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Gene network inference

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https://www.readbyqxmd.com/read/28938012/f-map-a-bayesian-approach-to-infer-the-gene-regulatory-network-using-external-hints
#1
Maryam Shahdoust, Hamid Pezeshk, Hossein Mahjub, Mehdi Sadeghi
The Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which applies the knowledge about gene interactions from related species. Our algorithm sets a Bayesian framework to estimate the precision matrix of one species microarray gene expressions dataset to infer the Gaussian Graphical model of the network...
2017: PloS One
https://www.readbyqxmd.com/read/28934252/three-way-interaction-model-to-trace-the-mechanisms-involved-in-alzheimer-s-disease-transgenic-mice
#2
Nasibeh Khayer, Sayed-Amir Marashi, Mehdi Mirzaie, Fatemeh Goshadrou
Alzheimer's disease (AD) is the most common cause for dementia in human. Currently, more than 46 million people in the world suffer from AD and it is estimated that by 2050 this number increases to more than 131 million. AD is considered as a complex disease. Therefore, understanding the mechanism of AD is a universal challenge. Nowadays, a huge number of disease-related high-throughput "omics" datasets are freely available. Such datasets contain valuable information about disease-related pathways and their corresponding gene interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28928672/micrornas-clustered-within-the-14q32-locus-are-associated-with-endothelial-damage-and-microparticle-secretion-in-bicuspid-aortic-valve-disease
#3
Neus Martínez-Micaelo, Raúl Beltrán-Debón, Gerard Aragonés, Marta Faiges, Josep M Alegret
Background: We previously described that PECAM(+) circulating endothelial microparticles (EMPs) are elevated in bicuspid aortic valve (BAV) disease as a manifestation of endothelial damage. In this study, we hypothesized that this endothelial damage, is functionally related to the secretion of a specific pattern of EMP-associated miRNAs. Methods: We used a bioinformatics approach to correlate the PECAM(+) EMP levels with the miRNA expression profile in plasma in healthy individuals and BAV patients (n = 36)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28915238/a-high-resolution-atlas-of-gene-expression-in-the-domestic-sheep-ovis-aries
#4
Emily L Clark, Stephen J Bush, Mary E B McCulloch, Iseabail L Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C Bruce Whitelaw, Tom C Freeman, Kim M Summers, Alan L Archibald, David A Hume
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28898266/translating-natural-genetic-variation-to-gene-expression-in-a-computational-model-of-the-drosophila-gap-gene-regulatory-network
#5
Vitaly V Gursky, Konstantin N Kozlov, Ivan V Kulakovskiy, Asif Zubair, Paul Marjoram, David S Lawrie, Sergey V Nuzhdin, Maria G Samsonova
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/28893852/root-architecture-shaping-by-the-environment-is-orchestrated-by-dynamic-gene-expression-in-space-and-time
#6
Liam Walker, Clare Boddington, Dafyd Jenkins, Ying Wang, Jesper T Grønlund, Jo Hulsmans, Sanjeev Kumar, Dhaval Patel, Jonathan D Moore, Anthony Carter, Siva Samavedam, Giovanni Bomono, David S Hersh, Gloria M Coruzzi, Nigel J Burroughs, Miriam L Gifford
Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response non-redundancy...
September 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/28883405/modeling-a-linkage-between-blood-transcriptional-expression-and-activity-in-brain-regions-to-infer-the-phenotype-of-schizophrenia-patients
#7
El Chérif Ibrahim, Vincent Guillemot, Magali Comte, Arthur Tenenhaus, Xavier Yves Zendjidjian, Aida Cancel, Raoul Belzeaux, Florence Sauvanaud, Olivier Blin, Vincent Frouin, Eric Fakra
Hundreds of genetic loci participate to schizophrenia liability. It is also known that impaired cerebral connectivity is directly related to the cognitive and affective disturbances in schizophrenia. How genetic susceptibility and brain neural networks interact to specify a pathological phenotype in schizophrenia remains elusive. Imaging genetics, highlighting brain variations, has proven effective to establish links between vulnerability loci and associated clinical traits. As previous imaging genetics works in schizophrenia have essentially focused on structural DNA variants, these findings could be blurred by epigenetic mechanisms taking place during gene expression...
September 7, 2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28860069/gernet-a-gene-regulatory-network-tool
#8
J S Dussaut, C A Gallo, F Cravero, M J Martínez, J A Carballido, I Ponzoni
Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene networks are hard to be mapped with accuracy by any other mathematical model. A highly abstract model-free approach, called rule-based approach, offers several advantages performing data-driven analysis; such as the requirement of the least amount of data...
