Graphlet laplacians for topology-function and topology-disease relationships
Visualitza/Obre
10.1093/bioinformatics/btz455
Inclou dades d'ús des de 2022
Cita com:
hdl:2117/327319
Tipus de documentArticle
Data publicació2019-12-15
EditorOxford University Press (OUP)
Condicions d'accésAccés obert
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Abstract
Motivation
Laplacian matrices capture the global structure of networks and are widely used to study biological networks. However, the local structure of the network around a node can also capture biological information. Local wiring patterns are typically quantified by counting how often a node touches different graphlets (small, connected, induced sub-graphs). Currently available graphlet-based methods do not consider whether nodes are in the same network neighbourhood. To combine graphlet-based topological information and membership of nodes to the same network neighbourhood, we generalize the Laplacian to the Graphlet Laplacian, by considering a pair of nodes to be ‘adjacent’ if they simultaneously touch a given graphlet.
Results
We utilize Graphlet Laplacians to generalize spectral embedding, spectral clustering and network diffusion. Applying Graphlet Laplacian-based spectral embedding, we visually demonstrate that Graphlet Laplacians capture biological functions. This result is quantified by applying Graphlet Laplacian-based spectral clustering, which uncovers clusters enriched in biological functions dependent on the underlying graphlet. We explain the complementarity of biological functions captured by different Graphlet Laplacians by showing that they capture different local topologies. Finally, diffusing pan-cancer gene mutation scores based on different Graphlet Laplacians, we find complementary sets of cancer-related genes. Hence, we demonstrate that Graphlet Laplacians capture topology-function and topology-disease relationships in biological networks.
CitacióWindels, S.F.L.; Malod Dognin, N.; Pržulj, N. Graphlet laplacians for topology-function and topology-disease relationships. "Bioinformatics", 15 Desembre 2019, vol. 35, núm. 24, p. 5226-5234.
ISSN1367-4803
1460-2059
1460-2059
Col·leccions
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main_revision_submitted.pdf | 2,281Mb | Visualitza/Obre |