Windels, SFL;
Malod-Dognin, N;
Przulj, N;
(2019)
Graphlet Laplacians for topology-function and topology-disease relationships.
Bioinformatics
, 35
(24)
pp. 5226-5234.
10.1093/bioinformatics/btz455.
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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. Availability and implementation: http://www0.cs.ucl.ac.uk/staff/natasa/graphlet-laplacian/index.html
| Type: | Article |
|---|---|
| Title: | Graphlet Laplacians for topology-function and topology-disease relationships |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/bioinformatics/btz455 |
| Publisher version: | http://dx.doi.org/10.1093/bioinformatics/btz455 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10097890 |
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