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https://www.readbyqxmd.com/read/28819298/transcriptome-based-network-analysis-reveals-renal-cell-type-specific-dysregulation-of-hypoxia-associated-transcripts
#1
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/28799567/identification-of-breast-cancer-mechanism-based-on-weighted-gene-coexpression-network-analysis
#2
X Guo, H Xiao, S Guo, L Dong, J Chen
Our gene expression-profiling analysis aimed to explain the mechanism of breast cancer development by identifying key pathways and constructing networks of related transcription factors (TFs) and microRNAs (miRNAs) in breast cancer tissues. Gene expression profiles of normal and breast cancer tissues were downloaded to identify differentially expressed genes (DEGs). Coexpression modules were explored using weighted gene coexpression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to discover the enriched functionally associated gene groups and define pathways in breast cancer, respectively...
August 11, 2017: Cancer Gene Therapy
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
#3
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/28782835/identification-and-functional-analysis-of-a-potential-key-lncrna-involved-in-fat-loss-of-cancer-cachexia
#4
Huiquan Liu, Ting Zhou, Bangyan Wang, Lu Li, Dawei Ye, Shiying Yu
Cancer cachexia is a devastating, multifactorial and irreversible syndrome characterized by skeletal muscle reduction with or without fat loss. Although much attention has been focused on muscle wasting, fat loss may occur earlier and accelerate muscle wasting in cachexia. The cause of 20% of cancer related death makes it urgent to discover molecular mechanisms behind cancer cachexia. Here we applied weighted gene co-expression network analysis(WGCNA) to identify cachexia related gene modules using differentially expressed 3289 genes and 59 long non-coding RNAs based on microarray data of cachectic and non-cachectic subcutaneous adipose tissue...
August 7, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28776273/combining-metabolomics-and-network-analysis-to-improve-tacrolimus-production-in-streptomyces-tsukubaensis-using-different-exogenous-feedings
#5
Cheng Wang, Jiao Liu, Huanhuan Liu, Shaoxiong Liang, Jianping Wen
Tacrolimus is widely used as an immunosuppressant in the treatment of various autoimmune diseases. However, the low fermentation yield of tacrolimus has thus far restricted its industrial applications. To solve this problem, the time-series response mechanisms of the intracellular metabolism that were highly correlated with tacrolimus biosynthesis were investigated using different exogenous feeding strategies in S. tsukubaensis. The metabolomic datasets, which contained 93 metabolites, were subjected to weighted correlation network analysis (WGCNA), and eight distinct metabolic modules and seven hub metabolites were identified to be specifically associated with tacrolimus biosynthesis...
August 3, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28745372/systems-level-organization-of-non-alcoholic-fatty-liver-disease-progression-network
#6
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...
July 26, 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
#7
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
#8
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/28684781/characterization-of-transcriptional-modules-related-to-fibrosing-nafld-progression
#9
Yi Lou, Guo-Yan Tian, Yu Song, Yin-Lan Liu, Yi-Dan Chen, Jun-Ping Shi, Jin Yang
Based on the severity of liver fibrosis, low or high-risk profile of developing end-stage liver disease was present in nonalcoholic fatty liver disease (NAFLD). However, the mechanisms inducing transition from mild to advanced NAFLD are still elusive. We performed a system-level study on fibrosing-NAFLD by weighted gene co-expression network analysis (WGCNA) to identify significant modules in the network, and followed by functional and pathway enrichment analyses. Moreover, hub genes in the module were analyzed by network feature selection...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28669080/identification-of-potential-gene-network-associated-with-hcv-related-hepatocellular-carcinoma-using-microarray-analysis
#10
Yang Cheng, Jian Ping, Jianjie Chen
In order to identify potential specific gene networks of Hepatitis C virus (HCV) related hepatocellular carcinoma (HCC), weighted gene co-expression network analysis (WGCNA) was performed, which may provide an insight into the potential mechanism of the HCC development. HCV-related HCC and normal sample data were downloaded from GEO, T test of limma package was used to screen different expression genes (DEGs); KEGG pathway was used to analyze related biochemical pathways, and WGCNA was used to construct clustering trees and screen hub genes in the HCC-specific modules...
