The expression of DCLK1 in colorectal cancers and normal mucosa was calculated from previously published Affymetrix exon array data (refs. 12‒ 14 accession numbers GSE24550 and GSE29638; GEO).
The expression level of the target gene was standardised with that of the house-keeping beta-actin gene and the ratio of each gene expression in paired samples (adenoma or adenocarcinoma/adjacent mucosa) was calculated.
The overmethylation rate of each transitional-CpG site in the H. pylori-positive and -negative gastric mucosa was calculated by the relative proportion of overmethylated cases to the total sum of the over- and under-methylated cases.
When the expression of each gene was compared between the tumour (t) and the matched normal mucosa (n), the decrease or increase factor φ in the tumour vs the normal mucosa was calculated with the formula φ= 2 I Δ C t(n -Δ C t(t) I -1, with Δ Ct(n -ΔCt(n)gene− Ct(n)TOP1, Δ Ct(t)= Ct(t)gene− Ct(t)TOP1, and I the absolute value of the term Δ Ct(n)−Δ Ct(t).
The target-to-background ratios (T/B) of peptide binding to adenomas versus normal-appearing adjacent mucosa for each peptide were calculated by dividing the average mean intensity from adenomas by that from normal mucosa for each mouse.
The threshold cycles (CT's) for GAPDH and p16 INK4A of nontumour mucosa (N) and UC carcinoma (T) were calculated.
From the measured unidirectional net flux rates (Jms = flux rate from mucosa to serosa; Jsm = flux rate from serosa to mucosa), the net ion flux rates (Jnet) were calculated according to Jnet = Jms - Jsm (nmol/h/cm) from the mean unidirectional flux rates.
The methylation dosage ratios (Dm) were calculated separately for each normal mucosa and tumor sample (Additional file 1: Table S1) as described [ 51].
Peptides identified by LC-MS/MS analyses were quantified in individual samples (12 CRC tissue-healthy mucosa pairs) using a label-free approach and modification intensities were calculated for each of the detected sites (see Methods).
