Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Sev...

The yeast two-hybrid (Y2H) system is currently one of the most important techniques for protein-protein interaction (PPI) discovery. Here, we describe a stringent three-step Y2H matrix interaction approach that is suitable for systematic PPI screening on a proteome scale. We start with the identification and elimination of autoactivating strains that would lead to false-positive signals and pre...

Protein complexes are fundamental for understanding principles of cellular organizations. Accurate and fast protein complex prediction from the PPI networks of increasing sizes can serve as a guide for biological experiments to discover novel protein complexes. However, protein complex prediction from PPI networks is a hard problem, especially in situations where the PPI network is noisy. We kn...

Cellular signal transduction is a complex process involving protein-protein interactions (PPIs) that transmit information. For example, signals from the plasma membrane may be transduced to transcription factors to regulate gene expression. To obtain a global view of cellular signaling and to predict potential signal modulators, we searched for protein interaction partners of more than 450 sign...

Essential proteins are those that are indispensable to cellular survival and development. Existing methods for essential protein identification generally rely on knock-out experiments and/or the relative density of their interactions (edges) with other proteins in a Protein-Protein Interaction (PPI) network. Here, we present a computational method, called EW, to first rank protein-protein inter...

MOTIVATION Recent advances in technology have dramatically increased the availability of protein-protein interaction (PPI) data and stimulated the development of many methods for improving the systems level understanding the cell. However, those efforts have been significantly hindered by the high level of noise, sparseness and highly skewed degree distribution of PPI networks. Here, we present...

We aimed to investigate the mechanism of action Zhimu in treatment ovarian cancer (OC) using network pharmacology. OC targets were screened DisGeNET and Online Mendelian Inheritance Man databases. Common identified Traditional Chinese Medicine System Pharmacology, UniProt databases, Venny 2.1.0. The protein-protein interaction (PPI) Search Tool for Retrieval Interacting Genes/Proteins database ...

Introduction: Psoriasis is a chronic, inflammatory skin disorder. Studies suggested dysregulations in cell programmed death keratinocytes may play role psoriasis. Previously, we found Oncostatin M (OSM) was overexpressed psoriatic lesions, and related to the expressions of cellular senescence autophagy markers. Therefore, hypothesized that OSM-regulated senescence-autophagy interaction maintena...

Stephaniae Tetrandrae Radix (STR) is a commonly used herb with history of thousands years. Accumulating evidence shows the therapeutic effect on breast cancer (BC) STR. Here, we aimed to elucidate active components and mechanisms STR against BC. The targets were retrieved screened from corresponding databases. A target protein–protein interaction (PPI) network was built Ingenuity Pathway Analys...

Objectives This study aimed to determine the pathophysiology of recurrent benign paroxysmal positional vertigo (BPPV) in young patients using gene expression profiling combined with bioinformatics analysis. Methods Total RNA was extracted from whole blood four BPPV and controls. The differentially expressed genes (DEGs) between groups were screened a microarray analysis based on cutoff criteria...