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Gene network inference

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https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#1
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/28629365/evaluation-and-improvement-of-the-regulatory-inference-for-large-co-expression-networks-with-limited-sample-size
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28623589/aranet-a-network-biology-server-for-arabidopsis-thaliana-and-other-non-model-plant-species
#5
Tak Lee, Insuk Lee
Functional gene networks link genes based on their functional relatedness, which is inferred from various complementary biological datasets. Gene networks comprising vast amounts of data can be used to predict which genes are associated with complex traits. Decades of studies in plant biology using the model organism Arabidopsis thaliana have generated large amounts of information, enabling the development of a system-level molecular network. AraNet (currently version 2) is a genome-scale functional gene network for Arabidopsis thaliana, constructed by integrating 19 types of genomics data and can be explored through a web-server (http://www...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623316/revealing-protein-networks-and-gene-drug-connectivity-in-cancer-from-direct-information
#6
Xian-Li Jiang, Emmanuel Martinez-Ledesma, Faruck Morcos
The connection between genetic variation and drug response has long been explored to facilitate the optimization and personalization of cancer therapy. Crucial to the identification of drug response related genetic features is the ability to separate indirect correlations from direct correlations across abundant datasets with large number of variables. Here we analyzed proteomic and pharmacogenomic data in cancer tissues and cell lines using a global statistical model connecting protein pairs, genes and anti-cancer drugs...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620222/nitric-oxide-mediated-transcriptional-modulation-enhances-plant-adaptive-responses-to-arsenic-stress
#7
Pradyumna Kumar Singh, Yuvraj Indoliya, Abhisekh Singh Chauhan, Surendra Pratap Singh, Amit Pal Singh, Sanjay Dwivedi, Rudra Deo Tripathi, Debasis Chakrabarty
Arsenic (As) contamination in rice leads to yield decline and causes carcinogenic risk to human health. Although the role of nitric oxide (NO) in reducing As toxicity is known, NO-mediated genetic modulation in the plant during arsenic toxicity has not yet been established. We analyzed the key components of NO metabolism and the correlations between NO interaction and arsenic stress using rice as a relevant model plant. Illumina sequencing was used to investigate the NO-mediated genome-wide temporal transcriptomic modulation in rice root upon AsIII exposure during 12 days (d) of the growth period...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28617955/expression-atlas-and-comparative-coexpression-network-analyses-reveal-important-genes-involved-in-the-formation-of-lignified-cell-wall-in-brachypodium-distachyon
#8
Richard Sibout, Sebastian Proost, Bjoern Oest Hansen, Neha Vaid, Federico M Giorgi, Severine Ho-Yue-Kuang, Frédéric Legée, Laurent Cézart, Oumaya Bouchabké-Coussa, Camille Soulhat, Nicholas Provart, Asher Pasha, Philippe Le Bris, David Roujol, Herman Hofte, Elisabeth Jamet, Catherine Lapierre, Staffan Persson, Marek Mutwil
While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function...
June 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/28617232/tigeri-modeling-and-visualizing-the-responses-to-perturbation-of-a-transcription-factor-network
#9
Namshik Han, Harry A Noyes, Andy Brass
BACKGROUND: Transcription factor (TF) networks play a key role in controlling the transfer of genetic information from gene to mRNA. Much progress has been made on understanding and reverse-engineering TF network topologies using a range of experimental and theoretical methodologies. Less work has focused on using these models to examine how TF networks respond to changes in the cellular environment. METHODS: In this paper, we have developed a simple, pragmatic methodology, TIGERi (Transcription-factor-activity Illustrator for Global Explanation of Regulatory interaction), to model the response of an inferred TF network to changes in cellular environment...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28603022/variation-analysis-of-norovirus-among-children-with-diarrhea-in-rural-hebei-province-north-of-china
#10
Niu Qiao, Song-Mei Wang, Jin-Xia Wang, Bin Kang, Shan-Shan Zhen, Xin-Jiang Zhang, Zhi-Yong Hao, Jing-Chen Ma, Chao Qiu, Yu-Liang Zhao, Lei Liu, Xuan-Yi Wang
To understand the distribution of genotyping, as well as evolution of norovirus circulating among children<5yrs., a population-based diarrhea surveillance targeted children<5yrs. was conducted in rural Zhengding County, Hebei Province, China between October 2011 and March 2012. RT-PCR was used to amplify the capsid-encoding region of GI and GII norovirus to identify norovirus infection. All PCR products were sequenced and analyzed for genotyping and constructing phylogenetic tree. Dynamic distribution network was constructed by TempNet to illustrate the genetic relationships at two different time points...
June 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28602808/in-silico-cardiac-aging-regulatory-model-including-microrna-post-transcriptional-regulation
#11
Gianfranco Politano, Federica Logrand, Mara Brancaccio, Stefano Di Carlo
In most developed countries, cardiovascular diseases are among the top causes of death and their development has been shown closely related to aging. In this context, because of their ability to pervasively influence gene networks, miRs have been found as possible key players in the development of cardiac pathologies, suggesting their potential role as therapeutic targets or diagnostic markers. Based on these assumptions, we hereby present a computational study that applies data fusion techniques coupled with network analysis theory to identify a regulatory model able to represent the relationship between key genes and miRs involved in cardiac senescence processes...
