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Gene network inference

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https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#1
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28712341/genetic-analysis-of-bactrocera-zonata-diptera-tephritidae-populations-from-india-based-on-cox1-and-nad1-gene-sequences
#2
Jaipal S Choudhary, Naiyar Naaz, Moanaro Lemtur, Bikash Das, Arun Kumar Singh, Bhagwati P Bhatt, Chandra S Prabhakar
The peach fruit fly, Bactrocera zonata, is among the most serious and polyphagous insect pest of fruit crops in many parts of the world under genus Bactrocera. In the present study, the genetic structure, diversity and demographic history of B. zonata in India were inferred from mitochondrial cytochrome oxidase 1 (cox1) and NADH dehydrogenase 1 (nad1) sequences. The efficiency of DNA barcodes for identification of B. zonata was also tested. Genetic diversity indices [number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π) and average number of nucleotide differences (k)] of B...
July 15, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28705469/systematic-prioritization-of-functional-hotspot-in-rig-1-domains-using-pattern-based-conventional-molecular-dynamic-simulation
#3
P Raghuraman, R Jesu Jaya Sudan, J Lesitha Jeeva Kumari, C Sudandiradoss
BACKGROUND: Retinoic acid inducible gene 1 (RIG-1), multi-domain protein has a role-play in detecting viral nucleic acids and stimulates the antiviral response. Dysfunction of this protein due to mutations makes the route vulnerable to viral diseases. AIM: Identification of functional hotspots that maintains conformational stability in RIG-1 domains. METHODS: In this study, we employed a systematic in silico strategy on RIG-1 protein to understand the mechanism of structural changes upon mutation...
July 10, 2017: Life Sciences
https://www.readbyqxmd.com/read/28700035/excavation-of-attractor-modules-for-nasopharyngeal-carcinoma-via-integrating-systemic-module-inference-with-attract-method
#4
T Jiang, C-Y Jiang, J-H Shu, Y-J Xu
The molecular mechanism of nasopharyngeal carcinoma (NPC) is poorly understood and effective therapeutic approaches are needed. This research aimed to excavate the attractor modules involved in the progression of NPC and provide further understanding of the underlying mechanism of NPC. Based on the gene expression data of NPC, two specific protein-protein interaction networks for NPC and control conditions were re-weighted using Pearson correlation coefficient. Then, a systematic tracking of candidate modules was conducted on the re-weighted networks via cliques algorithm, and a total of 19 and 38 modules were separately identified from NPC and control networks, respectively...
July 10, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28697314/grainyhead-like-transcription-factors-in-craniofacial-development
#5
M R Carpinelli, M E de Vries, S M Jane, S Dworkin
Craniofacial development in vertebrates involves the coordinated growth, migration, and fusion of several facial prominences during embryogenesis, processes governed by strict genetic and molecular controls. A failure in any of the precise spatiotemporal sequences of events leading to prominence fusion often leads to anomalous facial, skull, and jaw formation-conditions termed craniofacial defects (CFDs). Affecting approximately 0.1% to 0.3% of live births, CFDs are a highly heterogeneous class of developmental anomalies, which are often underpinned by genetic mutations...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28691107/network-based-approaches-that-exploit-inferred-transcription-factor-activity-to-analyze-the-impact-of-genetic-variation-on-gene-expression
#6
Harmen J Bussemaker, Helen C Causton, Mina Fazlollahi, Eunjee Lee, Ivor Muroff
Over the past decade, a number of methods have emerged for inferring protein-level transcription factor activities in individual samples based on prior information about the structure of the gene regulatory network. We discuss how this has enabled new methods for dissecting trans-acting mechanisms that underpin genetic variation in gene expression.
April 2017: Current opinion in systems biology
https://www.readbyqxmd.com/read/28684624/cell-interactions-signals-and-transcriptional-hierarchy-governing-placode-progenitor-induction
#7
Mark Hintze, Ravindra Singh Prajapati, Monica Tambalo, Nicolas A D Christophorou, Maryam Anwar, Timothy Grocott, Andrea Streit
In vertebrates, cranial placodes contribute to all sense organs and sensory ganglia and arsise from a common pool of Six1/Eya2+ progenitors. Here we dissect the events that specify ectodermal cells as placode progenitors using newly identified genes upstream of the Six/Eya complex. We show that two different tissues, the lateral head mesoderm and the prechordal mesendoderm, gradually induce placode progenitors: cells pass through successive transcriptional states, each identified by distinct factors and controlled by different signals...
