Table 1.
Characteristics of study population.
Figure 1.
PCA analyses of differentially-expressed probes (≥2 fold change in expression and P<1.12E-06) between matched BE, NE, and NC tissues from BE patients.
PCA was applied to each set of differentially-expressed probes to reduce the dimensionality of the microarray data with respect to individual samples. Phenotypic subgroups or tissues (BE, NE, and NC) can be differentiated from each other in BE patients, although there is some mixing of the phenotypes, particularly between BE and NC, which are more similar in terms of gene expression profiles. Color key: Blue = NC, Yellow = NE, Red = BE.
Figure 2.
Paired analyses of significant differential gene expression (≥2 fc and P<1.12E-06) in BE vs NE and BE vs NC and enrichment in known biological processes.
A. The left Venn diagram represents the total number of genes with significant differential expression between BE and NE (≥2 fc and P<1.12E-06), whereas the right Venn diagram represents the total number with genes significant differential expression between BE and NC (≥2 fc and P<1.12E-06). The overlap between the two differentially-expressed sets contained 205 genes used for functional classification and pathway-based analyses. B. Enrichment of the 205 genes in known biological processes (GO, Ariadne Genomics, MD). The columns entitled: ‘Total no of genes in process’ and ‘Number of genes involved in process (% overlap)’ refer to the total number of genes currently known in each process according to the database (Pathway Studio 9.00), and the % overlap of the 205 genes with the total gene number in each process, respectively. Enrichment of the 205 genes identified in each process relative to the whole gene set is also shown. The largest proportion of genes (7.3%) out of the 205 genes were involved in response to drugs and cell adhesion; however, relative to the overall number of genes in the identified process, cellular response to insulin showed the greatest enrichment.
Table 2.
Summary showing top 50 differentially expressed genes in BE vs NE (the complete list is reported in Table S4).
Table 3.
Summary showing top 50 differentially expressed genes in BE vs NC (the complete list is reported in Table S5).
Figure 3.
Pathway-based analyses of common differentially expressed genes in BE vs NE and BE vs NC comparisons.
Two hundred and five overlapping genes were identified between BE vs. NE and BE vs. NC tissues after Bonferroni correction (P<1.12-E06) and with a 2-fold or greater differential expression. Diagram illustrates the TGF-β1 signaling pathway in BE vs NE and BE vs NC comparative groups. The direction and/or magnitude of expression is inverse for thirty two genes in the TGF-β1 network between the comparative groups. Genes include: SERPINB2, TMOD3, EPHA2, KRT15, ADCY7, SST, FMOD, CD36, CA9, ALCAM, IL1RN, TIMP2, CAST, MITF, SPRR1A, BHLHE40, MCL1, IL13RA1, ACPP, SRD5A1, NR2F2, ALDH1A1, DST, TJP1, CD9, TGFA, MUC4, PMAIP1, ZFP36, CCNG2, IL18 and CHGA. Data source: Signaling Pathways, Ariadne Pathways. Primary red and blue colors and shading indicate the direction and degree of differential expression with pink to red indicating degrees of increasing upregulation and light blue to darker blue indicating increasing downregulation. Grey indicates a gene product that is part of the pathway, but is absent in the experimental list tested. Abbreviations: BE, Barrett's; NE, normal squamous epithelium; NC, normal gastric cardia epithelium.