.Therefore, to identify the responsive genes for progression of oral dysplasia or OSCC, we here performed CGH analysis to DNA from oral dysplasia and OSCC by microdissection Copy number analysis of Affymetrix 250K SNP arrays was performed for 8 oral dysplasia samples, 8 oral squamous cell carcinoma samples, using microdissection
Project description:Identification of genes that are differentially regulated in fibroblasts derived from dysplastic oral mucosa and oral squamous cell carcinoma compared to fibroblasts derived from normal oral mucosa. Affymetrix microarrays were used to define differential gene expression. Populations of fibroblasts were isolated from human normal oral mucosa, oral dysplasia and oral squamous cell carcinoma, maintained in 3D collagen I biomatrices, RNA extracted and processed for Affymetrix arrays. Fibroblasts maintained as monolayers were also included as comparators.
Project description:Strand-specific, paired-end, total RNA-sequencing data for fifteen Australian, HPV-negative, young oral squamous cell carcinoma patients of primary tumour and adjacent normal.
Project description:Identification of genes that are differentially regulated in fibroblasts derived from dysplastic oral mucosa and oral squamous cell carcinoma compared to fibroblasts derived from normal oral mucosa. Affymetrix microarrays were used to define differential gene expression.