Key network approach reveals new insight into Alzheimer's disease
In this study, the authors propose a closed network that uses a set of nodes (amyloid beta, tau, beta-secretase, glutamate, cyclin-dependent kinase 5, phosphoinositide 3-kinase and hypoxia-induced factor 1 alpha) as key elements of importance to the pathogenesis of AD. The proposed network, in total 39 nodes, is able to become a novel tool capable of providing new insights into AD, such as feedback loops. Further, it highlights interconnections between pathways and identifies their combination for therapy of AD. (Source: IET Systems Biology)
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Knowledge discovery for pancreatic cancer using inductive logic programming
Pancreatic cancer is a devastating disease and predicting the status of the patients becomes an important and urgent issue. The authors explore the applicability of inductive logic programming (ILP) method in the disease and show that the accumulated clinical laboratory data can be used to predict disease characteristics, and this will contribute to the selection of therapeutic modalities of pancreatic cancer. The availability of a large amount of clinical laboratory data provides clues to aid in the knowledge discovery of diseases. In predicting the differentiation of tumour and the status of lymph node metastasis in panc...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Systematic study on G-protein couple receptor prototypes: did they really evolve from prokaryotic genes?
G-protein couple receptor (GPCR) is one of the most striking examples of signalling proteins and it is only observed in eukaryotes. Based on various GPCR identification methods and classification systems, several evolutionary presumptions of different GPCR families have been reported. However, the prototype of GPCR still limits our knowledge. By investigating its structure and domain variance, the authors propose that GPCR might be evolved from prokaryotic world. The results given by the authors indicate that metabotropic glutamate receptor family would be the ancestor of GPCR. Phylogenetic analysis hints that one of metab...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago
This study provides a timely comparative genomic and transcriptomic analysis of the terpene synthase (TPS) gene family in Medicago truncatula (bears glandular and non-glandular trichomes) and Arabidopsis thaliana (bears non-glandular trichomes). The authors' efforts aimed to gain insight into TPS function, phylogenetic relationships and the role of trichomes in terpene biosynthesis and function. In silico analysis identified 33 and 23 putative full-length TPS genes in Arabidopsis and Medicago, respectively. All AtTPS and MtTPS fall into the five established angiosperm TPS subfamilies, with lineagespecific expansion of Subf...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon
In this study, the authors found that the steady-state behaviour of the system will have a great effect on the occurrence of overshoot. They showed that overshoot in general cannot occur in systems that will finally approach an equilibrium steady state. They further classified overshoot into two types, named as simple overshoot and oscillating overshoot. They showed that except for extreme cases, oscillating overshoot will occur if the system is far from equilibrium. All these results clearly show that overshoot is a non-equilibrium dynamic phenomenon with energy consumption. In addition, the main result in this study is v...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Cell commitment motif composed of progenitor-specific transcription factors and mutual-inhibition regulation
In this study, the authors represent the cell commitment motifs composed of mutual-inhibition regulation and progenitor-specific transcription factors, and develop associated mathematical model to understand how specific cell fate decisions are made. Bifurcation analysis and numerical simulation show that the model could exhibit multiple stable steady states corresponding to progenitor and committed cell states. The transitions between different cell states correspond to different commitment processes. Furthermore, the authors demonstrate that different commitment patterns, for example, haematopoietic and neural fate decis...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Editorial - Selected papers from The 7th IEEE International Conference on Systems Biology (ISB 2013)
Computational systems biology has become an intensive research topic in the past decade due to the emergence of high-throughput biological experiments. The generated genomics, epigenomics, transcriptomics, proteomics, and metabolomics data have provided new ways to decipher the biological systems in a more detailed and comprehensive manner. These research topics have also attracted many leading scientists in Biology, Systems Science, Physics, Mathematics, Computer Science, Control Science and Statistics. Many computational and mathematical methodologies have been developed to meet the request of the unprecedented opportuni...
