Transcriptomics

Dataset Information

177

Transcription profiling of human colon biopsy samples from healthy individuals and patients with colon adenomas, colorectal cancer or inflammatory bowel disease


ABSTRACT: Background and Aims: Gene expression analysis of colon biopsies using high-density oligonucleotide microarray can contribute to the understanding of local pathophysiological alterations and to functional classification of precancerous adenoma, different stage colorectal carcinomas (CRC) and inflammatory bowel diseases (IBD). Results: Significant overexpression of collagen IV1, lipocalin-2, caveolin-1, calumenin genes, and significant dowregulation of aquaporin-8, amnionless homolog, prostaglandin D2 receptor genes were detected in CRC patients compared to normal. Adenoma samples were characterized by upregulated CD44 antigen, met proto-oncogene and downregulated chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette A8 discriminatory genes. In IBD samples significantly increased lipocalin-2, interferon induced transmembrane protein 1 and 3 mRNA levels, decreased zinc finger protein 91 and transient receptor potential cation channel M6 mRNA levels were found. Ulcerative colitis and Crohn’s disease can be distinguished according to the top five genes: cyclin-G2; tripartite motif-containing-31; TNFR shedding aminopeptidase regulator-1; C-type lectin superfamily member-14 and AMICA. 88.3-97.8% of the cases was correctly classified according to discriminatory genes. Conclusions: Our whole genomic microarray analysis of biopsy samples provides discriminative signatures, and an insight into pathophysiological background of colonic diseases. The results afford a data warehouse which can be further mined for in-depth pathway analyses. Experiment Overall Design: Total RNA was extracted, amplified and biotinylated from frozen colonic biopsies of 15 patients with CRC, 15 with adenoma, 15 with IBD and 8 healthy normal controls. Genome-wide gene expression profile was evaluated by HGU133 Plus 2.0 microarrays. Gene expression was also measured by real-time PCR.

REANALYSED by: E-GEOD-4183

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Homo sapiens  

SUBMITTER: Balazs Györffy  

PROVIDER: E-GEOD-4183 | ArrayExpress | 2008-06-12

SECONDARY ACCESSION(S): GSE4183PRJNA95145

REPOSITORIES: GEO, ArrayExpress

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Publications

Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples.

Gyorffy Balazs B   Molnar Bela B   Lage Hermann H   Szallasi Zoltan Z   Eklund Aron C AC  

PloS one 20090521 5


Several preprocessing algorithms for Affymetrix gene expression microarrays have been developed, and their performance on spike-in data sets has been evaluated previously. However, a comprehensive comparison of preprocessing algorithms on samples taken under research conditions has not been performed.We used TaqMan RT-PCR arrays as a reference to evaluate the accuracy of expression values from Affymetrix microarrays in two experimental data sets: one comprising 84 genes in 36 colon biopsies, and  ...[more]

Publication: 1/2

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