Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series. We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the validation series.

2011-05-19 | E-GEOD-24550 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples (test sample series).

2011-05-19 | E-GEOD-24549 | biostudies-arrayexpress

Exon-level expression profiling of normal colonic mucosa samples.

Project description:These samples have been analyzed for global alternative splicing variation on exon-level expression data using the FIRMA algorithm. We have identified and described transcriptome instability as a genome-wide, pre-mRNA splicing related characteristic of solid cancers. This Series consists of 19 normal colonic mucosa samples from colorectal cancer patients, and is an amendment to a larger series of colorectal cancer and adjacent normal colonic mucosa samples analyzed for gene expression at the exon-level (GSE24550).

2014-08-13 | E-GEOD-42690 | biostudies-arrayexpress

Exon level expression profiling of colorectal cancer tissue samples (test sample series).

2011-05-19 | GSE24549 | GEO

Exon level expression profiling of colorectal cancer tissue samples (validation sample series).

2011-05-19 | GSE24550 | GEO