However, as group sizes were limited, gene regulation in DN of some genes defined as ����false positives���� can not be excluded. In summary, the single probe based analysis of oligonucleotide based arrays demonstrated clear advantages over the common probe set-based approach used in this study, most notably resulting in improved sensitivity and specificity of the biological findings . This was highlighted by the unique detection of a number of categories directly linked to clinical observations . In addition, the highlighted involvement of the Wnt pathway was in line with a larger body of data from the same microarray . Human renal biopsies from controls and patients with DN were collected from the European Renal cDNA Bank – Kro��ner- Fresenius Biopsy Bank , a multi-center study on renal gene expression in human nephropathies. Diagnostic renal biopsies were obtained from patients after informed consent and with approval of the local ethics committees. Microdissected samples taken from the tubulo-interstitial compartment were processed as described . For oligonucleotide array based gene expression profiling of DN a total of 9 kidney biopsies from individual patients were included: Biopsies from patients with advanced DN were analyzed and compared with pretransplantation kidney biopsies from living donors as control renal tissue . For confirmation of MMP7 induction, predicted by both array analysis approaches, an additional independent cohort from the ERCB-KFB was analyzed . The biopsies were stratified by reference pathologists according to their histological diagnosis. Following renal biopsy, the tissue was transferred to RNase inhibitor and microdissected into glomerular and tubular fragments. Total RNA was isolated from microdissected tubulointerstitial tissue . 300�C800 ng of total RNA was reverse-transcribed and linearly amplified according to a protocol previously reported . The fragmentation, hybridization, staining and imaging were performed according the Affymetrix Expression Analysis Technical Manual. RMA consists of three steps: background adjustment, quantile normalization, and summarization . RMA utilizes the Affymetrix provided probe set annotation to Y-27632 identify genes directly from the CEL files. The following settings were taken from previous studies : a background filter cut-off was defined to lower the count of false positive calls using the highest SB431542 signal value obtained from nonhuman Affymetrix control oligonucleotides multiplied by a factor of 1.2, corresponding in the current data set to a log based 2 value of 5.8. ChipInspector is a novel single probe-based analysis tool for microarray data that consists of four steps: single probe-transcript annotation, total intensity normalization, SAM analysis and transcript identification based on significantly changed probes.