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Clinical Oral Investigations
Published in: Clinical Oral Investigations 6/2015

01-07-2015 | Original Article

A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases

Authors: Antonio Barone, Paolo Toti, Maria Rita Giuca, Giacomo Derchi, Ugo Covani

Published in: Clinical Oral Investigations | Issue 6/2015

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Abstract

Objective

In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network.

Methods

The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of ‘leader’ genes.

Results

Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved.

Conclusions

Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database.

Clinical relevance

The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.
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Metadata
Title
A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases
Authors
Antonio Barone
Paolo Toti
Maria Rita Giuca
Giacomo Derchi
Ugo Covani
Publication date
01-07-2015
Publisher
Springer Berlin Heidelberg
Published in
Clinical Oral Investigations / Issue 6/2015
Print ISSN: 1432-6981
Electronic ISSN: 1436-3771
DOI
https://doi.org/10.1007/s00784-014-1349-4

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