Network Coherence Calculator

Calculates the network coherence of differentially expressed genes within a network.
### Introduction *Network Coherence Calculator* is an app designed to calculate the network coherence of a set of differentially expressed genes within a biological network. As of version 2.0, the app is also able to accept a file containing expression data for multiple samples as an alternative to a list of genes. The app then offers a rudimentary functionality of computing sample-level gene sets with high expression levels and returns a network coherence for each such set. Network Coherence Calculator is able to use any network loaded into Cytoscape as the biological reference network, provided the nodes and gene sets follow a common naming scheme. ### Use of The Concept **Network coherence computations have been used in the following publications:** Sonnenschein, N., Geertz, M., Muskhelishvili, G., & Hütt, M. T. (2011). Analog regulation of metabolic demand. BMC Systems Biology, 5(1), 1-13. Knecht, C., Fretter, C., Rosenstiel, P., Krawczak, M., & Hütt, M. T. (2016). Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls. Scientific Reports, 6(1), 1-11. Schlicht, K., Nyczka, P., Caliebe, A., Freitag-Wolf, S., Claringbould, A., Franke, L., ... & Krawczak, M. (2019). The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus. Human Genetics, 138(4), 375-388. Kosmidis, K., Jablonski, K. P., Muskhelishvili, G., & Hütt, M. T. (2020). Chromosomal origin of replication coordinates logically distinct types of bacterial genetic regulation. NPJ Systems Biology and Applications, 6(1), 1-9. Perrin-Cocon, L., Vidalain, P. O., Jacquemin, C., Aublin-Gex, A., Olmstead, K., Panthu, B., ... & Diaz, O. (2021). A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity. Communications Biology, 4(1), 1-15. **Some theoretical work around network coherences is found in:** Nyczka, P., & Hütt, M. T. (2020). Generative network model of transcriptome patterns in disease cohorts with tunable signal strength. Physical Review Research, 2(3), 033130. Nyczka, P., Hütt, M. T., & Lesne, A. (2021). Inferring pattern generators on networks. Physica A: Statistical Mechanics and its Applications, 566, 125631.

2.1

Works with Cytoscape 3.0

Release Notes

Added a progress bar to show the user how far along the calculation is. Large restructuring of the code to allow the calculation to take place outside of the GUI thread.

2.0

Works with Cytoscape 3.0

Release Notes

Added an additional input method that allows the user to select a file containing gene expression data for several samples. The file is then used to calculate the highly expressed genes for each sample. The network coherence is computed for each sample individually.

1.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 2.1

Released 23 May 2022

Works with Cytoscape 3.0

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