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Background Gene co-expression network analysis (GCNA) is widely adopted in bioinformatics and biomedical research with applications such as gene function prediction, protein-protein interaction inference, disease markers identification, and copy number variance discovery. Currently there is a lack of rigorous analysis on the mathematical condition for which the co-expressed gene module should satisfy.MethodsIn this paper, we present a linear algebraic based Centralized Concordance Index (CCI) for evaluating the concordance of co-expressed gene modules from gene co-expression network analysis. The CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. We applied CCI in detecting lung tumor specific gene modules.Results and DiscussionSimulation showed that CCI is a robust indicator for evaluating the concordance of a group of co-expressed genes. The application to lung cancer datasets revealed interesting potential tumor specific genetic alterations including CNVs and even hints for gene-fusion. Deeper analysis required for understanding the molecular mechanisms of all such condition specific co-expression relationships.ConclusionThe CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. It is shown to be more robust to outliers and interfering modules than density based on Pearson correlation coefficients.

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During the past few years, a variety of composite materials have been made by introducing a second crystalline phase into the liquid BMG [4,5] or by in situ formation of a crystalline phase during partial crystallization [6−10]. The underlying goal of enhancing the plasticity of BMG composites is to prevent a single shear band from traversing through the sample. Among the existing different types of bulk metallic glass composites, ductile metal reinforced composites, prepared via an in situ processing method, i.e., by precipitation of ductile micrometer-sized particles upon cooling from the melt, seem to be most promising [11]. Such composites were first developed by Johnson's group. Composites with the composition of Zr 56.2 Ti 13.8 Nb 5.0 Cu 6.9 Ni 5.6 Be 12.5 exhibited a total compression strain of above 8% to fracture at room temperature, which were synthesized via water-cooled copper plate and vacuum die technology, and consist of dendritic bcc b-Zr (Ti, Nb) and BMG matrix [7−9]. Beginning with the work of Hays et al., various glassy (or nanocrystalline) matrix composites, whose plasticity was enhanced by in situ formed ductile dendritics, have currently been developed in several BMG forming systems [12,13].In this paper, we report a Zr 56.2 Ti 13.8 Nb 5.0 Cu 6.9 Ni 5.6 Be 12.5 BMG composite prepared by water quenching. Microstructural features were observed and uniaxial compression tests were carried out at room temperature. All of the examination results are to be compared with those reported elsewhere [7−9]. Experimental procedureMulticomponent master alloy ingots with a nominal composition of Zr 56.2 Ti 13.8 Nb 5.0 Cu 6.9 Ni 5.6 Be 12.5 (at.%) [7−9] were prepared by arc melting a mixture of pure metal chips of Zr (99.95%), Ti (99.95%), Nb (99.95%), Cu (99.99%), Ni (99.95%), and Be (98.5%) (wt.%) under a Ti-gettered argon atmosphere on a water-cooled copper crucible. After Abstract A Zr 56.2 Ti 13.8 Nb 5.0 Cu 6.9 Ni 5.6 Be 12.5 bulk metallic glass composite with enhanced plasticity by in situ formed bcc b-Zr solid solution was prepared by water quenching. The ductile b phase with a volume fraction of about 30% possesses a developed dendritic morphology. The composite exhibits a pure plastic strain of 10.2% combined with a large elastic strain limit of 2% and a high ultimate strength of 1778 MPa upon room-temperature compression. Microscopic observation shows numbers of wave-like shear bands distributed on the surface of the compressive samples.

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