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Wgcna transcriptome

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https://www.readbyqxmd.com/read/28566751/establishment-of-the-model-system-between-phytochemicals-and-gene-expression-profiles-in-macrosclereid-cells-of-medicago-truncatula
#1
Fuyou Fu, Wentao Zhang, Yuan-Yuan Li, Hong Li Wang
Macrosclereid cells, which are a layer in the seed coat of Medicago truncatula, accumulate large amounts of phytochemicals during their development. But little is known about the complex and dynamic changes during macrosclereid cell development. To characterize the phytochemicals and the related gene expression during the development of M. truncatula macrosclereid cells, a high performance liquid chromatography-mass spectrometry (HPLC-MS) assay and microarray study were conducted on transcriptome changes from macrosclereid cell during seed development...
May 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28542617/inflammatory-and-apoptotic-remodeling-in-autonomic-nervous-system-following-myocardial-infarction
#2
Chen Gao, Kimberly Howard-Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
BACKGROUND: Chronic myocardial infarction (MI) triggers pathological remodeling in the heart and cardiac nervous system. Abnormal function of the autonomic nervous system (ANS), including stellate ganglia (SG) and dorsal root ganglia (DRG) contribute to increased sympathoexcitation, cardiac dysfunction and arrythmogenesis. ANS modulation is a therapeutic target for arrhythmia associated with cardiac injury. However, the molecular mechanism involved in the pathological remodeling in ANS following cardiac injury remains to be established...
2017: PloS One
https://www.readbyqxmd.com/read/28477104/using-scale-and-feather-traits-for-module-construction-provides-a-functional-approach-to-chicken-epidermal-development
#3
Weier Bao, Matthew J Greenwold, Roger H Sawyer
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis...
May 5, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28467969/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#4
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28438154/network-based-analysis-reveals-novel-gene-signatures-in-peripheral-blood-of-patients-with-chronic-obstructive-pulmonary-disease
#5
Ma'en Obeidat, Yunlong Nie, Virginia Chen, Casey P Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rotzschke, Peter J Castaldi, Craig P Hersh, Nick Fishbane, Raymond T Ng, Bruce McManus, Bruce E Miller, Stephen Rennard, Peter D Paré, Don D Sin
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death and there is a huge unmet clinical need to identify disease biomarkers in peripheral blood. Compared to gene level differential expression approaches to identify gene signatures, network analyses provide a biologically intuitive approach which leverages the co-expression patterns in the transcriptome to identify modules of co-expressed genes. METHODS: A weighted gene co-expression network analysis (WGCNA) was applied to peripheral blood transcriptome from 238 COPD subjects to discover co-expressed gene modules...
April 24, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28266556/integrative-diffusion-weighted-imaging-and-radiogenomic-network-analysis-of-glioblastoma-multiforme
#6
Dieter Henrik Heiland, Carl Philipp Simon-Gabriel, Theo Demerath, Gerrit Haaker, Dietmar Pfeifer, Elias Kellner, Valerij G Kiselev, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
In the past, changes of the Apparent Diffusion Coefficient in glioblastoma multiforme have been shown to be related to specific genes and described as being associated with survival. The purpose of this study was to investigate diffusion imaging parameters in combination with genome-wide expression data in order to obtain a comprehensive characterisation of the transcriptomic changes indicated by diffusion imaging parameters. Diffusion-weighted imaging, molecular and clinical data were collected prospectively in 21 patients...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197160/digital-gene-expression-analysis-provides-insight-into-the-transcript-profile-of-the-genes-involved-in-aporphine-alkaloid-biosynthesis-in-lotus-nelumbo-nucifera
#7
Mei Yang, Lingping Zhu, Ling Li, Juanjuan Li, Liming Xu, Ji Feng, Yanling Liu
The predominant alkaloids in lotus leaves are aporphine alkaloids. These are the most important active components and have many pharmacological properties, but little is known about their biosynthesis. We used digital gene expression (DGE) technology to identify differentially-expressed genes (DEGs) between two lotus cultivars with different alkaloid contents at four leaf development stages. We also predicted potential genes involved in aporphine alkaloid biosynthesis by weighted gene co-expression network analysis (WGCNA)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28104750/gene-networks-in-skeletal-muscle-following-endurance-exercise-are-coexpressed-in-blood-neutrophils-and-linked-with-blood-inflammation-markers
#8
James Broadbent, Dayle Sampson, Surendran Sabapathy, Luke J Haseler, Karl-Heinz Wagner, Andrew C Bulmer, Jonathan M Peake, Oliver Neubauer
It remains incompletely understood whether there is an association between the transcriptome profiles of skeletal muscle and blood leukocytes in response to exercise or other physiological stressors. We have previously analyzed the changes in the muscle and blood neutrophil transcriptome in eight trained men before and 3, 48, and 96 h after 2 h cycling and running. Because we collected muscle and blood in the same individuals and under the same conditions, we were able to directly compare gene expression between the muscle and blood neutrophils...
April 1, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/27907186/inter-tissue-gene-co-expression-networks-between-metabolically-healthy-and-unhealthy-obese-individuals
#9
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
#10
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
#11
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
#12
RANDOMIZED CONTROLLED TRIAL
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
#13
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 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
#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/27506548/transcriptome-profiling-of-the-rumen-epithelium-of-beef-cattle-differing-in-residual-feed-intake
#16
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
#17
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
#18
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
#19
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
#20
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
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