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...

Intervertebral disc (IVD) degeneration is a pathological process, which may lead to lower back pain. The present study aimed to investigate the pathogenesis of IVD degeneration. GSE42611 was downloaded from Gene Expression Omnibus, including 4 nucleus pulposus samples isolated from degenerated IVDs and 4 nucleus pulposus samples separated from normal IVDs. The differentially expressed genes (DE...

Abdominal aortic aneurysm (AAA) is frequently lethal and has no effective pharmaceutical treatment, posing a great threat to human health. Previous bioinformatics studies of the mechanisms underlying AAA relied largely on the detection of direct protein-protein interactions (level-1 PPI) between the products of reported AAA-related genes. Thus, some proteins not suspected to be directly linked ...

The present study aimed to investigate potential gene markers for predicting the formation of carotid atheroma plaques using high‑throughput bioinformatics methods. The GSE43292 gene expression profile was downloaded from the Gene Expression Omnibus database. Following data processing, differentially expressed genes (DEGs) were screened using a paired t‑test in the Linear Models for Microarray ...

Advances in modern technologies for measuring protein-protein interaction (PPI) has boosted research in PPI networks analysis and comparison. One of the challenging problems in comparative analysis of PPI networks is the comparison of networks across species for discovering conserved modules. Approaches for this task generally merge the considered networks into one new weighted graph, called al...

Empirical study of networks has enlightened our understanding of many application domains including the topology of biological systems. The Markov clustering algorithm (MCL), originally developed for clustering graphs, has been adopted to clustering protein-protein interaction (PPI) networks. MCL is also becoming an effective algorithm for the extraction of complexes from interaction networks. ...

SMYD3 is a member of the SET and myeloid-Nervy-DEAF-1 (MYND) domain-containing protein family of methyltransferases, which are known to play critical roles in carcinogenesis. Expression of SMYD3 is elevated in various cancers, including esophageal squamous cell carcinoma (ESCC), and is correlated with the survival time of patients with ESCC. Here, we dissect gene expression data, from a previou...

Pediatric adrenocortical carcinoma (ACC) is a rare malignancy with a poor outcome. Molecular mechanisms of pediatric ACC oncogenesis and advancement are not well understood. Accurate and timely diagnosis of the disease requires identification of new markers for pediatric ACC. Differentially expressed genes (DEGs) were identified from the gene expression profile of pediatric ACC and obtained fro...

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normal...