Analysis for biological network properties of Alzheimers disease associated gene set by enrichment and topological examinations

AbstractGene-set analyses measure the association between a disease of interest and a set of genes related to a biological pathway. These analyses often incorporate gene network properties to account for the differential contributions of each gene. Extending this concept further, mathematical models of biology can be leveraged to define gene interactions based on biophysical principles by predicting the effects of genetic perturbations on a particular downstream function. We present a method that combines gene weights from model predictions and gene ranks from genome-wide association studies into a weighted gene-set test. Using publicly-available summary data from the Psychiatric Genetics Consortium (n=41,653; ~9) million SNPs), we examine an a priori hypothesis that intracellular calcium ion concentrations contribute to bipolar disorder. In this case study, we are able to strengthen inferences from a P-value of 0.081 to 1.7×10−4 by moving from a general calcium signaling pathway to a specific model-predicted function.

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Faculty Opinions recommendation of Distinct biological network properties between the targets of natural products and disease genes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.4055956.3829054 ◽

2010 ◽

Author(s):

David Triggle

Keyword(s):

Natural Products ◽

Biological Network ◽

Disease Genes ◽

Network Properties

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PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Journal of Integrative Bioinformatics ◽

10.1515/jib-2016-284 ◽

2016 ◽

Vol 13 (1) ◽

pp. 1-6 ◽

Cited By ~ 1

Author(s):

Diogo Almeida ◽

Vasco Azevedo ◽

Artur Silva ◽

Jan Baumbach

Keyword(s):

Petri Nets ◽

Petri Net ◽

Biological Networks ◽

Computational Analysis ◽

Biological Network ◽

Global Network ◽

Data Sets ◽

Biological Network Analysis ◽

Network Properties ◽

Sbml Format

SummarySystems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape. Although discrete Petri nets are quite simplistic models, they are capable of modeling global network properties and simulating their behaviour. In addition, they are easily understood and well visualizable. PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization of the token flow in Cytoscape. PetriScape is the first Cytoscape plugin for Petri nets. It allows a straightforward Petri net model creation, simulation and visualization with Cytoscape, providing clues about the activity of key components in biological networks.

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