This study integrated four microarray datasets by Robust Rank Aggregation (RRA) method to identify the differentially expressed genes (DEG) in bovine mammary epithelial (BME) cells response Escherichia coli and Staphylococcus aureus infection. Furthermore, GO function KEGG pathway enrichment analysis of DEG were performed. Finally, protein-protein interaction (PPI) network was constructed. A to...

Proteins carry out their function in a cell through interactions with other proteins. A large scale Protein-Protein Interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction method...

Hypertension is one of the silent killers in human life which characterized by uncontrolled blood pressure. Although many therapeutic drugs have demonstrated success treating hypertension, these treatments their own drawbacks, most notably terms cost and side effects. treatment with natural products has lately been proposed. This study focused on potential Allium schoenoprasum against hypertens...

abstractintroduction: cancer is caused by genetic abnormalities, such as mutation of ontogenesis or tumor suppressor genes which alter downstream signaling pathways and protein-protein interactions. comparison of protein interactions in cancerous and normal cells can be of help in mechanisms of disease diagnoses and treatments. methods: we constructed protein interaction networks of cancerous a...

background: numerous studies used microarray gene expression data to extract metastasis-driving gene signatures for the prediction of breast cancer relapse. however, the accuracy and generality of the previously introduced biomarkers are not acceptable for reliable usage in independent datasets. this inadequacy is attributed to ignoring gene interactions by simple feature selection methods, due...

Characterization of protein–protein interactions (PPIs) is essential for understanding cellular signal transduction pathways. However, quantitative measurement the binding strength remains challenging. Building upon classical bacterial adenylate cyclase two-hybrid (BACTH) system, we previously demonstrated that relative reporter protein expression (RRPE), defined as level normalized to interact...

Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Pre...

Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein^protein interaction (PPI) networks. We first describe issues an...

Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues an...

The topology behind biological interaction networks has been studied for over a decade. Yet, there is no definite agreement on the theoretical models which best describe protein-protein interaction (PPI) networks. Such models are critical to quantifying the significance of any empirical observation regarding those networks. Here, we perform a comprehensive analysis of yeast PPI networks in orde...