2 network from more comprehensive aspects: variation of gene expression level, gene co-expression between directly connected proteins and the topology of the sub-network, whereas many other existing methods only take a part of these factors into account. By the edge-based searching procedure utilizing connected edges, instead of vertices, what we construct is a sub-network with the topology str...

OBJECTIVE Current protein-protein interaction (PPI) detection via high-throughput experimental methods, such as yeast-two-hybrid has been reported to be highly erroneous, leading to potentially costly spurious discoveries. This work introduces a novel measure called IRAP, i.e. "interaction reliability by alternative path", for assessing the reliability of protein interactions based on the under...

The aim of the present study was to explore the function and interaction of differentially expressed genes (DEGs) in pulmonary embolism (PE). The gene expression profile GSE13535, was downloaded from the Gene Expression Omnibus database. The DEGs 2 and 18 h post‑PE initiation were identified using the affy package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the...

OBJECTIVE This study was performed to evaluate the therapeutic effect of cisplatin-gemcitabine combination chemotherapy for advanced non-small cell lung cancer (NSCLC). MATERIALS AND METHODS Dataset GSE39345 from patients who underwent cisplatin-gemcitabine combination chemotherapy and normal controls was downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were iden...

Gene expression data were analysed using bioinformatic tools to demonstrate molecular mechanisms underlying the glioma CpG island methylator phenotype (CIMP). A gene expression data set (accession no. GSE30336) was downloaded from Gene Expression Omnibus, including 36 CIMP+ and 16 CIMP- glioma samples. Differential analysis was performed for CIMP+ vs. CIMP‑ samples using the limma package in R....

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...

Domain-domain interactions are a critical type of the mechanisms mediating protein-protein interactions (PPIs). For a given protein domain, its ability to combine with distinct domains is usually referred to as promiscuity or versatility. Interestingly, a previous study has reported that a domain's promiscuity may reflect its ability to interact with other domains in human proteins. In this wor...

The prediction of protein function is one of the most challenging problems in bioinformatics. Several studies have shown that the prediction using PPI is promising. However, the PPI data generated from highthroughput experiments are very noisy, which renders great challenges to the existing methods. In this paper, we propose an algorithm, MFC, to efficiently mine maximal frequent dense subgraph...

An enduring theme in the literature exploring patient and public involvement (PPI) in research has been the focus on evaluating impact, defined usually in terms of participants' practical contribution to enhancing research processes. By contrast, there has been less emphasis on the perspectives and experiences of those involved in PPI. Drawing on qualitative data with people involved in the Nat...