Figure 1.
Principal component analysis of microarray gene expression profiles.
(A) Discovery microarray dataset: 222 normal, black; 42 colitis/IBD, green; 29 adenomas, blue; and 161 adenocarcinomas, red. (B) Validation microarray dataset: 30 normal, black; 19 adenomas, blue; and 19 adenocarcinomas, red.
Table 1.
Summary of microarray discovery probesets.
Figure 2.
NFE2L3 – prototypical ‘switched ON’ gene in colorectal neoplastic tissue relative to non-neoplastic tissue specimens.
(A) Discovery data set, 222 normal, black; 42 IBDs, green; 29 adenomas, blue; 161 adenocarcinomas, red. (B) Validation data set: 30 normal, black; 19 adenomas, blue; 19 adenocarcinomas, red. Y-axis: Normalized probeset intensity (log2).
Table 2.
Summary of microarray discovery and validation studies.
Figure 3.
KIAA1199 expression in colon tissue specimens.
(A) KIAA1199 expression measured via probeset 212942_s_at in the discovery dataset of 454 colorectal tissue specimens (x-axis indexed by phenotype); Norm: 222 normal specimens, black; IBD: 42 ‘colitis’ specimens, green; ADE: 29 adenomas, blue; CA: 161 cancer specimens, red. Y-axis: normalized probeset intensity (log2). (B) KIAA1199 expression measured via probeset 1008852-HuGene_st in the validation dataset in 68 colorectal tissue specimens. X-axis; Norm: 30 normal colon tissue specimens, black; ADE: 19 adenomas, blue; CA: 19 colorectal cancer specimens, red. Y-axis: normalized probeset intensity (log2). (C) A quantitative real-time SYBR-green KIAA1199 PCR assay applied to RNA extracts used for the validation microarray data: 30 normal, black; 21 adenomas, blue; 20 colorectal cancer, red specimens. Data are mean values of duplicates, normalized against HPRT1 and depicted as delta-delta-Ct values. Note that three additional neoplastic specimens were available for the PCR experiments which were not tested by custom microarray.
Figure 4.
Measurement of RNA levels in plasma specimens.
(A) GAPDH and (B) KIAA1199 RNA levels in plasma from 20 healthy subjects (black) and from 20 patients with colon adenomas (blue) and 20 CRC patients (red). Data are mean Ct values (triplicates) normalized for extraction yield differences and depicted as fold-change differences relative to the median expression measured in the 20 normal subjects. P values were calculated using two-tailed Mann-Whitney t-test.
Table 3.
Phenotypic breakdown of clinical specimens used in this study.
Table 4.
A description of tumor specimens by stage for discovery tissues.