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Wgcna transcriptome

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https://www.readbyqxmd.com/read/29025019/differing-molecular-response-of-young-and-advanced-maternal-age-human-oocytes-to-ivm
#1
J M Reyes, E Silva, J L Chitwood, W B Schoolcraft, R L Krisher, P J Ross
STUDY QUESTION: What effect does maternal age have on the human oocyte's molecular response to in vitro oocyte maturation? SUMMARY ANSWER: Although polyadenylated transcript abundance is similar between young and advanced maternal age (AMA) germinal vesicle (GV) oocytes, metaphase II (MII) oocytes exhibit a divergent transcriptome resulting from a differential response to in vitro oocyte maturation. WHAT IS KNOWN ALREADY: Microarray studies considering maternal age or maturation stage have shown that either of these factors will affect oocyte polyadenylated transcript abundance in human oocytes...
September 15, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28970079/human-kidney-tubule-specific-gene-expression-based-dissection-of-chronic-kidney-disease-traits
#2
Pazit Beckerman, Chengxiang Qiu, Jihwan Park, Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Sang-Youb Han, Peter Choi, Matthew Palmer, Katalin Susztak
Chronic kidney disease (CKD) has diverse phenotypic manifestations including structural (such as fibrosis) and functional (such as glomerular filtration rate and albuminuria) alterations. Gene expression profiling has recently gained popularity as an important new tool for precision medicine approaches. Here we used unbiased and directed approaches to understand how gene expression captures different CKD manifestations in patients with diabetic and hypertensive CKD. Transcriptome data from ninety-five microdissected human kidney samples with a range of demographics, functional and structural changes were used for the primary analysis...
October 2017: EBioMedicine
https://www.readbyqxmd.com/read/28912681/divergence-in-morris-water-maze-based-cognitive-performance-under-chronic-stress-is-associated-with-the-hippocampal-whole-transcriptomic-modification-in-mice
#3
Seung H Jung, Milene L Brownlow, Matteo Pellegrini, Ryan Jankord
Individual susceptibility determines the magnitude of stress effects on cognitive function. The hippocampus, a brain region of memory consolidation, is vulnerable to stressful environments, and the impact of stress on hippocampus may determine individual variability in cognitive performance. Therefore, the purpose of this study was to define the relationship between the divergence in spatial memory performance under chronically unpredictable stress and an associated transcriptomic alternation in hippocampus, the brain region of spatial memory consolidation...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28903352/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...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28886704/differentiated-transcriptional-signatures-in-the-maize-landraces-of-chiapas-mexico
#5
Matthew A Kost, Hugo R Perales, Saranga Wijeratne, Asela J Wijeratne, Eric Stockinger, Kristin L Mercer
BACKGROUND: Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. RESULTS: Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico...
September 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28872670/tcr-pmhc-encounter-differentially-regulates-transcriptomes-of-tissue-resident-cd8-t%C3%A2-cells
#6
Akihiro Yoshizawa, Kevin Bi, Derin B Keskin, Guanglan Zhang, Bruce Reinhold, Ellis L Reinherz
To investigate the role of TCR-pMHC interaction in regulating lung CD8 tissue-resident T cell (TR ) differentiation, polyclonal responses were compared against NP366-374 /D(b) and PA224-233 /D(b) , two immunodominant epitopes that arise during influenza A infection in mice. Memory niches distinct from iBALTs develop within the lamina propria, supporting CD103(+) and CD103(-) CD8 TR generation and intraepithelial translocation. Gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis (WGCNA) identify dominant TCR, adherens junction, RIG-I-like and NOD-like pattern recognition receptor as well as TGF-β signaling pathways and memory signatures among PA224-233 /D(b) T cells consistent with T resident memory (TRM ) status...
