Many complex networks such as computer and social networks exhibit modular structures, where links between nodes are much denser within modules than between modules. It is widely believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. While many authors have claimed that observations from the yeast protein-pro...

PURPOSE CRC (Colorectal cancer) is a lethal cancer for death worldwide and the underlying pathological mechanisms for CRC progression remain unclear. We aimed to explore the regulatory mechanism of CRC and provide novel biomarkers for CRC screening. METHODS Downloading from GEO (Gene Expression Omnibus) database, Microarray data GSE44861 were consisted of 111 colon tissues samples including 5...

Alzheimer’s disease (AD) is the most common dementia characterized by tangles and plaques that hippocampus as one of the primary regions of the brain affected by AD. In this study investigated network-based Protein-Protein Interactions (PPI) for hippocampal proteins that altered in AD patient's comparison with healthy control. Altered protein data were extracted from beforehand investigation wh...

Traditional approaches for homology detection rely on finding sufficient similarities between protein sequences. Motivated by studies demonstrating that from non-sequence based sources of biological information, such as the secondary or tertiary molecular structure, we can extract certain types of biological knowledge when sequence-based approaches fail, we hypothesize that protein-protein inte...

Motivation: DNA microarray has become an important tool to help identify biomarker genes for improving the prognosis of metastatic breast cancer a leading cause of cancer-related deaths in women worldwide. Recently, pathway-level relationships between genes have been increasingly used to build more robust classification models which also can provide useful biological insights. Due to the unavai...

The present study aimed to identify altered genes and pathways associated with four histotypes of ovarian cancer, according to the systematic tracking of dysregulated modules of reweighted protein‑protein interaction (PPI) networks. Firstly, the PPI network and gene expression data were initially integrated to infer and reweight normal ovarian and four types of ovarian cancer (endometrioid, ser...

MOTIVATION A wealth of protein-protein interaction (PPI) data has recently become available. These data are organized as PPI networks and an efficient and biologically meaningful method to compare such PPI networks is needed. As a first step, we would like to compare observed networks to established network models, under the aspect of small subgraph counts, as these are conjectured to relate to...

The present study aimed to identify the genes directly or indirectly correlated with the amplification of MYCN in neuroblastoma (NB). Microarray data (GSE53371) were downloaded from Gene Expression Omnibus, and included 10 NB cell lines with MYCN amplification and 10 NB cell lines with normal MYCN copy numbers. Differentially expressed genes (DEGs) were identified using the Linear Models for Mi...

BACKGROUND The pathological mechanism of Barrett's esophagus (BE) is still unclear. In the present study, pathway cross-talks were analyzed to identify hub pathways for BE, with the purpose of finding an efficient and cost-effective detection method to discover BE at its early stage and take steps to prevent its progression. MATERIAL AND METHODS We collected and preprocessed gene expression pro...

Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we investigate how gene conservation, essentiality and functional repertoire are reflected in the connectivity k of the corresponding proteins in the PPI networks of 42 evolutionarily unrelated bacterial species. We investigate three issues: i) the degree distribution and densities of the ...