This document summarizes the results obtained by SICS in project GENFUNK (2001). The project was carried out in collaboration with Global Genomics AB (Stockholm, Sweden). Jointly obtained results will be presented separately. Main funding was provided by Swedish Research Agency VINNOVA. Project GENFUNK studied a novel approach of measuring the global gene expression. In the method, mRNA is extracted from a tissue sample and transformed into cDNA captured on magnetic beads. This is then acted on by type IIS restriction endonucleases, which recognize certain short DNA sequences and cut the DNA close to those sequences. The resulting fragments are amplified in PCR with selected ligation fragments, and displayed in capillary electrophoresis. Determining the gene expression levels from the peak data is combinatorial optimization problem, which can in principle be solved, to give expression levels of most genes active in sampled cells, with good accuracy.