The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF‑β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co‑expressed DEGs were selected using Venn Di...

The increasing availability of biological networks (proteinprotein interaction graphs, metabolic and transcriptional networks, etc.) is offering new opportunities to analyze their topological properties and possibly gain new insights in their design principles. Here we concentrate on the problem of de novo identification of the building modules of networks, which we refer to as network modules....

BACKGROUND Acute coronary syndrome (ACS), referring to any group of symptoms attributed to obstruction of the coronary arteries, affects millions of patients annually and requires immediate diagnosis and therapy. OBJECTIVE The purpose of this study was to find more biomarkers through identifying the genes which are related to ACS with samples from normal and diseased blood vessel. MATERIALS...

6 The increasing growth of data on protein-protein interaction (PPI) networks has boosted research 7 on their comparative analysis. In particular, recent studies proposed models and algorithms for 8 performing network alignment, that is, the comparison of networks across species for discovering 9 conserved functional complexes. In this paper, we present an algorithm for dividing PPI networks, 1...

The evaluation of the biological networks is considered the essential key to understanding the complex biological systems. Meanwhile, the graph clustering algorithms are mostly used in the protein-protein interaction (PPI) network analysis. The complexes introduced by the clustering algorithms include noise proteins. The error rate of the noise proteins in the PPI network researches is about 40...

It has been claimed that protein-protein interaction (PPI) networks are scale-free, and that identifying high-degree "hub" proteins reveals important features of PPI networks. In this paper, we evaluate the claims that PPI node degree sequences follow a power law, a necessary condition for networks to be scale-free. We provide two PPI network examples which clearly do not have power laws when a...

Proteins interact in complex protein-protein interaction (PPI) networks whose topological properties-such as scale-free topology, hierarchical modularity, and dissortativity-have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supportin...

High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. The PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserved subnetworks, and provides extra information for functional annotations. Although a few methods have been developed for multiple PPI network alignment, th...

Colorectal cancer (CRC) is one of the most common malignant diseases worldwide, but the involved signaling pathways and driven-genes are largely unclear. This study integrated four cohorts profile datasets to elucidate the potential key candidate genes and pathways in CRC. Expression profiles GSE28000, GSE21815, GSE44076 and GSE75970, including 319 CRC and 103 normal mucosa, were integrated and...

For the reconstruction of signaling pathways from RNAi data, an integer linear optimization model is proposed. The aim is to reconstruct the signaling network from the given protein protein interaction (PPI) network satisfying RNAi data by making minimum changes on the given network. For evaluation, 1000 reference PPI networks each with seven, eight, or nine proteins, and RNAi data for each of ...