The protocols related to array printing and hybridization in this paper generally can be found in microarrays.org (http://derisilab.ucsf.edu/microarray/protocols.html).html
This study has demonstrated that PSCA is overexpressed in pancreatic cancer and poorly expressed in normal pancreas and chronic pancreatitis, and similar results have been found in microarray and real-time studies (Argani et al, 2001; Ryu et al, 2002; Missiaglia et al, 2004; Grubbs et al, 2006).
Additional analysis and data can be found in Supplemental Microarray Analysis S1 and Tables S1, S3, S3, and S4.
The set of pathways obtained from the MSigDB covers more than 5,000 distinct genes, where 3,271 of them can be found in both microarray platforms used by the two breast cancer gene expression studies in [10], [11].
In total, we identified 217 common TGs of E2F1 3 and MYC that can be found in the microarray dataset GSE5550 (Table S1).
In line with this, AIF expression level is positively correlated with overall survival in our cohort of colon cancer patients, which can also be found in several microarray datasets for colon, breast, and lung cancers.
One explanation for these effects can be found in DNA microarray studies (Coser et al. 2003; Shioda et al. 2006), where increasing doses of estrogens, from low to higher levels, result in entirely different arrays of genes that are turned on or off.
The log2 fold-changes and p-values for all genes present on the microarray can be found in Additional file 1: Table S1, also including the microarray data for ∆luxI 1 versus wild-type [ 27] for comparison.
The hybridization setup can be found in Additional file 1. Microarrays were scanned using the Agilent DNA Microarray Scanner (Agilent Technologies, Part Number G2505B), and scans were quantified using the Agilent Feature Extraction software (version 8.5.1).
The full list of miRNA probes can be found in the GEO database where microarray data are submitted with an accession number of: GSE24106.
