doing centralized and coherent activities between governmental agencies is essential at any level. creating suitable institutional structure for appropriate solutions of policy problem in natural resources at multiple levels is possible using application of network governance. the aim of this paper is institutional network analysis with co-management of zagros dry forests in regional (county) l...

Abstract Background Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description each the network modules is therefore a critical step understand underlying processes contributing disease or phenotype. Biological integration, topology study and ...

Digital transcriptome analysis by next-generation sequencing discovers substantial mRNA variants. Variation in gene expression underlies many biological processes and holds a key to unravelling mechanism of common diseases. However, the current methods for construction of co-expression networks using overall gene expression are originally designed for microarray expression data, and they overlo...

The inference of network topologies from relational data is an important problem in data analysis. Exemplary applications include the reconstruction of social ties from data on human interactions, the inference of gene co-expression networks from DNA microarray data, or the learning of semantic relationships based on co-occurrences of words in documents. Solving these problems requires techniqu...

We modify the Google Page-Rank algorithm, which is primarily used for ranking web pages, to analyze the gene reachability in complex gene co-expression networks. Our modification is based on the average connections per gene. We propose a new method to compute the metric of average connections per gene, inspired by the PageRank algorithm. We calculate this average as eight for human genome data ...

The present study performed an integral analysis of the gene expression and DNA methylation profile of pilocytic astrocytomas (PAs). Weighted gene co-expression network analysis (WGCNA) was also performed to examine and identify the genes correlated to PAs, to identify candidate therapeutic targets for the treatment of PAs. The DNA methylation profile and gene expression profile were downloaded...

MOTIVATION The noisy nature of transcriptomic data hinders the biological relevance of conventional network centrality measures, often used to select gene candidates in co-expression networks. Therefore, new tools and methods are required to improve the prediction of mechanistically important transcriptional targets. RESULTS We propose an original network centrality measure, called annotation...

Recently, rapid advances in bioinformatics analysis have expanded our understanding of the transcriptome to a genome-wide level. miRNA-mRNA-lncRNA interactions have been shown to play critical regulatory role in cancer biology. In this study, we discussed the use of an integrated systematic approach to explore new facets of the oestrogen receptor (ER)-regulated transcriptome. The identification...

Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of ti...