Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling

In medical genetics, each genetic variant is evaluated as an independent entity regarding its clinical importance. However, in most complex diseases, variant combinations in specific gene networks, rather than the presence of a particular single variant, predominates. In the case of complex diseases, disease status can be evaluated by considering the success level of a team of specific variants. We propose a high dimensional modelling based method to analyse all the variants in a gene network together, which we name “Computational Gene Network Analysis” (CoGNA).To evaluate our method, we selected two gene networks, mTOR and TGF-$beta$. For each pathway, we generated 400 control and 400 patient group samples. mTOR and TGF-$beta$ pathways contain 31 and 93 genes of varying sizes, respectively. We produced Chaos Game Representation images for each gene sequence to obtain 2-D binary patterns. These patterns were arranged in succession, and a 3-D tensor structure was achieved for each gene network. Features for each data sample were acquired by exploiting Enhanced Multivariance Products Representation to 3-D data. Features were split as training and testing vectors. Training vectors were employed to train a Support Vector Machines classification model. We achieved more than $96$ and $99$ classification accuracies for mTOR and TGF-$beta$ networks, respectively, using a limited amount of training samples

P-selectin expression in a colon tumor model exposed by sinusoidal electromagnetic fields

P-selectin is mainly involved in the initial process of tumor cell adhesion to platelets. The aim of the present study was to determine the expression level of P-selectin in a colon tumor model affected by sinusoidal electromagnetic fields (SMF). Male Wistar albino rats aged 2-2.5 months were used. The animals were divided into the I [N-Methyl-N-Nitrosurea (MNU)], II (SMF-MNU), III (SMF) and IV (control) groups. The rats were housed five per polycarbonate cage. Sixty milligrams of MNU was dissolved in 6 ml sterile 0.9% NaCl. Prepared solutions were administered intra rectally (i.r.) to the 1st and 3rd groups as 0.2 ml/per animal. The same procedure was applied to the 2nd and 4th groups, although 0.2 ml/per animal sterile isotonic solution was administered instead. This procedure was repeated once a week for 10 weeks. Following the administration of MNU, the 2nd and 3rd groups were exposed to a sinusoidal magnetic field (SMF, 50 Hz, 5 mT) for 6 h/day for 8 months. P-selectin expression of the four groups of rat colon tissues was determined using immunohistochemistry on paraffin sections. The labeled streptavidin biotin method was performed. Fisher’s exact test was used for differences between proportions. Results showed that there was no statistically significant (P>0.05) change in the expression level of P-selectin. However, this result should be verified by both in vivo and in vitro experiments to determine the effects of the magnetic fields on P-selectin