Publication: Integrating omics data from phenotypically-related genodermatoses. A Cytoscape approach using biological networks
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2019-02
Defense date
2019-03-04
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Abstract
The ongoing advance of high-throughput sequencing technologies is bringing to the biomedical
research community the opportunity to disclose relatively uncharted and poorly addressed
domains in genetic disorders. Specifically, this project aims to shed new light on the molecular
mechanisms of three rare skin diseases: Recessive Dystrophic Epidermolysis Bullosa (RDEB),
Kindler Syndrome (KS) and Xeroderma pigmentosum type C (XPC). To accomplish this, biological
network construction is leveraged herein, by providing a convenient approach to integrate and
downstream analyze molecular omics data obtained from the comparison of these three
genodermatoses (RDEB, KS & XPC) against healthy control samples. Concretely, microRNAs,
RNAs and protein datasets are conjointly combined in the form of graphs whose structure and
arrangement can be analyzed. On this basis, and upon computational procedures, the
representation of high-throughput omics data across networks serves for both a topological and
functional characterization of the molecular entities embedded within the graphs. Cytoscape
software harbors the toolkits needed to exploit the massive omics information presented in this
work, closely operating with online ontologies containing crucial annotations on the molecular
entities under the network conglomerates. Cytoscape platform is going to carry out the
bioinformatics computational endeavours, conducting then to new insights where common
mechanisms and candidate biomarkers shared by the three genodermatoses will be highlighted.
In this manner, STRING, BiNGO and ClueGO (Cytoscape plug-ins) will assist in the finding of
enriched functions (such as “cell adhesions” and “epidermal growth factor signaling”), whereas
the topological analysis will rely on STRING and NetworkAnalyzer, following the principles of
graph theory to identify candidate molecules like TFAP2A and L1CAM. With the aid of manual
curations, these two approaches will stand for a narrowing-down strategy from which biological
interpretations are obtained.
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Keywords
Bioinformatics, Recessive Dystrophic Epidermolysis Bullosa, Kindler Syndrome, Xeroderma pigmentosum type C, Biological networks, Cytoscape, Network medicine