Transcriptomics

Dataset Information

3

Gene Expression Analysis of Thymic Neoplasms


ABSTRACT: Histologic classification of thymomas has significant limitations since complete surgical excision can be curative. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 36 patients with thymomas and follow-up data was available. Gene expression data was correlated with clinicopathological data. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed by Partek®, and Ingenuity Pathways Analysis (IPA). Validation of the chosen genes was performed using quantitative real-time RT-PCR (qRT-PCR). Unsupervised clustering resulted in identification of four clusters of tumors (C1-C4). Using IPA, the top significant biological functions and pathways displayed cell cycle related category and genes in C1 and C2. Carbohydrate metabolism and cellular growth and proliferation were among the most significant for C3 and C4, respectively. On the other hand, cancer and metabolism related functions and pathways were prominent in clinical outcome including metastasis and stage. Our gene expression analysis representing one of the largest series in literature, revealed at least four distinct clusters of thymic tumors. The study identified number of metastasis-associated genes that are potential candidates for therapeutics 41 Samples, 3 Cell Line samples with 1 duplicate (total = 4). 37 Patient samples including 1 duplicate (total = 37).

ORGANISM(S): Homo sapiens  

TISSUE(S): Cell Line, Fresh Frozen Human Tumors

SUBMITTER: Chirayu P Goswami   Sunil Badve  Yesim G Polar 

PROVIDER: E-GEOD-29695 | ArrayExpress | 2012-06-30

SECONDARY ACCESSION(S): GSE29695PRJNA141117

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-29695.README.txt Txt
E-GEOD-29695.additional.1.zip Other
E-GEOD-29695.idf.txt Idf
E-GEOD-29695.processed.1.zip Processed
E-GEOD-29695.sdrf.txt Txt
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