es functional relations between AGS genes themselves and between AGS and outside pathways. Hence, it is desirable to go beyond a simple overlap between AGS and members of FGS. For this purpose, IPA attempts to identify differentially expressed genes grouped in compact modules in the network. However, DE genes not necessarily group like this. In contrast to other network methods, the NEA does not expect any ready modules in the network and considers functional links between any genes of AGS and FGS in the whole gene interaction network. In other words, it uses available network links scattered over the network to test enrichment hypotheses of functional associations between an experimentally defined gene set and known pathways and biological processes. Hence, NEA acts in the most straightforward and robust GSEA-like manner with the difference that, unlike conventional GSEA, it employs DE genes which are not necessarily members of any already known functional category; but they are connected to such members in the network. Due to the availability of gene network links to nearly every gene, the sensitivity of the method exceeds that of GSEA around 510 fold. In the following, we systematically apply the GSEA, IPA, and NEA to our research problem. By combining these methods we highlight the most crucial biological processes controlled by Sodium laureth sulfate web syndecan-1 in malignant mesothelioma. Materials and Methods Cell Culture Conditions Human malignant mesothelioma cells were grown in RPMI 1640 medium supplemented with 10% human AB serum, 1% L-Glutamine and 25 mM HEPES buffer under standardized incubation conditions, in humidified atmosphere containing 5% CO2 at 37uC. The cells display epithelioid morphology and express low endogenous syndecan-1. Syndecan-1 Overexpression Syndecan-1 was stably overexpressed by transfection with a pEGFP-N1 plasmid carrying the human full-length syndecan-1 gene. Transfection was performed using Effectene Transfection Reagent. The plasmid and subsequent stable transfection of STAV-AB cells have previously been described in detail by us in a recent publication. Cells transfected with the pEGFP-N1 vector were used as negative control. Syndecan-1 Silencing Three hundred thousand STAV-AB cells/well were seeded and after one day transfected using LipofectamineTM 2000. Three siRNA constructs specific for syndecan-1 were used with an optimized concentration of 40 nM. Scrambled siRNA, with no target mRNA, was used as negative control. Syndecan-1 specific siRNA or scrambled control siRNA and lipofectamine were diluted in antibiotics- and serum- free medium according to the manufacturer’s instructions and incubated for 25 minutes. The different mediums containing the siRNA-lipofectamine complexes were then added separately to the cells and incubated at 37uC and 5% CO2. After 24 or 48 hours the samples were harvested and RNA was extracted. Experiments were performed in triplicates or more. RNA Isolation Total RNA was isolated from sub-confluent cells, using 
the High Pure RNA Isolation Kit according to the manufacturer’s protocol. The yield and purity of the RNA were determined spectrophotometrically by measuring the UV absorbances at 260 and 280 nm with a NanoDrop spectrophotometer. Validation a. Quantitative real time polymerase chain reaction. Verification of the syndecan-1 overexpression and silencing, as well as validation of the Affimetryx results, were done by quantitative RT-PCR. cDNA synthesis was performed by reverse transcriptio