Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease.

Hdl Handle:
http://hdl.handle.net/10675.2/68
Title:
Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease.
Authors:
Mojica, Wilfrido; Hawthorn, Lesleyann
Abstract:
BACKGROUND: Studies using microarray analysis of colorectal cancer have been generally beleaguered by the lack of a normal cell population of the same lineage as the tumor cell. One of the main objectives of this study was to generate a reference gene expression data set for normal colonic epithelium which can be used in comparisons with diseased tissues, as well as to provide a dataset that could be used as a baseline for studies in alternative splicing. RESULTS: We present a dependable expression reference data set for non-neoplastic colonic epithelial cells. An enriched population of fresh colon epithelial cells were obtained from non-neoplastic, colectomy specimens and analyzed using Affymetrix GeneChip EXON 1.0 ST arrays. For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and matched normal colon data. This analysis allowed an assessment of global gene expression alterations and demonstrated that adjacent normal tissues, with a high degree of cellular heterogeneity, are not always representative of normal cells for comparison to tumors which arise from the colon epithelium. We also examined alternative splicing events in tumors compared to normal colon epithelial cells. CONCLUSIONS: The findings from this study represent the first comprehensive expression profile for non-neoplastic colonic epithelial cells reported. Our analysis of splice variants illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data. It is projected that the contribution of this set of data derived from pure colonic epithelial cells will enhance studies in colon-related disease and offer a vital baseline for studies aimed at elucidating the mechanisms of alternative splicing.
Citation:
BMC Genomics. 2010 Jan 4; 11:5
Issue Date:
18-Feb-2010
URI:
http://hdl.handle.net/10675.2/68
DOI:
10.1186/1471-2164-11-5
PubMed ID:
20047688
PubMed Central ID:
PMC2823691
Type:
Journal Article; Research Support, Non-U.S. Gov't
ISSN:
1471-2164
Appears in Collections:
Georgia Cancer Center: Faculty Research and Presentations

Full metadata record

DC FieldValue Language
dc.contributor.authorMojica, Wilfridoen_US
dc.contributor.authorHawthorn, Lesleyannen_US
dc.date.accessioned2010-09-24T21:39:15Z-
dc.date.available2010-09-24T21:39:15Z-
dc.date.issued2010-02-18en_US
dc.identifier.citationBMC Genomics. 2010 Jan 4; 11:5en_US
dc.identifier.issn1471-2164en_US
dc.identifier.pmid20047688en_US
dc.identifier.doi10.1186/1471-2164-11-5en_US
dc.identifier.urihttp://hdl.handle.net/10675.2/68-
dc.description.abstractBACKGROUND: Studies using microarray analysis of colorectal cancer have been generally beleaguered by the lack of a normal cell population of the same lineage as the tumor cell. One of the main objectives of this study was to generate a reference gene expression data set for normal colonic epithelium which can be used in comparisons with diseased tissues, as well as to provide a dataset that could be used as a baseline for studies in alternative splicing. RESULTS: We present a dependable expression reference data set for non-neoplastic colonic epithelial cells. An enriched population of fresh colon epithelial cells were obtained from non-neoplastic, colectomy specimens and analyzed using Affymetrix GeneChip EXON 1.0 ST arrays. For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and matched normal colon data. This analysis allowed an assessment of global gene expression alterations and demonstrated that adjacent normal tissues, with a high degree of cellular heterogeneity, are not always representative of normal cells for comparison to tumors which arise from the colon epithelium. We also examined alternative splicing events in tumors compared to normal colon epithelial cells. CONCLUSIONS: The findings from this study represent the first comprehensive expression profile for non-neoplastic colonic epithelial cells reported. Our analysis of splice variants illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data. It is projected that the contribution of this set of data derived from pure colonic epithelial cells will enhance studies in colon-related disease and offer a vital baseline for studies aimed at elucidating the mechanisms of alternative splicing.en_US
dc.rightsThe PMC Open Access Subset is a relatively small part of the total collection of articles in PMC. Articles in the PMC Open Access Subset are still protected by copyright, but are made available under a Creative Commons or similar license that generally allows more liberal redistribution and reuse than a traditional copyrighted work. Please refer to the license statement in each article for specific terms of use. The license terms are not identical for all articles in this subset.en_US
dc.subject.meshAgeden_US
dc.subject.meshAged, 80 and overen_US
dc.subject.meshAlternative Splicingen_US
dc.subject.meshColon / metabolism / pathologyen_US
dc.subject.meshColonic Diseases / geneticsen_US
dc.subject.meshColorectal Neoplasms / geneticsen_US
dc.subject.meshEpithelium / metabolism / pathologyen_US
dc.subject.meshExonsen_US
dc.subject.meshFemaleen_US
dc.subject.meshGene Expression Profilingen_US
dc.subject.meshHumansen_US
dc.subject.meshMaleen_US
dc.subject.meshMiddle Ageden_US
dc.subject.meshOligonucleotide Array Sequence Analysisen_US
dc.subject.meshPrincipal Component Analysisen_US
dc.subject.meshReference Standardsen_US
dc.titleNormal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease.en_US
dc.typeJournal Articleen_US
dc.typeResearch Support, Non-U.S. Gov'ten_US
dc.identifier.pmcidPMC2823691en_US
dc.contributor.corporatenameGHSU Cancer Centeren_US

Related articles on PubMed

All Items in Scholarly Commons are protected by copyright, with all rights reserved, unless otherwise indicated.