Abstract: Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.
Abstract: Complex assemblies of interacting proteins carry out
most of the interesting jobs in a cell, such as metabolism, DNA
synthesis, mitosis and cell division. These physiological properties
play out as a subtle molecular dance, choreographed by underlying
regulatory networks that control the activities of cyclin-dependent
kinases (CDK). The network can be modeled by a set of nonlinear
differential equations and its behavior predicted by numerical
simulation. In this paper, an innovative approach has been proposed
that uses genetic algorithms to mine a set of behavior data output by
a biological system in order to determine the kinetic parameters of
the system. In our approach, the machine learning method is
integrated with the framework of existent biological information in a
wiring diagram so that its findings are expressed in a form of system
dynamic behavior. By numerical simulations it has been illustrated
that the model is consistent with experiments and successfully shown
that such application of genetic algorithms will highly improve the
performance of mathematical model of the cell division cycle to
simulate such a complicated bio-system.
Abstract: A New features are extracted and compared to
improve the prediction of protein-protein interactions. The basic idea
is to select and use the best set of features from the Tensor matrices
that are produced by the frequency vectors of the protein sequences.
Three set of features are compared, the first set is based on the
indices that are the most common in the interacting proteins, the
second set is based on the indices that tend to be common in the
interacting and non-interacting proteins, and the third set is
constructed by using random indices. Moreover, three encoding
strategies are compared; that are based on the amino asides polarity,
structure, and chemical properties. The experimental results indicate
that the highest accuracy can be obtained by using random indices
with chemical properties encoding strategy and support vector
machine.
Abstract: The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.