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https://www.readbyqxmd.com/read/28710486/comprehensive-transcriptomics-and-proteomics-analyses-of-pollinated-and-parthenocarpic-litchi-litchi-chinensis-sonn-fruits-during-early-development
#1
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
#2
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
#3
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
#4
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
#5
Qing Liu, Chao Jiang, Jin Xu, Mingtao 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 (i.e. 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. Methods and Results: We profiled the temporal changes in transcriptome and chromatin accessibility at genome-wide levels during cardiomyocyte differentiation derived from two hiPSC lines and two hESC lines at four stages: pluripotent stem cells, mesoderm, cardiac mesoderm, and differentiated cardiomyocytes...
June 29, 2017: Circulation Research
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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/28467779/identification-of-a-rna-seq-based-prognostic-signature-with-five-lncrnas-for-lung-squamous-cell-carcinoma
#16
Rui-Xue Tang, Wen-Jie Chen, Rong-Quan He, Jiang-Hui Zeng, Liang Liang, Shi-Kang Li, Jie Ma, Dian-Zhong Luo, Gang Chen
Long non-coding RNAs (lncRNAs) expression profile signature for survival assessment in lung squamous cell carcinoma (LUSC) are largely inconsistent due to distinct detecting approaches and small sample size. Systematic and integrative investigation of RNA-Seq based data from The Cancer Genome Atlas (TCGA) herein was performed to determine candidate lncRNAs for prognosis evaluation of LUSC. A total of 60483 genes, including 7589 lncRNAs were assessed in a cohort including 478 LUSC cases with follow-up data. Firstly, 4225 differentially expressed lncRNAs were obtained via R packages...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28460420/identification-of-key-gene-modules-of-neuropathic-pain-by-co-expression-analysis
#17
Yang Zhang, Jinlin Wang, Li-Juan Ji, Lin Li, Meng Wei, Su Zhen, Cheng-Cai Wen
Neuropathic pain (NP) is a substantial clinical problem causing great injury to people word-widely. Although gene expression analyses had been performed previously, the mechanisms underlying the etiology and development of NP are still poorly understood. To understand the function genes involved in the etiology and development of NP, we built the co-expression modules and performed function enrichment analysis for neuropathic pain. In the present study, from a public microarray data set (GSE69901) from NCBI, gene co-expression modules were contributed with the help of WGCNA for 12 neuropathic pain samples and 13 control samples, respectively...
April 29, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28444190/biological-aging-and-the-human-gut-microbiota
#18
Vincent J Maffei, Sangkyu Kim, Eugene Blanchard, Meng Luo, S Michal Jazwinski, Christopher M Taylor, David A Welsh
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity...
April 25, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28440393/identification-of-key-genes-associated-with-schmid-type-metaphyseal-chondrodysplasia-based-on-microarray-data
#19
Bing Wang, Li He, Wusheng Miao, Ge Wu, Hai Jiang, Yongtao Wu, Jining Qu, Min Li
This study aimed to gain a better understanding of the molecular circuitry of Schmid-type metaphyseal chondrodysplasia (SMCD), and to identify more potential genes associated with the pathogenesis of SMCD. Microarray data from GSE72261 were downloaded from the NCBI GEO database, including collagen X p.Asn617Lys knock-in mutation (ColXN617K), ablated XBP1 activity (Xbp1CartΔEx2), compound mutant (C/X), and wild-type (WT) specimens. Differentially expressed genes (DEGs) were screened in Xbp1 vs. WT, Col vs...
June 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28440025/identifying-key-genes-in-rheumatoid-arthritis-by-weighted-gene-co-expression-network-analysis
#20
Chunhui Ma, Qi Lv, Songsong Teng, Yinxian Yu, Kerun Niu, Chengqin Yi
PURPOSE: This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. METHODS: Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status...
April 25, 2017: International Journal of Rheumatic Diseases
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