Source: IET Systems Biology - August 1, 2014 Category: Biology Source Type: research
Anti-triangle centrality-based community detection in complex networks
Community detection has been extensively studied in the past decades largely because of the fact that community exists in various networks such as technological, social and biological networks. Most of the available algorithms, however, only focus on the properties of the vertices, ignoring the roles of the edges. To explore the roles of the edges in the networks for community discovery, the authors introduce the novel edge centrality based on its antitriangle property. To investigate how the edge centrality characterises the community structure, they develop an approach based on the edge antitriangle centrality with the i...
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes
The maintenance of the diverse cell types in a multicellular organism is one of the fundamental mysteries of biology. Modelling the dynamic regulatory relationships between the histone modifications and the gene expression across the diverse cell types is essential for the authors to understand the mechanisms of the epigenetic regulation. Here, the authors thoroughly assessed the histone modification enrichment profiles at the promoters and constructed quantitative models between the histone modification abundances and the gene expression in 12 human cell types. The author??s results showed that the histone modifications a...
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
Construction and investigation of breast-cancer-specific ceRNA network based on the mRNA and mirna expression data
It has been proved and widely acknowledged that messenger RNAs can talk to each other by competing for a limited pool of miRNAs. The competing endogenous RNAs are called as ceRNAs. Although some researchers have recently used ceRNAs to do biological function annotations, few of them have investigated the ceRNA network on specific disease systematically. In this work, using both miRNA expression data and mRNA expression data of breast cancer patient as well as the miRNA target relations, the authors proposed a computational method to construct a breast-cancer-specific ceRNA network by checking whether the shared miRNA spong...
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
Using graphical adaptive lasso approach to construct transcription factor and microRNA??s combinatorial regulatory network in breast cancer
Discovering the regulation of cancer-related gene is of great importance in cancer biology. Transcription factors and microRNAs are two kinds of crucial regulators in gene expression, and they compose a combinatorial regulatory network with their target genes. Revealing the structure of this network could improve the authors?? understanding of gene regulation, and further explore the molecular pathway in cancer. In this article, the authors propose a novel approach graphical adaptive lasso (GALASSO) to construct the regulatory network in breast cancer. GALASSO use a Gaussian graphical model with adaptive lasso penalties to...
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
Construction and analysis of microRNA-transcription factor regulation network in arabidopsis
In this study, they analysed the properties of the GRN in Arabidopsis, and discussed their biological implications, as well as their potential applications. (Source: IET Systems Biology)
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
Part 2: network construction and mining for systems biology [Editorial]
The molecular networks provide the context in which the molecules interact with each other and can therefore help us understand the functions of these molecules. Unfortunately, the current knowledge about molecular networks is far from complete. It is time consuming and expensive to screen possible interactions between distinct molecules in a lab. Furthermore, the current interactomes deposited in popular public databases are generally static snapshots of the dynamic molecular interactions that change with time. Therefore, some computational approaches have been proposed for reverse-engineering andmining the interactomes. ...
Source: IET Systems Biology - June 1, 2014 Category: Biology Source Type: research
MPGraph: multi-view penalised graph clustering for predicting drug-target interactions
Identifying drug-target interactions has been a key step for drug repositioning, drug discovery and drug design. Since it is expensive to determine the interactions experimentally, computational methods are needed for predicting interactions. In this work, the authors first propose a single-view penalised graph (SPGraph) clustering approach to integrate drug structure and protein sequence data in a structural view. The SPGraph model does clustering on drugs and targets simultaneously such that the known drug-target interactions are best preserved in the clustering results. They then apply the SPGraph to a chemical view wit...
Source: IET Systems Biology - April 1, 2014 Category: Biology Source Type: research
In silico identification of potential targets and drugs for non-small cell lung cancer
In conclusion, this study provides a systematic strategy to discover potential drugs and target genes for lung cancer. (Source: IET Systems Biology)
Source: IET Systems Biology - April 1, 2014 Category: Biology Source Type: research
