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https://www.readbyqxmd.com/read/27907186/inter-tissue-gene-co-expression-networks-between-metabolically-healthy-and-unhealthy-obese-individuals
#1
Lisette J A Kogelman, Jingyuan Fu, Lude Franke, Jan Willem Greve, Marten Hofker, Sander S Rensen, Haja N Kadarmideen
BACKGROUND: Obesity is associated with severe co-morbidities such as type 2 diabetes and nonalcoholic steatohepatitis. However, studies have shown that 10-25 percent of the severely obese individuals are metabolically healthy. To date, the identification of genetic factors underlying the metabolically healthy obese (MHO) state is limited. Systems genetics approaches have led to the identification of genes and pathways in complex diseases. Here, we have used such approaches across tissues to detect genes and pathways involved in obesity-induced disease development...
2016: PloS One
https://www.readbyqxmd.com/read/27898768/transcriptome-and-small-rnaome-dynamics-during-a-resistant-and-susceptible-interaction-between-cucumber-and-downy-mildew
#2
Alyssa Burkhardt, Brad Day
Cucumber ( L.) downy mildew, caused by the obligate oomycete pathogen (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible ('Vlaspik') cucumber during a time course of infection using Illumina sequencing...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27896962/adaptive-testing-of-snp-brain-functional-connectivity-association-via-a-modular-network-analysis
#3
Chen Gao, Junghi Kim, Wei Pan
Due to its high dimensionality and high noise levels, analysis of a large brain functional network may not be powerful and easy to interpret; instead, decomposition of a large network into smaller subcomponents called modules may be more promising as suggested by some empirical evidence. For example, alteration of brain modularity is observed in patients suffering from various types of brain malfunctions. Although several methods exist for estimating brain functional networks, such as the sample correlation matrix or graphical lasso for a sparse precision matrix, it is still difficult to extract modules from such network estimates...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27894806/genetic-divergence-in-the-transcriptional-engram-of-chronic-alcohol-abuse-a-laser-capture-rna-seq-study-of-the-mouse-mesocorticolimbic-system
#4
Megan K Mulligan, Khyobeni Mozhui, Ashutosh K Pandey, Maren L Smith, Suzhen Gong, Jesse Ingels, Michael F Miles, Marcelo F Lopez, Lu Lu, Robert W Williams
Genetic factors that influence the transition from initial drinking to dependence remain enigmatic. Recent studies have leveraged chronic intermittent ethanol (CIE) paradigms to measure changes in brain gene expression in a single strain at 0, 8, 72 h, and even 7 days following CIE. We extend these findings using LCM RNA-seq to profile expression in 11 brain regions in two inbred strains - C57BL/6J (B6) and DBA/2J (D2) - 72 h following multiple cycles of ethanol self-administration and CIE. Linear models identified differential expression based on treatment, region, strain, or interactions with treatment...
October 15, 2016: Alcohol
https://www.readbyqxmd.com/read/27824868/drug-repositioning-through-systematic-mining-of-gene-coexpression-networks-in-cancer
#5
Alexander E Ivliev, Peter A C 't Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G Sergeeva
Gene coexpression network analysis is a powerful "data-driven" approach essential for understanding cancer biology and mechanisms of tumor development. Yet, despite the completion of thousands of studies on cancer gene expression, there have been few attempts to normalize and integrate co-expression data from scattered sources in a concise "meta-analysis" framework. We generated such a resource by exploring gene coexpression networks in 82 microarray datasets from 9 major human cancer types. The analysis was conducted using an elaborate weighted gene coexpression network (WGCNA) methodology and identified over 3,000 robust gene coexpression modules...
2016: PloS One
https://www.readbyqxmd.com/read/27819739/identification-of-significantly-different-modules-between-permanent-and-deciduous-teeth-by-network-and-pathway-analyses
#6
J Kang, R Bai, K Liu, X P Ji, Y Li, J Y Han
The differences in genetic backgrounds between deciduous and permanent teeth might contribute to the differences in developmental processes, histological characteristics, and tooth life cycles. Here, we attempted to identify significantly different modules between permanent and deciduous teeth via network and pathway analyses. We identified 291 differentially expressed genes (DEGs) between permanent and deciduous teeth using significance analysis of microarray methods. Co-expression networks of DEGs were constructed by weighted gene co-expression network analysis (WGCNA)...