July 6, 2017: Development
https://www.readbyqxmd.com/read/28676075/sgnesr-an-r-package-for-simulating-gene-expression-data-from-an-underlying-real-gene-network-structure-considering-delay-parameters
#8
Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
BACKGROUND: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles...
July 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28674972/genetic-variation-and-phylogenetic-relationships-of-the-ectomycorrhizal-floccularia-luteovirens-on-the-qinghai-tibet-plateau
#9
Rui Xing, Qing-Bo Gao, Fa-Qi Zhang, Peng-Cheng Fu, Jiu-Li Wang, Hui-Ying Yan, Shi-Long Chen
Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations...
July 4, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28659815/multi-level-integration-of-environmentally-perturbed-internal-phenotypes-reveals-key-points-of-connectivity-between-them
#10
Nirupama Benis, Soumya K Kar, Vitor A P Martins Dos Santos, Mari A Smits, Dirkjan Schokker, Maria Suarez-Diez
The genotype and external phenotype of organisms are linked by so-called internal phenotypes which are influenced by environmental conditions. In this study, we used five existing -omics datasets representing five different layers of internal phenotypes, which were simultaneously measured in dietarily perturbed mice. We performed 10 pair-wise correlation analyses verified with a null model built from randomized data. Subsequently, the inferred networks were merged and literature mined for co-occurrences of identified linked nodes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28659000/recurrent-neural-network-based-modeling-of-gene-regulatory-network-using-elephant-swarm-water-search-algorithm
#11
Sudip Mandal, Goutam Saha, Rajat Kumar Pal
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN)...
June 13, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28649444/reverse-engineering-highlights-potential-principles-of-large-gene-regulatory-network-design-and-learning
#12
Clément Carré, André Mas, Gabriel Krouk
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#13
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#14
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E M Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#15
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#16
Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A Lussier, Maria Gabriella Cusella De Angelis, Riccardo Bellazzi
The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties...
June 21, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28634987/dietary-tio2-particles-modulate-expression-of-hormone-related-genes-in-bombyx-mori
#17
Guofang Shi, Pengfei Zhan, Weiming Jin, JianMing Fei, Lihua Zhao
Silkworm (Bombyx mori) is an economically beneficial insect. Its growth and development are regulated by endogenous hormones. In the present study, we found that feeding titanium dioxide nanoparticles (TiO2 NP) caused a significant increase of body size. TiO2 NP stimulated the transcription of several genes, including the insulin-related hormone bombyxin, PI3K/Akt/TOR (where PI3K is phosphatidylinositol 3-kinase and TOR is target of rapamycin), and the adenosine 5'-monophosphateactivated protein kinase (AMPK)/target of rapamycin (TOR) pathways...
August 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/28629365/evaluation-and-improvement-of-the-regulatory-inference-for-large-co-expression-networks-with-limited-sample-size
#18
Wenbin Guo, Cristiane P G Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W S Brown, Runxuan Zhang
BACKGROUND: Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a few hundred nodes. For large networks, simulated expression data usually consist of hundreds or thousands of profiles with different perturbations or knock-outs, which is uncommon in real experiments due to their cost and the amount of work required...
June 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28623595/inferring-gene-regulatory-networks-in-the-arabidopsis-root-using-a-dynamic-bayesian-network-approach
#19
Maria Angels de Luis Balaguer, Rosangela Sozzani
Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623592/computational-approaches-to-study-gene-regulatory-networks
#20
Nooshin Omranian, Zoran Nikoloski
The goal of the gene regulatory network (GRN) inference is to determine the interactions between genes given heterogeneous data capturing spatiotemporal gene expression. Since transcription underlines all cellular processes, the inference of GRN is the first step in deciphering the determinants of the dynamics of biological systems. Here, we first describe the generic steps of the inference approaches that rely on similarity measures and group the similarity measures based on the computational methodology used...
2017: Methods in Molecular Biology
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