September 5, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28819298/transcriptome-based-network-analysis-reveals-renal-cell-type-specific-dysregulation-of-hypoxia-associated-transcripts
#7
Natallia Shved, Gregor Warsow, Felix Eichinger, David Hoogewijs, Simone Brandt, Peter Wild, Matthias Kretzler, Clemens D Cohen, Maja T Lindenmeyer
Accumulating evidence suggests that dysregulation of hypoxia-regulated transcriptional mechanisms is involved in development of chronic kidney diseases (CKD). However, it remains unclear how hypoxia-induced transcription factors (HIFs) and subsequent biological processes contribute to CKD development and progression. In our study, genome-wide expression profiles of more than 200 renal biopsies from patients with different CKD stages revealed significant correlation of HIF-target genes with eGFR in glomeruli and tubulointerstitium...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798764/root-transcriptomic-analysis-revealing-the-importance-of-energy-metabolism-to-the-development-of-deep-roots-in-rice-oryza-sativa-l
#8
Qiaojun Lou, Liang Chen, Hanwei Mei, Kai Xu, Haibin Wei, Fangjun Feng, Tiemei Li, Xiaomeng Pang, Caiping Shi, Lijun Luo, Yang Zhong
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28745372/systems-level-organization-of-non-alcoholic-fatty-liver-disease-progression-network
#9
K Shubham, L Vinay, P K Vinod
Non-Alcoholic Fatty Liver Disease (NAFLD) is a complex spectrum of diseases ranging from simple steatosis to Non-Alcoholic Steatohepatitis (NASH) with fibrosis, which can progress to cirrhosis and hepatocellular carcinoma. The pathogenesis of NAFLD is complex, involving crosstalk between multiple organs, cell-types, and environmental and genetic factors. Dysfunction of the adipose tissue plays a central role in NAFLD progression. Here, we analysed transcriptomics data obtained from the Visceral Adipose Tissue (VAT) of NAFLD patients to understand how the VAT metabolism is altered at the genome scale and co-regulated with other cellular processes during the progression from obesity to NASH with fibrosis...
August 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28710486/comprehensive-transcriptomics-and-proteomics-analyses-of-pollinated-and-parthenocarpic-litchi-litchi-chinensis-sonn-fruits-during-early-development
#10
Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Nonghui Jiang, Junsheng Zhao, Shuaipeng Ma, Xu Xiang
Litchi (Litchi chinensis Sonn.) is an important fruit that is widely cultivated in tropical and subtropical areas. In this study, we used RNA-Seq and iTRAQ technologies to compare the transcriptomes and proteomes of pollinated (polLFs) and parthenocarpic (parLFs) litchi fruits during early development (1 day, 2 days, 4 days and 6 days). We identified 4,864 DEGs in polLFs and 3,672 in parLFs, of which 2,835 were shared and 1,051 were specifically identified in parLFs. Compared to po1LFs, 768 DEGs were identified in parLFs...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693416/whole-transcriptome-analysis-delineates-the-human-placenta-gene-network-and-its-associations-with-fetal-growth
#11
Maya A Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J Marsit, Jia Chen
BACKGROUND: The placenta is the principal organ regulating intrauterine growth and development, performing critical functions on behalf of the developing fetus. The delineation of functional networks and pathways driving placental processes has the potential to provide key insight into intrauterine perturbations that result in adverse birth as well as later life health outcomes. RESULTS: We generated the transcriptome-wide profile of 200 term human placenta using the Illumina HiSeq 2500 platform and characterized the functional placental gene network using weighted gene coexpression network analysis (WGCNA)...
July 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28663367/genome-wide-temporal-profiling-of-transcriptome-and-open-chromatin-of-early-cardiomyocyte-differentiation-derived-from-hipscs-and-hescs
#12
Qing Liu, Chao Jiang, Jin Xu, Ming-Tao Zhao, Kevin Van Bortle, Xun Cheng, Guangwen Wang, Howard Y Chang, Joseph C Wu, Michael P Snyder
RATIONALE: Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited. OBJECTIVE: To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs...
August 4, 2017: Circulation Research
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#13
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28566751/establishment-of-the-model-system-between-phytochemicals-and-gene-expression-profiles-in-macrosclereid-cells-of-medicago-truncatula
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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