November 3, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27818889/discovery-of-the-molecular-mechanisms-of-the-novel-chalcone-based-magnaporthe-oryzae-inhibitor-c1-using-transcriptomic-profiling-and-co-expression-network-analysis
#7
Hui Chen, Xiaoyun Wang, Hong Jin, Rui Liu, Taiping Hou
BACKGROUND: In our previous studies, we discovered a series of chalcone-based phytopathogenic fungus inhibitors. However, knowledge of their effects, detailed targets and molecular mechanisms in Magnaporthe oryzae (M. oryzae) remained limited. METHODS: To explore the expression and function of differentially expressed genes in M. oryzae after treatment with compound C1, we analyzed the expression profile of mRNAs using a microarray analysis and GO, KEGG and WGCNA analysis, followed by qRT-PCR and Western blots to validate our findings...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27814717/differential-dna-methylation-marks-and-gene-comethylation-of-copd-in-african-americans-with-copd-exacerbations
#8
Robert Busch, Weiliang Qiu, Jessica Lasky-Su, Jarrett Morrow, Gerard Criner, Dawn DeMeo
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort...
November 5, 2016: Respiratory Research
https://www.readbyqxmd.com/read/27793094/network-analysis-of-psoriasis-reveals-biological-pathways-and-roles-for-coding-and-long-non-coding-rnas
#9
Richard Ahn, Rashmi Gupta, Kevin Lai, Nitin Chopra, Sarah T Arron, Wilson Liao
BACKGROUND: Psoriasis is an immune-mediated, inflammatory disorder of the skin characterized by chronic inflammation and hyperproliferation of the epidermis. Differential expression analysis of microarray or RNA-seq data have shown that thousands of coding and non-coding genes are differentially expressed between psoriatic and healthy control skin. However, differential expression analysis may fail to detect perturbations in gene coexpression networks. Sensitive detection of such networks may provide additional insight into important disease-associated pathways...
October 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27725221/fresh-frozen-plasma-modulates-brain-gene-expression-in-a-swine-model-of-traumatic-brain-injury-and-shock-a-network-analysis
#10
Martin Sillesen, Theodore Bambakidis, Simone Dekker, Yongqing Li, Hasan B Alam
BACKGROUND: Resuscitation with Fresh Frozen Plasma (FFP) decreases brain lesion size and swelling in a swine model of Traumatic Brain Injury (TBI) and hemorrhagic shock (HS). We hypothesized that brain gene expression profiles following TBI+HS would be modulated by FFP resuscitation. STUDY DESIGN: 15 swine underwent a protocol of TBI and HS, two hours of shock followed by resuscitation with FFP, Normal Saline (NS) or hetastarch (Hextend, HEX, 5/group). After 6 hours, brain RNA was isolated and hybridized onto a Porcine Gene ST 1...
October 7, 2016: Journal of the American College of Surgeons
https://www.readbyqxmd.com/read/27711190/the-role-of-vitamin-d-in-the-transcriptional-program-of-human-pregnancy
#11
Amal Al-Garawi, Vincent J Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky-Su, Weiliang Qiu, Nancy Laranjo, Augusto A Litonjua, Scott T Weiss
BACKGROUND: Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. OBJECTIVE: Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels...
2016: PloS One
https://www.readbyqxmd.com/read/27704223/gene-co-expression-network-analysis-reveals-the-correlation-patterns-among-genes-in-euryhaline-adaptation-of-crassostrea-gigas
#12
Xuelin Zhao, Hong Yu, Lingfeng Kong, Qi Li
The Pacific oyster Crassostrea gigas is a dominant aquaculture species in many intertidal zones throughout the Pacific and Atlantic Oceans and can tolerate a wide range of salinity. Studying the gene expression profiles of oyster gills had found differentially expressed genes (DEGs) involved in salinity tolerance. A systematic study of cellular response to salinity stress may provide insights into the mechanism of acquired salinity tolerance. Here, weighted gene co-expression network analysis (WGCNA) was carried out using RNA-seq data from gill transcriptome in response to different salinity...
October 4, 2016: Marine Biotechnology
https://www.readbyqxmd.com/read/27613830/molecular-differences-between-cerebral-blood-volume-and-vessel-size-in-glioblastoma-multiforme
#13
Dieter Henrik Heiland, Theo Demerath, Elias Kellner, Valerij G Kiselev, Dietmar Pfeifer, Oliver Schnell, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
The purpose of this study was to investigate the molecular background of cerebral blood volume (CBV) and vessel size (VS) of capillaries in glioblastoma multiforme (GBM). Both parameters are derived from extended perfusion MR imaging.A prospective case study including 21 patients (median age 66 years, 10 females) was performed. Before operation, CBV and VS of contrast enhancing tumor were assessed. Tissue was sampled from the assessed areas under neuronavigation control. After RNA extraction, transcriptional data was analyzed by Weighted Gene Co-Expression Network Analysis (WGCNA) and split into modules based on its network affiliations...
