Specialty Molecular Biomedicine Mechanisms of Disease, Molecular and Cellular Therapies, and Bioinnovation
Library of the School of Health Sciences

2020-06-15

2020

Koutrouli Mikaela

Γεώργιος Παυλόπουλος, Ερευνητής Β', Ερευνητικό Κέντρο Βιοϊατρικών Επιστημών "Αλέξανδρος Φλέμινγκ", Επιβλέπων
Γεώργιος Κόλλιας, Καθηγητής, Ιατρική Σχολή, ΕΚΠΑ
Χριστόφορος Νικολάου, Ερευνητής Β', Ερευνητικό Κέντρο Βιοϊατρικών Επιστημών "Αλέξανδρος Φλέμινγκ"

Bioinformatics approaches for the analysis and visualization of biological networks

English

Bioinformatics approaches for the analysis and visualization of biological networks

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this dissertation thesis, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several global network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns and models and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. In addition, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing and clustering as well as the current state-of-the-art tools. Furthermore, we provide demonstration examples for the STRING and Reactome databases and we highlight their features and functionality, discuss their front- and back-end interfaces and show a simple case study of how these tools can be combined for deeper biological analysis and functional enrichment. Finally, we propose NORMA and NAP, two web tools for interactive handling of multiple networks. Specifically, NORMA focuses on interactive network annotation visualization and topological analysis and it is able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g. Gene Ontology/Pathway enrichment or clustering results) can be uploaded and visualized in a network either as colored pie-chart nodes or as color-filled convex hulls in a Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Briefly, with NORMA, users can encode three types of information simultaneously. These are: i) the network, ii) the communities or annotations and iii) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at: http://bib.fleming.gr:3838/NORMA. Code is available at: https://github.com/PavlopoulosLab/NORMA. On the other hand, NAP directly compares the topological features of multiple networks simultaneously and currently offers both 2D and 3D network visualization as well as visual comparisons of node- and edge-based topological features both as bar charts or as a scatterplot matrix. NAP is fully interactive and users can easily export and visualize the intersection between any pair of networks using Venn diagrams or a 2D and a 3D multi-layer graph-based visualization. NAP supports weighted, unweighted, directed, undirected and bipartite graphs and is available at: http://bib.fleming.gr:3838/NAP/. Its code can be found at: https://github.com/PavlopoulosLab/NAP.

Health Sciences

Network annotation, Visualization, Topological analysis, Community detection, Functional enrichment visualization, Biological networks, Topology, Graph theory, Clustering

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File access is restricted only to the intranet of UoA.

https://pergamos.lib.uoa.gr/uoa/dl/object/2916451