Unravelling personalized dysfunctional gene network of complex diseases based on differential network model

Abstract

In the conventional analysis of complex diseases, the control and case samples are assumed to be of great purity. However, due to the heterogeneity of disease samples, many disease genes are even not always consistently up-/down-regulated, leading to be under-estimated. This problem will seriously influence effective personalized diagnosis or treatment. The expression variance and expression covariance can address such a problem in a network manner. But, these analyses always require multiple samples rather than one sample, which is generally not available in clinical practice for each individual. To extract the common and specific network characteristics for individual patients in this paper, a novel differential network model, e.g. personalized dysfunctional gene network, is proposed to integrate those genes with different features, such as genes with the differential gene expression (DEG), genes with the differential expression variance (DEVG) and gene-pairs with the differential expression covariance (DECG) simultaneously, to construct personalized dysfunctional networks. This model uses a new statistic-like measurement on differential information, i.e., a differential score (DEVC), to reconstruct the differential expression network between groups of normal and diseased samples; and further quantitatively evaluate different feature genes in the patient-specific network for each individual. This DEVC-based differential expression network (DEVC-net) has been applied to the study of complex diseases for prostate cancer and diabetes. (1) Characterizing the global expression change between normal and diseased samples, the differential gene networks of those diseases were found to have a new bi-coloured topological structure, where their non hub-centred sub-networks are mainly composed of genes/proteins controlling various biological processes. (2) The differential expression variance/covariance rather than differential expression is new informative sources, and can be used to identify genes or gene-pairs with discriminative power, which are ignored by traditional methods. (3) More importantly, DEVC-net is effective to measure the expression state or activity of different feature genes and their network or modules in one sample for an individual. All of these results support that DEVC-net indeed has a clear advantage to effectively extract discriminatively interpretable features of gene/protein network of one sample (i.e. personalized dysfunctional network) even when disease samples are heterogeneous, and thus can provide new features like gene-pairs, in addition to the conventional individual genes, to the analysis of the personalized diagnosis and prognosis, and a better understanding on the underlying biological mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-015-0546-5) contains supplementary material, which is available to authorized users.

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Clinical trans-omics: an integration of clinical phenomes with molecular multiomics

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