Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Authors: Chen, Haifen; Maduranga, D. A. K.; Mundra, Piyushkumar A.; Zheng, Jie
Abstract
Accurately reconstructing gene regulatory networks (GRNs) from high-throughput gene expression data has been a major challenge in systems biology for decades. Many approaches have been proposed to solve this problem. However, there is still much room for the improvement of GRN inference. Integrating data from different sources is a promising strategy. Epigenetic modifications have a close relationship with gene regulation. Hence, epigenetic data such as histone modification profiles can provide useful information for uncovering regulatory interactions between genes. In this paper, we propose a method to integrate epigenetic data into the inference of GRNs. In particular, a dynamic Bayesian network (DBN) is employed to infer gene regulations from time-series gene expression data. Epigenetic data (histone modification profiles here) are integrated into the prior probability distribution of the Bayesian model. Our method has been validated on both synthetic and real datasets. Experimental results show that the integration of epigenetic data can significantly improve the performance of GRN inference. As more epigenetic datasets become available, our method would be useful for elucidating the gene regulatory mechanisms driving various cellular activities. The source code and testing datasets are available at https://github.com/Zheng-Lab/MetaGRN/tree/master/histonePrior.
Variability of clinical syndromes and cerebral glucose metabolism in symptomatic frontotemporal lobar degeneration associated with progranulin mutations
AMYOTROPHIC LATERAL SCLEROSIS AND FRONTOTEMPORAL DEGENERATION
Authors: Licata, Abigail; Grimmer, Timo; Winkelmann, Juliane; Wagner, Matias; Goldhardt, Oliver; Riedl, Lina; Rossmeier, Carola; Yakushev, Igor; Diehl-Schmid, Janine
Abstract
Objective: The aims of our study were to describe the clinical phenotype and to characterize the cerebral glucose metabolism patterns as measured with fluordesoxyglucose-positron emission tomography (FDG-PET) in symptomatic FTLD-patients with differentGRNvariants.Methods: For this study, data were included from all patients (n = 10) of a single-center FTLD registry study who had a pathogenic GRN variant and who had undergone a cerebral FDG-PET scan.Results: An overt variability of clinical phenotypes was identified with half of the cases being not unambiguously classifiable into one of the clinical FTLD subtypes. Furthermore, GRN + patients showed a considerable inter-individual variability of FDG uptake pattern. In half of the GRN + patients, metabolic changes expanded from frontal and temporal brain regions to parietal brain regions including the posterior cingulate cortex. Striking asymmetry without a preference for either hemisphere was overt in half of GRN + cases.Conclusion: We conclude that GRN mutations cause variable patterns of neurodegeneration that often exceed the anatomical boundaries of the frontotemporal brain regions and produce clinical syndromes that cannot clearly be classified into one of the subtypes as defined by the diagnostic criteria.