In this article, we extend the Le et al. method so that we can integrate expression values and text when searching for matched array pairs.
For 114 of these samples there were matched mRNA array expression profiles available (Operon Human v.3 ~ 35 K 70-mer two-color oligonucleotide arrays, Gene Expression Omnibus accession [GEO GSE13876]).
An R-package to match array comparative genomic hybridization (CGH) and gene expression microarray features for integrative analysis purposes was provided by van Wieringen et al. (2012).
The cancer profiling array (CPA) I (Clontech) is a matched tumour/normal expression array consisting of cDNA synthesised from 50 breast carcinomas, 50 normal breast tissues and 3 breast cancer lymph node metastasis specimens.
Since there is a higher than 95% chance that cluster assignments are accurate (Supplemental File S2), and our validation analysis shows that 90.7% of the array expression patterns match the RNA analysis results using other techniques (e.g., Q-PCR), we estimate that more than 86% of the genes in a cluster follow the corresponding average expression profile.
For example, tiling array expression data that does not match an exon, a weak splice site in the existing structure and an incomplete Interpro domain in the existing structure, all indicating that the structure needs attention.
Exon array data from paired normal and adenoma samples were available for 18 patients, and for five of these patients exon array expression data were available for a matched carcinoma sample as well.
Validation of array expression using qRT-PCR.
For gene and protein expression analyses, northern blot, dot blot hybridization of matched tumor/normal arrays (cancer profiling arrays), quantitative RT-PCR, non-radioisotopic RNA in situ hybridization and immunohistochemistry were used.
Analysis of the raw array hybridization data for these transcripts revealed consistent hybridization profiles between duplicate spots on individual arrays and between distinct bio-replicates, these matching the expression trends of the group normalised data.
