Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of colorectal cancer and paired normal tissues using Affymetrix HGU133-X3P arrays

ABSTRACT: Transcriptome profiling of colorectal cancer and paired normal tissues using Affymetrix HGU133-X3P arrays

PROVIDER: PRJNA1132983 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome profiling of colorectal cancer and paired normal tissues using Affymetrix HGU133-X3P arrays

Project description:Background: Colorectal cancer (CRC) is a major global health concern, responsible for a significant number of cancer-related deaths. In this context, the development of accurate gene signatures is of paramount importance for predicting prognosis and guiding therapeutic decisions. This study was undertaken with the specific aim of creating an expression-based risk assessment model to predict overall survival (OS) in CRC patients. Methods: We analysed 49 paired FFPE tumours and normal tissue samples from sporadic CRC cases using Affymetrix HGU133-X3P arrays. We identified candidate prognostic genes by combining transcriptome profiling with public mRNA and miRNA microarray datasets. Univariate Cox regression analysis determined essential genes predicting OS. A prognostic risk score was developed using the expression of selected genes and patient stage, validated with two independent GEO datasets (GSE17536 and GSE40967). Results: We found 845 differentially expressed genes (FDR≤0.001, fold change ≥2) mainly enriched in the ECM-receptor interaction pathway. Four overexpressed genes in this pathway were identified as critical regulators of CRC. The high expression of these genes correlated with poor prognosis. Our four-gene prognostic signature, validated with independent datasets, stratified CRC patients into low- and high-risk groups with significant OS differences. Conclusion: Our risk-score model, developed and validated in this study, holds significant potential as a prognostic tool for predicting survival and clinicopathological features in CRC patients. Its successful application could enhance the precision of therapeutic decisions in clinical practice.

2025-07-21 | GSE271719 | GEO

Comparison of gene expression profiles between paired primary and metastasis colorectal carcinoma

2010-10-06 | GSE18462 | GEO

Drug Matrix Data - Affymetrix Arrays

Project description:Drug Matrix Data - Affymetrix Arrays

| PRJNA248180 | ENA

Gene expression data for tumor and paired adjacent normal tissues from colorectal cancer patients

Project description:We have employed whole genome microarray to compare the gene expression profile of tumor tissues and paired adjancent normal colonic tissues from six colorectal cancer patients.

2020-08-18 | GSE156355 | GEO

Comparison of gene expression profiles between paired primary and metastasis colorectal carcinoma

Project description:Paired tissues (normal colon, primary colorectal carcinoma, normal liver, liver metastasis of colorectal carcinoma) from 2 colorectal carcinoma patients in Taiwan were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays. Comparison of gene expression profiles between paired normal colon and primary colorectal carcinoma; between primary colorectal carcinoma and liver metastasis colorectal carcinoma

2010-10-06 | E-GEOD-18462 | biostudies-arrayexpress

Long noncoding RNA (lncRNA) expression profiles in colorectal cancer tissues and paired adjacent normal tissues

Project description:Long noncoding RNAs (lncRNAs) play important roles in the tumorigenesis and metastasis of colorectal cancer (CRC). This study used a lncRNA microarray to analyze the aberrant lncRNA expression profiles in CRC tissues compared with paired adjacent normal tissues as well as CRC with regional lymph nodes metastasis compared with CRC without regional lymph nodes metastasis.

2020-05-12 | GSE84983 | GEO

RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients

Project description:The RNA from two paired normal and colorectal tumor tissue were sequenced by Illumina genome analyzer. 0.8 to 1.1 million reads were generated. Sequencing data was aligned with human RNA, human mitochondrial DNA and human genomic DNA by BWA. Base calling and Phred-like score was calculated by SAMTools. Whole transcriptome sequence of paired normal and tumor tissues obtained from two colorectal cancer patients

2011-05-28 | E-GEOD-29580 | biostudies-arrayexpress

RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients

2011-05-28 | GSE29580 | GEO

Microsatellite stable (n=38) and instable-high (n=13) human colorectal tumors assayed with Affymetrix HuGeneFL arrays.

Project description:mRNA assays were performed on 51 samples of human colorectal tumors using Affymetrix HuGeneFL arrays containing 7129 probe-sets. We compared 38 microsatelite stable (MSS) tumors with 13 microsatellite instable-high (MSI) tumors to form a list of genes differing between the two types. In order to identify molecular signatures characterizing MSI tumors, we examined only MSI-high cancers and not MSI-low ones. Keywords: disease state analysis

2009-04-10 | GSE11543 | GEO

Colorectal adenocarcinomas and matched normal colonic tissues

Project description:Five colorectal adenocarcinomas and matched normal colonic tissues were analyzed with Affymetrix HG-U133-Plus-2.0 microarrays. Two labs independently generated microarray data with the same array platform on the same biological samples.

2012-10-03 | GSE41328 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data