Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

ABSTRACT: Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

PROVIDER: PRJNA565162 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

Project description:Methylation of CpG Islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. The northeastern states of India are leaders in the country for cancers of several sites. Almost no reports are available of any DNA methylation biomarker for oropharyngeal cancers of the northeastern states. The present study aimed to identify targets of CpG hypermethylation and hypomethylation in oropharyngeal cancer prevalent in northeast India. Using Illumina Infinium Human Methylation 450K microarray platform a genome wide screening has been done for differentially methylated genes, including genes not previously implicated in carcinogenesis. Differential gene expression correlated to their methylation status was elaborated using transcriptome profiling. The new genes identified may be used to develop promising panels of DNA Methylation biomarkers for oropharyngeal screening and detection at a very early stage.

2020-09-25 | GSE136704 | GEO

Identification and development of DNA methylation biomarkers for oral/oropharyngeal cancers prevalent in the North-Eastern states of India

Project description:Whole-genome DNA methylation profiling of oral cancer in patients from North-Eastern states of India. The Illumina Infinium 450k Human DNA methylation BeadChip was used to screen the entire DNA methylation profiles across approximately 485,577 CpGs in matched oral cancer samples. Samples included 12 paired samples (12 cancer and 12 normal).

2019-04-09 | GSE97784 | GEO

Proteomic analysis of Daboia russelli venom samples from Burdwan and Nadia districts of West Bengal, eastern India

Project description:Russell’s viper (Daboia russelii) (RV), a category I medically important snake as well as a member of the “Big Four”, is responsible for a heavy toll of snake bite mortality and morbidity in Indian sub-continent. Epidemiological studies suggest highest incidence of RV envenomation in eastern India (EI). In this study the RV venom proteomes from Burdwan and Nadia, the two districts of West Bengal, eastern India was deciphered for the first time using tandem mass spectrometry analysis.

2018-07-16 | PXD008607 | Pride

Gene expression profile analysis of non small cell lung cancer in North East India

2012-01-31 | GSE30118 | GEO

Gene expression profile analysis of non small cell lung cancer in North East India

Project description:The objective of this study was to identify the genes differentially expressed in non small cell lung carcinoma associated with prevalent risk factor such as smoking and betel quid chewing in high-risk north eastern Indian population. The tumor biopsies and matched normal tissue from distant site were collected in RNA later, snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical and pathologic report. Institutional human ethics committee approved the study. Total RNA was isolated from tumor biopsies and matched normal of five patients. Total RNA from normal tissue from three patients was pooled in one slide and normal tissue from another two patients was pooled in another slide. Individual slide were used for each tumor samples. Isolation Kit: RNeasy mini Kit (Qiagen) Scanner Used: AFFYMETRIX, 428 Array

2012-01-31 | E-GEOD-30118 | biostudies-arrayexpress

Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers.

Project description: Not available

| S-EPMC7578381 | biostudies-literature

OSCC CGH SriLanka vs India

Project description:In Asia, oral cancer (OC) and oral submucous fibrosis (OSF) constitute major health problems linked to use of betel quid. This work performed CGH genome-wide analysis of OC (12 from India, 12 from Sri Lanka) and OSF (6 from India) cases with normal controls.

2011-11-30 | E-MTAB-819 | biostudies-arrayexpress

STUDY OF SERUM AND BILE FROM PATIENTS OF CHOLELITHIASIS IN NORTH-EASTERN INDIA.

Project description: Not available

| S-EPMC5529796 | biostudies-other

Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-discovery peptidomic approach

Project description:Peptides and proteins were identified using a novel de novo-discovery approach in suspended and sinking organic particles from the eastern tropical North Pacific and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. De novo peptide sequencing, where the sequence of amino acids is determined directly from mass spectra rather than from comparison to theoretical spectra from a selected sequence database, was found to be a useful tool for discovery of peptides present in a sample but not initially included in the search database. Iterative de novo-informed database search results suggested the presence of fungal peptides and proteins in deep sinking particles, consistent with growing evidence that fungi play an important role in degradation of sinking material in the ocean. The de novo-discovery approach also allowed the tracking of modified autotrophic cyanobacterial peptides to the deep sea, where they contributed 0.63% of the phylum-level identifiable peptide pool in a bathymetric sediment trap sample. Overall, the amino acid composition of the peptides in the sinking material showed little change with depth, consistent with earlier observations of bulk organic matter and/or amino acid composition during the early stages of degradation. However, we identified an abundance of modified amino acids in sinking and suspended particles, including high levels of deamidation, suggesting that partial degradation of protein could potentially fuel observed anammox and contribute to observed pool of refractory organic nitrogen. We also observe methylation of arginine, which has previously been shown to slow degradation of peptides in seawater. Our results demonstrate several examples how de novo-discovery allows for a deeper evaluation of proteins and peptides in environmental systems undergoing degradation.

2022-01-10 | PXD023187 | Pride

human oropharyngeal metagenome

Project description:human oropharyngeal metagenome

| PRJNA428766 | ENA