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Wgcna transcriptome

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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/27818889/discovery-of-the-molecular-mechanisms-of-the-novel-chalcone-based-magnaporthe-oryzae-inhibitor-c1-using-transcriptomic-profiling-and-co-expression-network-analysis
#3
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/27711190/the-role-of-vitamin-d-in-the-transcriptional-program-of-human-pregnancy
#4
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
#5
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/27610074/comparative-gene-expression-analysis-of-two-mouse-models-of-autism-transcriptome-profiling-of-the-btbr-and-en2-hippocampus
#6
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
#7
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/27506548/transcriptome-profiling-of-the-rumen-epithelium-of-beef-cattle-differing-in-residual-feed-intake
#8
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/27331400/an-integrative-transcriptomic-analysis-for-identifying-novel-target-genes-corresponding-to-severity-spectrum-in-spinal-muscular-atrophy
#9
Chung-Wei Yang, Chien-Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh-Jyh Jong, Li-Kai Tsai, Chun-Yu Chuang
Spinal muscular atrophy (SMA) is an inherited neuromuscular disease resulting from a recessive mutation in the SMN1 gene. This disease affects multiple organ systems with varying degrees of severity. Exploration of the molecular pathological changes occurring in different cell types in SMA is crucial for developing new therapies. This study collected 39 human microarray datasets from ArrayExpress and GEO databases to build an integrative transcriptomic analysis for recognizing novel SMA targets. The transcriptomic analysis was conducted through combining weighted correlation network analysis (WGCNA) for gene module detection, gene set enrichment analysis (GSEA) for functional categorization and filtration, and Cytoscape (visual interaction gene network analysis) for target gene identification...
2016: PloS One
https://www.readbyqxmd.com/read/27295368/network-and-biosignature-analysis-for-the-integration-of-transcriptomic-and-metabolomic-data-to-characterize-leaf-senescence-process-in-sunflower
#10
Sebastián Moschen, Janet Higgins, Julio A Di Rienzo, Ruth A Heinz, Norma Paniego, Paula Fernandez
BACKGROUND: In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables, which has a strong impact on crop yield. Transcription factors (TFs) are key proteins in the regulation of gene expression, regulating different signaling pathways; their function is crucial for triggering and/or regulating different aspects of the leaf senescence process...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27215785/transcriptomic-network-analyses-of-leaf-dehydration-responses-identify-highly-connected-aba-and-ethylene-signaling-hubs-in-three-grapevine-species-differing-in-drought-tolerance
#11
Daniel W Hopper, Ryan Ghan, Karen A Schlauch, Grant R Cramer
BACKGROUND: Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant's response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that responded to dehydration in three different grapevine species differing in their drought tolerance...
2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27133569/understanding-the-progression-of-atherosclerosis-through-gene-profiling-and-co-expression-network-analysis-in-apob-tm2sgy-ldlr-tm1her-double-knockout-mice
#12
Vrushali Deshpande, Ankit Sharma, Rupak Mukhopadhyay, Lakshmi Narasimha Rao Thota, Madankumar Ghatge, Rajani Kanth Vangala, Vijay V Kakkar, Lakshmi Mundkur
The objective of the study was to gain molecular insights into the progression of atherosclerosis in Apob(tm2Sgy)Ldlr(tm1Her) mice, using transcriptome profiles. Weighted gene co network analysis (WGCNA) and time course analysis using limma were used to study disease progression from 0 to 20weeks. Five co-expression modules were identified by WGCNA using the expression values of 2153 genes. Genes associated with autophagy, endoplasmic reticulum stress, inflammation and lipid metabolism were differentially expressed at early stages of atherosclerosis...
June 2016: Genomics
https://www.readbyqxmd.com/read/27104786/genome-wide-identification-of-the-transcription-factors-involved-in-citrus-fruit-ripening-from-the-transcriptomes-of-a-late-ripening-sweet-orange-mutant-and-its-wild-type
#13
Juxun Wu, Lili Fu, Hualin Yi
Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (C. sinensis L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72-1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively...
2016: PloS One
https://www.readbyqxmd.com/read/26883038/coupled-electrophysiological-recording-and-single-cell-transcriptome-analyses-revealed-molecular-mechanisms-underlying-neuronal-maturation
#14
Xiaoying Chen, Kunshan Zhang, Liqiang Zhou, Xinpei Gao, Junbang Wang, Yinan Yao, Fei He, Yuping Luo, Yongchun Yu, Siguang Li, Liming Cheng, Yi E Sun
The mammalian brain is heterogeneous, containing billions of neurons and trillions of synapses forming various neural circuitries, through which sense, movement, thought, and emotion arise. The cellular heterogeneity of the brain has made it difficult to study the molecular logic of neural circuitry wiring, pruning, activation, and plasticity, until recently, transcriptome analyses with single cell resolution makes decoding of gene regulatory networks underlying aforementioned circuitry properties possible...
March 2016: Protein & Cell
https://www.readbyqxmd.com/read/26801403/post-weaning-blood-transcriptomic-differences-between-yorkshire-pigs-divergently-selected-for-residual-feed-intake
#15
Haibo Liu, Yet T Nguyen, Dan Nettleton, Jack C M Dekkers, Christopher K Tuggle
BACKGROUND: Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired...
