E-GEOD-13911 - Transcription profiling by array of human primary gastric tumors with microsatellite instability

Status
Released on 3 January 2009, last updated on 6 March 2012
Organism
Homo sapiens
Samples (69)
Array (1)
Protocols (3)
Description
Gastric cancers with mismatch repair (MMR) inactivation are characterised by microsatellite instability (MSI). In this study, the transcriptional profile of 38 gastric cancers with and without MSI was analysed. Unsupervised analysis showed that the immune and apoptotic gene networks efficiently discriminated these two cancer types. Hierarchical clustering analysis revealed numerous gene expression changes associated with the MSI phenotype. Amongst these, the p53-responsive genes maspin and 14-3-3 sigma were significantly more expressed in tumours with than without MSI. A tight immunosurveillance coupled with a functional p53 gene response is consistent with the better prognosis of MSI cancers. Frequent silencing of MLH1 and downregulation of MMR target genes, such as MRE11 and MBD4, characterised MSI tumours. The downregulation of SMUG1 was also a typical feature of these tumours. The DNA repair gene expression profile of gastric cancer with MSI is of relevance for therapy response. Experiment Overall Design: Genes differentially expressed between MSI and MSS tumours were identified as follows: (i) gene probe sets were pre-selected for being flagged as ‘PRESENT’ in at least 10 tumour samples (21,324 probe sets); (ii) the probe set signal values on the pre-selected probe sets were used to run a t-test between the two types of tumour samples; (iii) the false discovery rate (FDR) method was applied to the t-test calculated p-values to correct for multiple testing and (iv) a false discovery rate <0.05 and a t-test p-value < 0.01 were chosen as threshold criteria to identify the genes differentially expressed in tumours with and without MSI
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Genome-wide expression profile of sporadic gastric cancers with microsatellite instability. D'Errico M, de Rinaldis E, Blasi MF, Viti V, Falchetti M, Calcagnile A, Sera F, Saieva C, Ottini L, Palli D, Palombo F, Giuliani A, Dogliotti E. , Europe PMC 19081245
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-13911.idf.txt
Sample and data relationshipE-GEOD-13911.sdrf.txt
Raw data (2)E-GEOD-13911.raw.1.zip, E-GEOD-13911.raw.2.zip
Processed data (1)E-GEOD-13911.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-13911.eSet.r
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