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

Mojica W, Hawthorn L - BMC Genomics (2010)

Bottom Line: 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.For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and matched normal colon data.Our analysis of splice variants illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Oncology Program, Medical College of Georgia Cancer Center, Augusta, GA, USA.

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.

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Venn Diagram of gene expression alterations for three comparisons. The tumor vs cell comparison showed the largest number of transcript expression changes, while the tumor compared to the adjacent normal tissues showed the lowest number. The 77 genes which show alterations in both the tumor vs cell and tumor vs normal are of interest. All comparisons were performed following RMA normalization of all raw image files. Following a 3-way ANOVA the sources of variation were removed and the comparisons conducted. Cut-off values for gene expression differences were p = 0.05 and combined with a > 2-fold change.
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Figure 2: Venn Diagram of gene expression alterations for three comparisons. The tumor vs cell comparison showed the largest number of transcript expression changes, while the tumor compared to the adjacent normal tissues showed the lowest number. The 77 genes which show alterations in both the tumor vs cell and tumor vs normal are of interest. All comparisons were performed following RMA normalization of all raw image files. Following a 3-way ANOVA the sources of variation were removed and the comparisons conducted. Cut-off values for gene expression differences were p = 0.05 and combined with a > 2-fold change.

Mentions: Following this corrective processing, the various cut-off values for expression differences were set at p = 0.05 for the experimental sets compared to normal and combined with fold change values of 2. Genes showing differential expression using these analysis parameters are shown in the Venn diagram in Figure 2. This analysis reveals that there are more changes in the comparison between the isolated epithelial cells and the tumor than there were in the comparison between the matched tumor and normal tissue. Genes showing the highest increased expression levels in the tumor vs CELL comparison were OLFM4, FN1, ACTG2, IGJ, ACTA2, COL1A2, SPARC, RCN1, COL3A1 and COL1A1. The genes with the most significant decreases included TMIGD1, OTOP2, CA4, ZG16, MS4A12, GUCA2B, BEST4, CD177, HRASLS2, IFIT1 and MUC17.


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

Mojica W, Hawthorn L - BMC Genomics (2010)

Venn Diagram of gene expression alterations for three comparisons. The tumor vs cell comparison showed the largest number of transcript expression changes, while the tumor compared to the adjacent normal tissues showed the lowest number. The 77 genes which show alterations in both the tumor vs cell and tumor vs normal are of interest. All comparisons were performed following RMA normalization of all raw image files. Following a 3-way ANOVA the sources of variation were removed and the comparisons conducted. Cut-off values for gene expression differences were p = 0.05 and combined with a > 2-fold change.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823691&req=5

Figure 2: Venn Diagram of gene expression alterations for three comparisons. The tumor vs cell comparison showed the largest number of transcript expression changes, while the tumor compared to the adjacent normal tissues showed the lowest number. The 77 genes which show alterations in both the tumor vs cell and tumor vs normal are of interest. All comparisons were performed following RMA normalization of all raw image files. Following a 3-way ANOVA the sources of variation were removed and the comparisons conducted. Cut-off values for gene expression differences were p = 0.05 and combined with a > 2-fold change.
Mentions: Following this corrective processing, the various cut-off values for expression differences were set at p = 0.05 for the experimental sets compared to normal and combined with fold change values of 2. Genes showing differential expression using these analysis parameters are shown in the Venn diagram in Figure 2. This analysis reveals that there are more changes in the comparison between the isolated epithelial cells and the tumor than there were in the comparison between the matched tumor and normal tissue. Genes showing the highest increased expression levels in the tumor vs CELL comparison were OLFM4, FN1, ACTG2, IGJ, ACTA2, COL1A2, SPARC, RCN1, COL3A1 and COL1A1. The genes with the most significant decreases included TMIGD1, OTOP2, CA4, ZG16, MS4A12, GUCA2B, BEST4, CD177, HRASLS2, IFIT1 and MUC17.

Bottom Line: 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.For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and matched normal colon data.Our analysis of splice variants illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Oncology Program, Medical College of Georgia Cancer Center, Augusta, GA, USA.

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.

Show MeSH
Related in: MedlinePlus