Connectivity can be used to identify key genes in DNA microarray data: a study based on gene expression in nasal polyps before and after treatment with glucocorticoids

Abstract

In all, 166 genes were differentially expressed; 39 of these were previously defined as inflammatory and considered important for nasal polyposis. The connectivity of all differentially expressed genes was analysed using the PubGene literature co-citation network. Seventy-four of the 166 genes were connected to other genes. By contrast, the average number of connected genes among 100 sets of 166 randomly chosen genes was 31.5. A small number of the differentially expressed genes were highly connected, while most genes had few or no connections. This indicated a scale-free network. The most connected gene was interleukin-8, an inflammatory gene of known importance for nasal polyposis. Twenty-eight of the 74 connected genes were inflammatory (38%), compared with 11 of the 92 unconnected genes (12%), p < 0.0001. Since most evidence suggests that nasal polyps are inflammatory in their nature, this supports the hypothesis that connected genes have more disease relevance than unconnected genes.

Microsatellite DNA instability in nasal polyposis

“…The genetic background of nasal polyposis has been the focus of many recent studies 4–17. Nevertheless, the role of acquired somatic mutations in the pathogenesis of nasal polyposis has not received much attention.…”

Genes regulating molecular and cellular functions in noninfectious nonallergic rhinitis

“…This kind of investigation usually results in a set of differently expressed genes and the question arises how to identify which of these genes that might have key functions in the disease. One approach to this problem is to treat differentially expressed genes as nodes in a network (9–11). Interacting nodes are connected by their function to describe the architecture of the network.…”

Xanthorrhizol attenuates dextran sulfate sodium-induced colitis via the modulation of the expression of inflammatory genes in mice

“…The gene symbol 'Tgn' was represented as Tg in the PubGene tool. possible reason for this discrepancy is that some pivotal genes or protein like MPO are more likely to be studied, and therefore more co-cited (Benson et al, 2007). However, the exact reason for this discrepancy in the effect of XA on the MPO regulation in terms of gene, protein expressions and its functionality remains to be determined.…”

“…Since biological effects are often the result of multiple interacting genes, proteins and other molecules rather than single one, the identification of which genes, proteins and molecules are interconnected may be helpful to interpret the data (Benson et al, 2007). Therefore, we have further explored the possible biological relationships between XA-responsive genes and colonic inflammation using the PubGene co-citation literature network.…”