June 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28602483/a-hybrid-framework-for-reverse-engineering-of-robust-gene-regulatory-networks
#12
Mina Jafari, Behnam Ghavami, Vahid Sattari
The inference of Gene Regulatory Networks (GRNs) using gene expression data in order to detect the basic cellular processes is a key issue in biological systems. Inferring GRN correctly requires inferring predictor set accurately. In this paper, a fast and accurate predictor set inference framework which linearly combines some inference methods is proposed. The purpose of the combination of various methods is to increase the accuracy of inferred GRN. The proposed framework offers a linear weighted combination of Pearson Correlation Coefficient (PCC) and two different feature selection approaches, namely: Information Gain (IG) and ReliefF...
June 8, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28594840/phylogeography-on-the-rocks-the-contribution-of-current-and-historical-factors-in-shaping-the-genetic-structure-of-chthamalus-montagui-crustacea-cirripedia
#13
Federica G Pannacciulli, Ferruccio Maltagliati, Christian de Guttry, Yair Achituv
The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28592500/epistatic-networks-jointly-influence-phenotypes-related-to-metabolic-disease-and-gene-expression-in-diversity-outbred-mice
#14
Anna L Tyler, Bo Ji, Daniel M Gatti, Steven C Munger, Gary A Churchill, Karen L Svenson, Gregory W Carter
Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice...
June 2017: Genetics
https://www.readbyqxmd.com/read/28586048/modeling-osteosarcoma-progression-by-measuring-the-connectivity-dynamics-using-an-inference-of-multiple-differential-modules-algorithm
#15
Bin Liu, Zhi Zhang, E-Nuo Dai, Jia-Xin Tian, Jiang-Ze Xin, Liang Xu
Understanding the dynamic changes in connectivity of molecular pathways is important for determining disease prognosis. Thus, the current study used an inference of multiple differential modules (iMDM) algorithm to identify the connectivity changes of sub‑network to predict the progression of osteosarcoma (OS) based on the microarray data of OS at four Huvos grades. Initially, multiple differential co‑expression networks (M‑DCNs) were constructed, and weight values were assigned for each edge, followed by detection of seed genes in M‑DCNs according to the topological properties...
June 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28585919/transcriptional-networks-specifying-homeostatic-and-inflammatory-programs-of-gene-expression-in-human-aortic-endothelial-cells
#16
Nicholas T Hogan, Michael B Whalen, Lindsey K Stolze, Nizar K Hadeli, Michael T Lam, James R Springstead, Christopher K Glass, Casey E Romanoski
Endothelial cells (ECs) are critical determinants of vascular homeostasis and inflammation, but transcriptional mechanisms specifying their identities and functional states remain poorly understood. Here, we report a genome-wide assessment of regulatory landscapes of primary human aortic endothelial cells (HAECs) under basal and activated conditions, enabling inference of transcription factor networks that direct homeostatic and pro-inflammatory programs. We demonstrate that 43% of detected enhancers are EC-specific and contain SNPs associated to cardiovascular disease and hypertension...
June 6, 2017: ELife
https://www.readbyqxmd.com/read/28584165/phylogenomic-synteny-network-analysis-of-mads-box-transcription-factor-genes-reveals-lineage-specific-transpositions-ancient-tandem-duplications-and-deep-positional-conservation
#17
Tao Zhao, Rens Holmer, Suzanne de Bruijn, Gerco C Angenent, Harrold A van den Burg, M Eric Schranz
Conserved genomic context provides critical information for comparative evolutionary analysis. With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insight into gene family evolution. Here, we exploit a network analysis approach to organize and interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using fifty-one completed plant genomes. In combination with phylogenetic profiling, several novel evolutionary patterns were inferred and visualized from synteny network clusters...
June 5, 2017: Plant Cell
https://www.readbyqxmd.com/read/28584094/reconstructing-blood-stem-cell-regulatory-network-models-from-single-cell-molecular-profiles
#18
Fiona K Hamey, Sonia Nestorowa, Sarah J Kinston, David G Kent, Nicola K Wilson, Berthold Göttgens
Adult blood contains a mixture of mature cell types, each with specialized functions. Single hematopoietic stem cells (HSCs) have been functionally shown to generate all mature cell types for the lifetime of the organism. Differentiation of HSCs toward alternative lineages must be balanced at the population level by the fate decisions made by individual cells. Transcription factors play a key role in regulating these decisions and operate within organized regulatory programs that can be modeled as transcriptional regulatory networks...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28583129/co-expressed-pathways-database-for-tomato-a-database-to-predict-pathways-relevant-to-a-query-gene
#19
Takafumi Narise, Nozomu Sakurai, Takeshi Obayashi, Hiroyuki Ohta, Daisuke Shibata
BACKGROUND: Gene co-expression, the similarity of gene expression profiles under various experimental conditions, has been used as an indicator of functional relationships between genes, and many co-expression databases have been developed for predicting gene functions. These databases usually provide users with a co-expression network and a list of strongly co-expressed genes for a query gene. Several of these databases also provide functional information on a set of strongly co-expressed genes (i...
June 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28580005/investigating-the-genetic-diversity-population-differentiation-and-population-dynamics-of-cycas-segmentifida-cycadaceae-endemic-to-southwest-china-by-multiple-molecular-markers
#20
Xiuyan Feng, Jian Liu, Yu-Chung Chiang, Xun Gong
Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs), three nuclear genes (nDNAs) and 12 nuclear microsatellites (SSRs), we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China...
2017: Frontiers in Plant Science
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