August 28, 2017: Bio Systems
https://www.readbyqxmd.com/read/28854641/conserved-transcription-factors-steer-growth-related-genomic-programs-in-daphnia
#9
Katina I Spanier, Mieke Jansen, Ellen Decaestecker, Gert Hulselmans, Dörthe Becker, John K Colbourne, Luisa Orsini, Luc De Meester, Stein Aerts
Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28851837/rna-structure-inference-through-chemical-mapping-after-accidental-or-intentional-mutations
#10
Clarence Y Cheng, Wipapat Kladwang, Joseph D Yesselman, Rhiju Das
Despite the critical roles RNA structures play in regulating gene expression, sequencing-based methods for experimentally determining RNA base pairs have remained inaccurate. Here, we describe a multidimensional chemical-mapping method called "mutate-and-map read out through next-generation sequencing" (M2-seq) that takes advantage of sparsely mutated nucleotides to induce structural perturbations at partner nucleotides and then detects these events through dimethyl sulfate (DMS) probing and mutational profiling...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28851355/integrative-model-of-leukocyte-genomics-and-organ-dysfunction-in-heart-failure-patients-requiring-mechanical-circulatory-support-a-prospective-observational-study
#11
Nicholas Wisniewski, Galyna Bondar, Christoph Rau, Jay Chittoor, Eleanor Chang, Azadeh Esmaeili, Martin Cadeiras, Mario Deng
BACKGROUND: The implantation of mechanical circulatory support devices in heart failure patients is associated with a systemic inflammatory response, potentially leading to death from multiple organ dysfunction syndrome. Previous studies point to the involvement of many mechanisms, but an integrative hypothesis does not yet exist. Using time-dependent whole-genome mRNA expression in circulating leukocytes, we constructed a systems-model to improve mechanistic understanding and prediction of adverse outcomes...
August 29, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28835615/logic-programming-reveals-alteration-of-key-transcription-factors-in-multiple-myeloma
#12
Bertrand Miannay, Stéphane Minvielle, Olivier Roux, Pierre Drouin, Hervé Avet-Loiseau, Catherine Guérin-Charbonnel, Wilfried Gouraud, Michel Attal, Thierry Facon, Nikhil C Munshi, Philippe Moreau, Loïc Campion, Florence Magrangeas, Carito Guziolowski
Innovative approaches combining regulatory networks (RN) and genomic data are needed to extract biological information for a better understanding of diseases, such as cancer, by improving the identification of entities and thereby leading to potential new therapeutic avenues. In this study, we confronted an automatically generated RN with gene expression profiles (GEP) from a cohort of multiple myeloma (MM) patients and normal individuals using global reasoning on the RN causality to identify key-nodes. We modeled each patient by his or her GEP, the RN and the possible automatically detected repairs needed to establish a coherent flow of the information that explains the logic of the GEP...
August 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28835260/genomic-insights-into-potential-interdependencies-in-microbial-hydrocarbon-and-nutrient-cycling-in-hydrothermal-sediments
#13
Nina Dombrowski, Kiley W Seitz, Andreas P Teske, Brett J Baker
BACKGROUND: Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data...
August 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28830924/cone-community-oriented-network-estimation-is-a-versatile-framework-for-inferring-population-structure-in-large-scale-sequencing-data
#14
Markku O Kuismin, Jon Ahlinder, Mikko J Sillanpää
Estimation of genetic population structure based on molecular markers is a common task in population genetics and ecology. We apply a generalized linear model with LASSO regularization to infer relationships between individuals and populations from molecular marker data. Specifically, we apply a neighborhood selection algorithm to infer population genetic structure and gene flow between populations. The resulting relationships are used to construct an individual-level population graph. Different network substructures known as communities are then dissociated from each other using a community detection algorithm...
August 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28830434/rational-confederation-of-genes-and-diseases-ngs-interpretation-via-genecards-malacards-and-varelect
#15
Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, Doron Lancet
BACKGROUND: A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses...
August 18, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28830343/divergence-of-functional-effects-among-bacterial-srna-paralogs
#16
I-Chen Kimberly Chen, Gregory J Velicer, Yuen-Tsu Nicco Yu
BACKGROUND: Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus...
August 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28830337/a-history-of-hybrids-genomic-patterns-of-introgression-in-the-true-geese
#17
Jente Ottenburghs, Hendrik-Jan Megens, Robert H S Kraus, Pim van Hooft, Sipke E van Wieren, Richard P M A Crooijmans, Ronald C Ydenberg, Martien A M Groenen, Herbert H T Prins
BACKGROUND: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns...
August 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28827319/predicting-gene-regulatory-networks-by-combining-spatial-and-temporal-gene-expression-data-in-arabidopsis-root-stem-cells
#18
Maria Angels de Luis Balaguer, Adam P Fisher, Natalie M Clark, Maria Guadalupe Fernandez-Espinosa, Barbara K Möller, Dolf Weijers, Jan U Lohmann, Cranos Williams, Oscar Lorenzo, Rosangela Sozzani
Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference...
August 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28821731/stability-in-metabolic-phenotypes-and-inferred-metagenome-profiles-before-the-onset-of-colitis-induced-inflammation
#19
M Glymenaki, A Barnes, S O' Hagan, G Warhurst, A J McBain, I D Wilson, D B Kell, K J Else, S M Cruickshank
Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28815099/enabling-comprehension-of-patient-subgroups-and-characteristics-in-large-bipartite-networks-implications-for-precision-medicine
#20
Suresh K Bhavnani, Tianlong Chen, Archana Ayyaswamy, Shyam Visweswaran, Gowtham Bellala, Divekar Rohit, Bassler Kevin E
A primary goal of precision medicine is to identify patient subgroups based on their characteristics (e.g., comorbidities or genes) with the goal of designing more targeted interventions. While network visualization methods such as Fruchterman-Reingold have been used to successfully identify such patient subgroups in small to medium sized data sets, they often fail to reveal comprehensible visual patterns in large and dense networks despite having significant clustering. We therefore developed an algorithm called ExplodeLayout, which exploits the existence of significant clusters in bipartite networks to automatically "explode" a traditional network layout with the goal of separating overlapping clusters, while at the same time preserving key network topological properties that are critical for the comprehension of patient subgroups...
2017: AMIA Summits on Translational Science Proceedings
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