2016: BMC Genomics
https://www.readbyqxmd.com/read/26679926/a-translational-systems-biology-approach-in-both-animals-and-humans-identifies-a-functionally-related-module-of-accumbal-genes-involved-in-the-regulation-of-reward-processing-and-binge-drinking-in-males
#16
David Stacey, Anbarasu Lourdusamy, Barbara Ruggeri, Matthieu Maroteaux, Tianye Jia, Anna Cattrell, Charlotte Nymberg, Tobias Banaschewski, Sohinee Bhattacharyya, Hamid Band, Gareth Barker, Arun Bokde, Christian Buchel, Fabiana Carvalho, Patricia Conrod, Sylvane Desrivieres, Alanna Easton, Mira Fauth-Buehler, Alberto Fernandez-Medarde, Herta Flor, Vincent Frouin, Jurgen Gallinat, Hugh Garavanh, Andreas Heinz, Bernd Ittermann, Mark Lathrop, Claire Lawrence, Eva Loth, Karl Mann, Jean-Luc Martinot, Frauke Nees, Tomas Paus, Zdenka Pausova, Marcella Rietschel, Andrea Rotter, Eugenio Santos, Michael Smolka, Wolfgang Sommer, Manuel Mameli, Rainer Spanagel, Jean-Antoine Girault, Christian Mueller, Gunter Schumann
BACKGROUND: The mesolimbic dopamine system, composed primarily of dopaminergic neurons in the ventral tegmental area that project to striatal structures, is considered to be the key mediator of reinforcement-related mechanisms in the brain. Prompted by a genome-wide association meta-analysis implicating the Ras-specific guanine nucleotide-releasing factor 2 (RASGRF2) gene in the regulation of alcohol intake in men, we have recently shown that male Rasgrf2(-/-) mice exhibit reduced ethanol intake and preference accompanied by a perturbed mesolimbic dopamine system...
April 2016: Journal of Psychiatry & Neuroscience: JPN
https://www.readbyqxmd.com/read/26558288/transcriptome-analysis-of-gelatin-seed-treatment-as-a-biostimulant-of-cucumber-plant-growth
#17
H T Wilson, K Xu, A G Taylor
The beneficial effects of gelatin capsule seed treatment on enhanced plant growth and tolerance to abiotic stress have been reported in a number of crops, but the molecular mechanisms underlying such effects are poorly understood. Using mRNA sequencing based approach, transcriptomes of one- and two-week-old cucumber plants from gelatin capsule treated and nontreated seeds were characterized. The gelatin treated plants had greater total leaf area, fresh weight, frozen weight, and nitrogen content. Pairwise comparisons of the RNA-seq data identified 620 differentially expressed genes between treated and control two-week-old plants, consistent with the timing when the growth related measurements also showed the largest differences...
2015: TheScientificWorldJournal
https://www.readbyqxmd.com/read/26460053/transcriptome-analyses-reveal-molecular-mechanisms-underlying-functional-recovery-after-spinal-cord-injury
#18
Hongmei Duan, Weihong Ge, Aifeng Zhang, Yue Xi, Zhihua Chen, Dandan Luo, Yin Cheng, Kevin S Fan, Steve Horvath, Michael V Sofroniew, Liming Cheng, Zhaoyang Yang, Yi E Sun, Xiaoguang Li
Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI...
October 27, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26435169/network-based-proteomic-analysis-for-postmenopausal-osteoporosis-in-caucasian-females
#19
Lan Zhang, Yao-Zhong Liu, Yong Zeng, Wei Zhu, Ying-Chun Zhao, Ji-Gang Zhang, Jia-Qiang Zhu, Hao He, Hui Shen, Qing Tian, Fei-Yan Deng, Christopher J Papasian, Hong-Wen Deng
Menopause is one of the crucial physiological events during the life of a woman. Transition of menopause status is accompanied by increased risks of various health problems such as osteoporosis. Peripheral blood monocytes can differentiate into osteoclasts and produce cytokines important for osteoclast activity. With quantitative proteomics LC-nano-ESI-MS(E) (where MS(E) is elevated-energy MS), we performed protein expression profiling of peripheral blood monocytes in 42 postmenopausal women with discordant bone mineral density (BMD) levels...
January 2016: Proteomics
https://www.readbyqxmd.com/read/26417021/transcriptome-analysis-of-an-apple-malus-%C3%A3-domestica-yellow-fruit-somatic-mutation-identifies-a-gene-network-module-highly-associated-with-anthocyanin-and-epigenetic-regulation
#20
Islam El-Sharkawy, Dong Liang, Kenong Xu
Using RNA-seq, this study analysed an apple (Malus×domestica) anthocyanin-deficient yellow-skin somatic mutant 'Blondee' (BLO) and its red-skin parent 'Kidd's D-8' (KID), the original name of 'Gala', to understand the molecular mechanisms underlying the mutation. A total of 3299 differentially expressed genes (DEGs) were identified between BLO and KID at four developmental stages and/or between two adjacent stages within BLO and/or KID. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered a network module of 34 genes highly correlated (r=0...
December 2015: Journal of Experimental Botany
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