Exon level expression profiling of colorectal cancer tissue samples
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ABSTRACT:
PROVIDER: PRJNA132583 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE24549: Exon level expression profiling of colorectal cancer tissue samples (test sample series). GSE24550: Exon level expression profiling of colorectal cancer tissue samples (validation sample series). Refer to individual Series
2011-05-19 | E-GEOD-24551 | biostudies-arrayexpress
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
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 test series.
2011-05-19 | E-GEOD-24549 | biostudies-arrayexpress
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.
2011-05-19 | GSE24549 | GEO
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.
2011-05-19 | GSE24550 | GEO
Project description:These colorectal cancer (CRC) samples have been analyzed by exon expression profiling to identify genes with overexpression of 3’ parts. By characterizing underlying transcript structures of such genes with a combination of rapid amplification of cDNA ends and deep-sequencing (RACE-seq), we identify and describe novel RNA-variants in CRC.
2016-04-12 | GSE69182 | GEO
Project description:By the use of whole genome transcription analysis, we aimed to develop a gene expression classifier to increase the likelihood of identifying stage II colorectal cancer (CRC) samples with a poor prognostic outcome. Gene expression measurement were measured by the GeneChip® Human Exon 1.0 ST Arrays from Affymetrix. We analyzed genome-wide expression at the gene-level for an independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform.
2012-01-06 | E-GEOD-29638 | biostudies-arrayexpress
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
Project description:By the use of whole genome transcription analysis, we aimed to develop a gene expression classifier to increase the likelihood of identifying stage II colorectal cancer (CRC) samples with a poor prognostic outcome. Gene expression measurement were measured by the GeneChip® Human Exon 1.0 ST Arrays from Affymetrix.
2012-01-06 | GSE29638 | GEO
Project description:Samples were taken from surgically resected tumor specimens/metastases from patients with colorectal cancer. The expression profiles were determined using the Affymetrix GeneChip Human Exon 1.0 ST Array version 2.
2017-09-24 | GSE90814 | GEO