August 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27610074/comparative-gene-expression-analysis-of-two-mouse-models-of-autism-transcriptome-profiling-of-the-btbr-and-en2-hippocampus
#14
Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, Maria L Scattoni, Yuri Bozzi
Autism spectrum disorders (ASD) are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity, and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD; however, a comprehensive approach to identify transcriptional abnormalities in different ASD models has never been performed...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27591185/decoding-the-long-noncoding-rna-during-cardiac-maturation-a-roadmap-for-functional-discovery
#15
Marlin Touma, Xuedong Kang, Yan Zhao, Ashley A Cass, Fuying Gao, Reshma Biniwale, Giovanni Coppola, Xinshu Xiao, Brian Reemtsen, Yibin Wang
BACKGROUND: Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects. Transcriptome programming during perinatal stages is an important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated. METHODS AND RESULTS: From comprehensive analysis of transcriptomes derived from neonatal mouse heart left and right ventricles, a total of 45 167 unique transcripts were identified, including 21 916 known and 2033 novel lncRNAs...
October 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27588126/construction-of-protein-interaction-network-involved-in-lung-adenocarcinomas-using-a-novel-algorithm
#16
Juan Chen, Hai-Tao Yang, Zhu Li, Ning Xu, Bo Yu, Jun-Ping Xu, Pei-Ge Zhao, Yan Wang, Xiu-Juan Zhang, Dian-Jie Lin
Studies that only assess differentially-expressed (DE) genes do not contain the information required to investigate the mechanisms of diseases. A complete knowledge of all the direct and indirect interactions between proteins may act as a significant benchmark in the process of forming a comprehensive description of cellular mechanisms and functions. The results of protein interaction network studies are often inconsistent and are based on various methods. In the present study, a combined network was constructed using selected gene pairs, following the conversion and combination of the scores of gene pairs that were obtained across multiple approaches by a novel algorithm...
September 2016: Oncology Letters
https://www.readbyqxmd.com/read/27536319/gene-coexpression-analyses-differentiate-networks-associated-with-diverse-cancers-harboring-tp53-missense-or-null-mutations
#17
Kathleen Oros Klein, Karim Oualkacha, Marie-Hélène Lafond, Sahir Bhatnagar, Patricia N Tonin, Celia M T Greenwood
In a variety of solid cancers, missense mutations in the well-established TP53 tumor suppressor gene may lead to the presence of a partially-functioning protein molecule, whereas mutations affecting the protein encoding reading frame, often referred to as null mutations, result in the absence of p53 protein. Both types of mutations have been observed in the same cancer type. As the resulting tumor biology may be quite different between these two groups, we used RNA-sequencing data from The Cancer Genome Atlas (TCGA) from four different cancers with poor prognosis, namely ovarian, breast, lung and skin cancers, to compare the patterns of coexpression of genes in tumors grouped according to their TP53 missense or null mutation status...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27523473/weighted-gene-co-expression-based-biomarker-discovery-for-psoriasis-detection
#18
Sudharsana Sundarrajan, Mohanapriya Arumugam
Psoriasis is a chronic inflammatory disease of the skin with an unknown aetiology. The disease manifests itself as red and silvery scaly plaques distributed over the scalp, lower back and extensor aspects of the limbs. After receiving scant consideration for quite a few years, psoriasis has now become a prominent focus for new drug development. A group of closely connected and differentially co-expressed genes may act in a network and may serve as molecular signatures for an underlying phenotype. A weighted gene coexpression network analysis (WGCNA), a system biology approach has been utilized for identification of new molecular targets for psoriasis...
November 15, 2016: Gene
https://www.readbyqxmd.com/read/27506548/transcriptome-profiling-of-the-rumen-epithelium-of-beef-cattle-differing-in-residual-feed-intake
#19
Rebecca S G Kong, Guanxiang Liang, Yanhong Chen, Paul Stothard, Le Luo Guan
BACKGROUND: Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach. RESULTS: The rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27496332/comparative-transcript-profiling-of-alloplasmic-male-sterile-lines-revealed-altered-gene-expression-related-to-pollen-development-in-rice-oryza-sativa-l
#20
Jihong Hu, Guanglong Chen, Hongyuan Zhang, Qian Qian, Yi Ding
BACKGROUND: Cytoplasmic male sterility (CMS) is an ideal model for investigating the mitochondrial-nuclear interaction and down-regulated genes in CMS lines which might be the candidate genes for pollen development in rice. In this study, a set of rice alloplasmic sporophytic CMS lines was obtained by successive backcrossing of Meixiang B, with three different cytoplasmic types: D62A (D type), ZS97A (WA type) and XQZ-A (DA type). RESULTS: Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expressed genes (DEGs) in each of the three CMS lines compared with the maintainer line Meixiang B...
2016: BMC Plant Biology
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