E-GEOD-30784
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA144305
PROVIDER: E-GEOD-30784 | ExpressionAtlas | 2015-08-17
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Gene Expression Profiling of Oral Leukoplakia (OPL) and Early Stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate gene/s clusters with potential to distinguish normal, OPL and tumor tissue from Gingivobuccal complex. All tissue samples were collected after obtaining written informed consent. The RNA profile of 15 OPL and 34 OSCC samples was compared with 1 independent controls Gingivobuccal complex tissue from healthy donors.
2017-04-26 | GSE85195 | GEO
Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent. The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F
2011-10-29 | E-GEOD-23558 | biostudies-arrayexpress
Project description:<a href="https://www.nature.com/articles/s41467-017-00493-9" target="_blank">Chen T-W, Lee C-C, Liu H, Wu C-S, Pickering CR, Huang P-J, et al., Nature Communications 8, Article number: 465 (2017) doi:10.1038/s41467-017-00493-9</a></p><p>Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n=188; p=0.004). The frequency of APOBEC3B-deletion alleles is ~50% in 143 genotyped oral squamous cell carcinoma -Taiwan samples (27A3B-/-:89A3B+/-:27A3B+/+), compared to the 5.8% found in 314 OSCC-TCGA samples. We thus report a frequent APOBEC mutational profile, which relates to a APOBEC3B-deletion germline polymorphism in Taiwanese oral squamous cell carcinoma that impacts expression of APOBEC3A, and is shown to be of clinical prognostic relevance. Our finding might be recapitulated by genomic studies in other cancer types.</p><br/><p>Mass Spectrometry Data Sets, Provided Below</p><p>The APOBEC-associated mutational signature enriched in the OSCC-Taiwan cohort was investigated to determine if this mutational signature might correlate with tumor-related alterations in APOBEC expression.</p><p>RNA-Seq results from normal / tumor paired tissue samples were analyzed and data may be obtain from NCBI (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA327548" target="_blank">BioProject:PRJNA327548</a> and <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP078156" target="_blank">SRA Study:SRP078156</a>). </p><p>Corresponding enrichment of A3A-specific peptides in tumor proteomes was assessed by iTRAQ (isobaric Tags for Relative and Absolute Quantification) mass spectrometry protein quantification methods in 38 normal / tumor paired tissue samples. Peptides were digested, labeled by iTRAQ, and fractionated by on-line 2D-HPLC to 44 fractions. Each dataset (labeled as OSCC-Pxx, example OSCC-P01) contains 44 raw mass spectrometry data files (LTQ-Orbitrap ELITE). The iTRAQ 114 reagent was used to label the digestion products of 30-pairs of OSCC tissues, and iTRAQ 115 and 116 reagents were used to label peptides of non-tumor tissue and tumor tissue, respectively. The APOBEC3A (A3A) coding region is part of a APOBEC3 gene cluster at 22q13.</p><ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S034">https://cptac-data-portal.georgetown.edu/cptac/s/S034</a> on 08/28/19</li></ul>
2019-08-28 | MSV000084250 | MassIVE
Project description:Interventions: Group 1: Quantitative Expression Analysis of the proteom and gene Expression of Primary Tumor, normal tissue, and metastases
Primary outcome(s): Disease associated Proteins and Genes
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: basic science
| 2431957 | ecrin-mdr-crc
Project description:Gene expression profile Colorectal Tumor and Normal tissue samples
| PRJNA305877 | ENA
Project description:Genomewide DNA methylation profiling of oral leukoplakia and oral sqamous cell carcinoma (OSCC) was performed to delineate candidate gene associated with progression and clinicopathological parameters. All tissue samples were collected after obtaining written informed consent. The DNA methylation profile of 74 OSCC and 22 leukoplakia were compared with 22 normal control tissues from healthy donor.
2023-06-05 | GSE204943 | GEO
Project description:RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance.
2010-02-25 | GSE20116 | GEO
Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent.
2011-10-30 | GSE23558 | GEO
Project description:OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls.
2011-07-22 | GSE30784 | GEO