July 1, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28663367/genome-wide-temporal-profiling-of-transcriptome-and-open-chromatin-of-early-cardiomyocyte-differentiation-derived-from-hipscs-and-hescs
#11
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
#12
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/28592500/epistatic-networks-jointly-influence-phenotypes-related-to-metabolic-disease-and-gene-expression-in-diversity-outbred-mice
#13
Anna L Tyler, Bo Ji, Daniel M Gatti, Steven C Munger, Gary A Churchill, Karen L Svenson, Gregory W Carter
Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice...
June 2017: Genetics
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/28562334/gene-co-expression-network-reveals-shared-modules-predictive-of-stage-and-grade-in-serous-ovarian-cancers
#15
Qian Sun, Haiyue Zhao, Cong Zhang, Ting Hu, Jianli Wu, Xingguang Lin, Danfeng Luo, Changyu Wang, Li Meng, Ling Xi, Kezhen Li, Junbo Hu, Ding Ma, Tao Zhu
Serous ovarian cancer (SOC) is the most lethal gynecological cancer. Clinical studies have revealed an association between tumor stage and grade and clinical prognosis. Identification of meaningful clusters of co-expressed genes or representative biomarkers related to stage or grade may help to reveal mechanisms of tumorigenesis and cancer development, and aid in predicting SOC patient prognosis. We therefore performed a weighted gene co-expression network analysis (WGCNA) and calculated module-trait correlations based on three public microarray datasets (GSE26193, GSE9891, and TCGA), which included 788 samples and 10402 genes...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28558655/the-common-transcriptional-subnetworks-of-the-grape-berry-skin-in-the-late-stages-of-ripening
#16
Ryan Ghan, Juli Petereit, Richard L Tillett, Karen A Schlauch, David Toubiana, Aaron Fait, Grant R Cramer
BACKGROUND: Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS: To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed...
May 30, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28542617/inflammatory-and-apoptotic-remodeling-in-autonomic-nervous-system-following-myocardial-infarction
#17
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/28529955/identification-of-transcriptional-modules-and-key-genes-in-chickens-infected-with-salmonella-enterica-serovar-pullorum-using-integrated-coexpression-analyses
#18
Bao-Hong Liu, Jian-Ping Cai
Salmonella enterica Pullorum is one of the leading causes of mortality in poultry. Understanding the molecular response in chickens in response to the infection by S. enterica is important in revealing the mechanisms of pathogenesis and disease progress. There have been studies on identifying genes associated with Salmonella infection by differential expression analysis, but the relationships among regulated genes have not been investigated. In this study, we employed weighted gene coexpression network analysis (WGCNA) and differential coexpression analysis (DCEA) to identify coexpression modules by exploring microarray data derived from chicken splenic tissues in response to the S...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28525545/gene-co-expression-network-analysis-for-identifying-modules-and-functionally-enriched-pathways-in-sca2
#19
Lance T Pflieger, Warunee Dansithong, Sharan Paul, Daniel Scoles, Karla P Figueroa, Pratap Meera, Thomas S Otis, Julio C Facelli, Stefan M Pulst
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the ATXN2 gene. The repeat resides in an encoded region of the gene resulting in polyglutamine (polyQ) expansion which has been assumed to result in gain of function, predominantly, for the ATXN2 protein. We evaluated temporal cerebellar expression profiles by RNA sequencing of ATXN2Q127 mice vs wildtype littermates. ATXN2Q127 mice are characterized by a progressive motor phenotype onset, and have progressive cerebellar molecular and neurophysiological (Purkinje cell firing frequency) phenotypes...
May 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28477104/using-scale-and-feather-traits-for-module-construction-provides-a-functional-approach-to-chicken-epidermal-development
#20
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
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