Empirical Bayes conditional independence graphs for regulatory network recovery

Mahdi, Rami N.; Madduri, Abishek Sainath; Wang, Guoqing; Strulovici-Barel, Yael; Salit, Jacqueline; Hackett, Neil R.; Crystal, Ronald G.; Mezey, Jason G.

doi:10.1093/bioinformatics/bts312

Cited by 8 publications

(6 citation statements)

References 39 publications

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“…nodes are the backbone of the network topological architecture and may improve our understanding of molecular integration. Similar results have been reported for transcriptional networks (27), protein-protein interaction networks (28), gene co-expression networks (29) and regulatory networks (30). The robustness of a hub gene network formed by various associated diseases is indicated by its highly connected components.…”

Section: Discussionsupporting

confidence: 85%

Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis

Zhao

Zhang

Gai

et al. 2016

Molecular Medicine Reports

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Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis strategy. The biomarker-target interrelated molecules associated with diabetes and its complications were identified via the Comparative Toxicogenomics Database (CTD); the Search Tool for Recurring Instances of Neighboring Genes was utilized for network construction. Functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery software to investigate connections between diabetes and its complications. A total of 142 (including 122 biomarkers, 10 therapeutic targets and 10 overlapping molecules) biomarker-target interrelated molecules associated with diabetes and its complications were identified via the CTD database, and analysis of the network yielded 1,087 biological processes and fifteen Kyoto Encyclopedia of Genes and Genomes pathways with significant P‑values. Various critical aspects of the networks were examined in the present study: a) Intermolecular horizontal and vertical combinations in biomarkers and therapeutic targets associated with diabetes and its complicationb) network topology properties associated with molecular pathological responsec) contribution of key molecules to integrated regulation; and d) crosstalk between multiple pathways. Based on a multi-dimensional analysis, it was concluded that the integrated molecular pathological development of diabetes and its complications does not proceed randomly, which suggests a requirement for integrated, multi-target intervention.

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Section: Discussionsupporting

confidence: 85%

Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis

Zhao

Zhang

Gai

et al. 2016

Molecular Medicine Reports

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“…Turnover juga telah menjadi agenda riset yang penting untuk diteliti bagi pengembangan sumber daya manusia dan pengembangan organisasional (Baek-Kyoo dan Sunyoung, 2009). Keputusan karyawan atau kemauan karyawan untuk keluar dari organisasi selalu menjadi tanda tanya besar bagi organisasi (Mahdi et al, 2012). Turnover menjadi kendala yang harus diterima oleh semua organisasi, karena saat ini sulit mencari tenaga kerja yang memiliki keterampilan serta komitmen yang tinggi terhadap organisasi (Jehanzeb, 2013).…”

Section: Pendahuluanunclassified

“…Kang et al (2012) Turnover intention diartikan sebagai keinginan seseorang untuk tetap tinggal atau pindah dari organisasinya (Lum et al, 1998) (Hanafiah, 2014). Kepuasan kerja telah berulang kali diidentifikasi sebagai alasan utama mengapa karyawan meninggalkan pekerjaan mereka (Mahdi et al, 2012). Namun banyak studi yang dilakukan di negara-negara barat secara konsisten menunjukkan pengaruh negatif dan signifikan antara kepuasan kerja dan turnover intention di kalangan karyawan (Salleh et al, 2012).…”

Section: Dua Teori Kepuasan Kerja Yang Menjadi Dasar Penelitian Adalaunclassified

Pengaruh Job Insecurity Dan Kepuasan Kerja Terhadap Turnover Intention Pada Karyawan Hotel

Januartha¹,

Adnyani²

2018

EJMUNUD

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Turnover intention will affect the performance and sustainability of the company for the future. The purpose of this research is to analyze the influence of job insecurity and job satisfaction toward turnover intention. The research was conducted at Hotel Grand Zuri Kuta, Badung regency, Bali. The number of respondents in use as many as 75 employees by using the census method. Data analysis method used is multiple linear regression analysis. Data collecting through, questionnaires and interviews. The results showed that job insecurity had positive and significant effect on turnovrer intention, and job satisfaction had negative and significant effect on turnover intention. To lower the turnover intention rate it is important to pay attention to safety and comfort in working. Therefore it is very necessary to minimize the threats of cyclical and psychological to employees because it will impact on performance and also a strong reference to minimize turnover intention. In addition to job security (job insecurity) job satisfaction is also a strong reference in mempenguruh intention turnover intention. Therefore it is very important to pay attention to job satisfaction from employees to high employee satisfaction level, thus will show the positive level of employees, both to the work and environment. Keywords: job insecurity, job satisfaction, intrntion turnover

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“…In this approach, many effective methods have been developed, for example, state space models (Beal et al, 2005;Hirose et al, 2008;Rangel et al, 2004) and Bayesian inference (Friedman et al, 2007;Mahdi et al, 2012;Watanabe et al, 2012). For restoring literaturebased GRNs, a concept, called network completion, has also been developed (Akutsu et al, 2009;Nakajima et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data

Hasegawa

Mori

Yamaguchi

et al. 2014

Journal of Computational Biology

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Gene regulatory networks (GRNs) play a central role in sustaining complex biological systems in cells. Although we can construct GRNs by integrating biological interactions that have been recorded in literature, they can include suspicious data and a lack of information. Therefore, there has been an urgent need for an approach by which the validity of constructed networks can be evaluated; simulation-based methods have been applied in which biological observational data are assimilated. However, these methods apply nonlinear models that require high computational power to evaluate even one network consisting of only several genes. Therefore, to explore candidate networks whose simulation models can better predict the data by modifying and extending literature-based GRNs, an efficient and versatile method is urgently required. We applied a combinatorial transcription model, which can represent combinatorial regulatory effects of genes, as a biological simulation model, to reproduce the dynamic behavior of gene expressions within a state space model. Under the model, we applied the unscented Kalman filter to obtain the approximate posterior probability distribution of the hidden state to efficiently estimate parameter values maximizing prediction ability for observational data by the EM-algorithm. Utilizing the method, we propose a novel algorithm to modify GRNs reported in the literature so that their simulation models become consistent with observed data. The effectiveness of our approach was validated through comparison analysis to the previous methods using synthetic networks. Finally, as an application example, a Kyoto Encyclopedia of Genes and Genomes (KEGG)-based yeast cell cycle network was extended with additional candidate genes to better predict the real mRNA expressions data using the proposed method.

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Empirical Bayes conditional independence graphs for regulatory network recovery

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 8 publications

References 39 publications

Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis

Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis

Pengaruh Job Insecurity Dan Kepuasan Kerja Terhadap Turnover Intention Pada Karyawan Hotel

An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data

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