A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

Tuikkala, Johannes; Vähämaa, Heidi; Salmela, Pekka; Nevalainen, Olli; Aittokallio, Tero

doi:10.1186/1756-0381-5-2

Cited by 11 publications

(6 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The betweeness centrality measures the number of shortest paths going through the node. Since metabolic networks are directed, we use relative-betweeness centrality for a metabolite importance measure (Tuikkala et al 2012 ). The degree centrality measures focus more on local connectivities, while the betweeness centrality measures focus more on global network topology.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive metabolome analyses reveal N-acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin

et al. 2015

View full text Add to dashboard Cite

Systemic lupus erythematosus (SLE) patients exhibit depletion of the intracellular antioxidant glutathione and downstream activation of the metabolic sensor, mechanistic target of rapamycin (mTOR). Since reversal of glutathione depletion by the amino acid precursor, N-acetylcysteine (NAC), is therapeutic in SLE, its mechanism of impact on the metabolome was examined within the context of a double-blind placebo-controlled trial. Quantitative metabolome profiling of peripheral blood lymphocytes (PBL) was performed in 36 SLE patients and 42 healthy controls matched for age, gender, and ethnicity of patients using mass spectrometry that covers all major metabolic pathways. mTOR activity was assessed by western blot and flow cytometry. Metabolome changes in lupus PBL affected 27 of 80 KEGG pathways at FDR p < 0.05 with most prominent impact on the pentose phosphate pathway (PPP). While cysteine was depleted, cystine, kynurenine, cytosine, and dCTP were the most increased metabolites. Area under the receiver operating characteristic curve (AUC) logistic regression approach identified kynurenine (AUC = 0.859), dCTP (AUC = 0.762), and methionine sulfoxide (AUC = 0.708), as top predictors of SLE. Kynurenine was the top predictor of NAC effect in SLE (AUC = 0.851). NAC treatment significantly reduced kynurenine levels relative to placebo in vivo (raw p = 2.8 × 10−7, FDR corrected p = 6.6 × 10−5). Kynurenine stimulated mTOR activity in healthy control PBL in vitro. Metabolome changes in lupus PBL reveal a dominant impact on the PPP that reflect greater demand for nucleotides and oxidative stress. The PPP-connected and NAC-responsive accumulation of kynurenine and its stimulation of mTOR are identified as novel metabolic checkpoints in lupus pathogenesis.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-015-0772-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Comprehensive metabolome analyses reveal N-acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Kerpedjiev et al 184 developed a tool called forna to display the secondary structure of RNA. In addition, Bang et al 185 and Tuikkala et al 186 proposed multilevel force-directed algorithms to visualise large protein networks and genetic interactions.…”

Section: Applications Of Force-directed Algorithmsmentioning

confidence: 99%

Force-directed algorithms for schematic drawings and placement: A survey

Cheong

2019

Information Visualization

View full text Add to dashboard Cite

Force-directed algorithms have been developed over the last 50 years and used in many application fields, including information visualisation, biological network visualisation, sensor networks, routing algorithms, scheduling, and graph drawing. Our survey provides a comprehensive summary of developments and a full roadmap for state-of-the-art force-directed algorithms in schematic drawings and placement. We classified the model of force-directed algorithms into classical and hybrid. The classical force-directed algorithms are further classified as follows: (a) accumulated force models, (b) energy function minimisation models and (c) combinatorial optimisation models. The hybrid force-directed algorithms are classified as follows: (a) parallel and hardware accelerated models, (b) multilevel force-directed models and (c) multidimensional scaling force-directed algorithms. Five categories of application domains in which force-directed algorithms have been adopted for schematic drawings and placement are also summarised: (a) aesthetic drawings for general networks, (b) component placement and scheduling in high-level synthesis of very-large-scale integration circuits design, (c) information visualisation, (d) biological network visualisation and (e) node placement and localisation for sensor networks.

show abstract

“…The first, yFiles organic , is a “force-directed” graph (Tuikkala et al 2012) that is optimized based on the principle that nodes are mutually repulsive, while ties constitute attractive forces. On force-directed optimized graphs, repulsive and attractive forces are balanced so that interconnected nodes become positioned close to each other.…”

Section: Social Network Analysismentioning

confidence: 99%

Mapping collaborative relations among Canada's chronic disease prevention organizations

Contandriopoulos

Hanusaik

Maximova

et al. 2015

European Journal of Public Health

View full text Add to dashboard Cite

In the field of chronic disease prevention (CDP), collaborations between organizations provide a vital framework for intersectoral engagement and exchanges of knowledge, expertise and resources. However, little is known about how the structures of preventive health systems actually articulate with CDP capacity and outcomes. Drawing upon data from the Public Health Organizational Capacity Study -a repeat census of all public health organizations in Canada -we used social network analysis to map and examine interorganizational collaborative relationships in the Canadian preventive health system. The network of relationships obtained through our study shows that provincial boundaries remain a major factor influencing collaborative patterns. Not only are collaborations scarce on the interprovincial level but they are also mostly limited to links with federal and multi-provincial organizations. Given this finding, federal or multi-provincial organizations that occupy central bridging positions in the Canadian CDP collaborative structure should serve as key players for shaping CDP practices in the country. RésuméDans le domaine de la prévention des maladies chroniques (PMC), la collaboration interorganisationnelle est un processus fondamental pour l' action intersectorielle ainsi que pour l'échange de connaissances, d' expertise et de ressources. Cependant, peu de connaissances existent sur les liens entre la structure de ces réseaux de collaboration et la capacité d' action ainsi qu' avec les résultats de la PMC. En nous appuyant sur des données tirées du Public Health Organizational Capacity Study -un recensement de tous les organismes canadiens de santé publique -nous avons utilisé des méthodes dérivées de l' analyse des réseaux sociaux pour cartographier et examiner les relations de collaboration interorganisationnelle dans le domaine de la PMC. Les résultats de notre étude montrent que les frontières provinciales demeurent un facteur d'influence important sur les schémas de collaboration. Non seulement les relations sont-elles rares au niveau interprovincial, mais elles se limitent presque exclusivement à des liens entre les organisations fédérales et multiprovinciales. À la lumière de ces résultats, les organisations fédérales et multiprovinciales qui occupent une position centrale dans la structure canadienne de collaboration pour la PMC devraient agir comme joueurs clés dans l'élaboration des pratiques de PMC au pays.

show abstract

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

Cited by 11 publications

References 65 publications

Comprehensive metabolome analyses reveal N-acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin

Comprehensive metabolome analyses reveal N-acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin

Force-directed algorithms for schematic drawings and placement: A survey

Mapping collaborative relations among Canada's chronic disease prevention organizations

Contact Info

Product

Resources

About