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https://www.readbyqxmd.com/read/29228631/identification-of-differentially-expressed-genes-lncrnas-and-mirnas-which-are-associated-with-tumor-malignant-phenotypes-in-hepatoblastoma-patients
#1
Sida Liu, Fujing Xie, Xiaohong Xiang, Sinan Liu, Shunbin Dong, Kai Qu, Ting Lin
Hepatoblastoma (HB) is one of the most common hepatic malignancies in the pediatric population. HB are composed of a variety of tumors, which derived from different origins and had varying clinical outcomes. However, the unclear underlying mechanisms of HB limited exploring novel biomarkers and effective therapeutic targets. We searched microarray datasets on Gene Expression Omnibus (GEO) database and selected GSE75271 and GSE75283 datasets for comprehensive analysis. Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226034/constructing-a-comprehensive-gene-co-expression-based-interactome-in-bos-taurus
#2
Yan Chen, Yining Liu, Min Du, Wengang Zhang, Ling Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Lingyang Xu, Junya Li, Min Zhao
Integrating genomic information into cattle breeding is an important approach to exploring genotype-phenotype relationships for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully understand and identify the functional relevant genes. To this end, we constructed a co-expression analysis of 92 tissues and this represents the systematic exploration of gene-gene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5,000 protein-coding genes with majority variations in expression across 92 tissues...
2017: PeerJ
https://www.readbyqxmd.com/read/29212967/integrated-bioinformatics-analysis-predicts-the-key-genes-involved-in-aortic-valve-calcification-from-hemodynamic-changes-to-extracellular-remodeling
#3
Mu Liu, Ming Luo, Haoliang Sun, Buqing Ni, Yongfeng Shao
In our aging world, increasing numbers of people are suffering from calcific aortic valve disease (CAVD). In this study, we used integrated bioinformatics analysis to predict several key genes that are involved in the initiation and progression of CAVD. Expression profiles of 15 calcific and 14 normal human aortic valve samples were generated from two gene expression datasets (GSE12644 and GSE51472). Dataset GSE26953 from the human aortic valve fibrosa-derived endothelial cells cultured under laminar or oscillatory shear stress was also evaluated...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29202516/-weighted-gene-co-expression-network-analysis-in-biomedicine-research
#4
Wei Liu, Li Li, Hua Ye, Wei Tu
High-throughput biological technologies are now widely applied in biology and medicine, allowing scientists to monitor thousands of parameters simultaneously in a specific sample. However, it is still an enormous challenge to mine useful information from high-throughput data. The emergence of network biology provides deeper insights into complex bio-system and reveals the modularity in tissue/cellular networks. Correlation networks are increasingly used in bioinformatics applications. Weighted gene co-expression network analysis (WGCNA) tool can detect clusters of highly correlated genes...
November 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29199037/potential-role-of-lncrnas-in-contributing-to-pathogenesis-of-chronic-glomerulonephritis-based-on-microarray-data
#5
Jia-Rong Gao, Xiu-Juan Qin, Hui Jiang, Ya-Chen Gao, Ming-Fei Guo, Nan-Nan Jiang
BACKGROUND: Chronic glomerulonephritis (CGN) is the most common form of primary glomerular disease with unclear molecular mechanisms, which related to immune-mediated inflammatory diseases. Our study intended to identify potential long non-coding RNAs (lncRNAs) and genes, and to determine the potential molecular mechanisms of CGN pathogenesis. METHODS: The microarray of GSE64265 and GSE46295 were downloaded from the Gene Expression Omnibus database, GSE64265 including 3 rats control kidney tissues and 5 rats model kidney tissues, GSE46295 including 3 rats control kidney tissues and 3 rats model kidney tissues, which was on the basis of GPL1355 platform...
November 30, 2017: Gene
https://www.readbyqxmd.com/read/29196862/voluntary-exposure-to-a-toxin-the-genetic-influence-on-ethanol-consumption
#6
Paula L Hoffman, Laura M Saba, Lauren A Vanderlinden, Boris Tabakoff
Ethyl alcohol is a toxin that, when consumed at high levels, produces organ damage and death. One way to prevent or ameliorate this damage in humans is to reduce the exposure of organs to alcohol by reducing alcohol ingestion. Both the propensity to consume large volumes of alcohol and the susceptibility of human organs to alcohol-induced damage exhibit a strong genetic influence. We have developed an integrative genetic/genomic approach to identify transcriptional networks that predispose complex traits, including propensity for alcohol consumption and propensity for alcohol-induced organ damage...
December 1, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29189710/non-additive-transcriptomic-responses-to-inoculation-with-rhizobia-in-a-young-allopolyploid-compared-with-its-diploid-progenitors
#7
Adrian F Powell, Jeff J Doyle
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2...
November 30, 2017: Genes
https://www.readbyqxmd.com/read/29188613/-exploration-of-common-biological-pathways-for-attention-deficit-hyperactivity-disorder-and-low-birth-weight
#8
Bo Xiang, Minglan Yu, Xuemei Liang, Wei Lei, Chaohua Huang, Jing Chen, Wenying He, Tao Zhang, Tao Li, Kezhi Liu
OBJECTIVE: To explore common biological pathways for attention deficit hyperactivity disorder (ADHD) and low birth weight (LBW). METHODS: Thei-Gsea4GwasV2 software was used to analyze the result of genome-wide association analysis (GWAS) for LBW (pathways were derived from Reactome), and nominally significant (P< 0.05, FDR< 0.25) pathways were tested for replication in ADHD.Significant pathways were analyzed with DAPPLE and Reatome FI software to identify genes involved in such pathways, with each cluster enriched with the gene ontology (GO)...
December 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29186495/sugar-metabolism-reprogramming-in-a-non-climacteric-bud-mutant-of-a-climacteric-plum-fruit-during-development-on-the-tree
#9
Macarena Farcuh, Bosheng Li, Rosa M Rivero, Lyudmila Shlizerman, Avi Sadka, Eduardo Blumwald
We investigated sugar metabolism in leaves and fruits of two Japanese plum (Prunus salicina Lindl.) cultivars, the climacteric Santa Rosa and its bud sport mutant the non-climacteric Sweet Miriam, during development on the tree. We previously characterized differences between the two cultivars. Here, we identified key sugar metabolic pathways. Pearson coefficient correlations of metabolomics and transcriptomic data and weighted gene co-expression network analysis (WGCNA) of RNA sequencing (RNA-Seq) data allowed the identification of 11 key sugar metabolism-associated genes: sucrose synthase, sucrose phosphate synthase, cytosolic invertase, vacuolar invertase, invertase inhibitor, α-galactosidase, β-galactosidase, galactokinase, trehalase, galactinol synthase, and raffinose synthase...
November 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29180012/weighted-gene-co-expression-network-analysis-reveals-potential-genes-involved-in-early-metamorphosis-process-in-sea-cucumber-apostichopus-japonicus
#10
Yongxin Li, Mani Kikuchi, Xueyan Li, Qionghua Gao, Zijun Xiong, Yandong Ren, Ruoping Zhao, Bingyu Mao, Mariko Kondo, Naoki Irie, Wen Wang
Sea cucumbers, one main class of Echinoderms, have a very fast and drastic metamorphosis process during their development. However, the molecular basis under this process remains largely unknown. Here we systematically examined the gene expression profiles of Japanese common sea cucumber (Apostichopus japonicus) for the first time by RNA sequencing across 16 developmental time points from fertilized egg to juvenile stage. Based on the weighted gene co-expression network analysis (WGCNA), we identified 21 modules...
November 24, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29177853/bioinformatic-assessment-of-macrophage-activation-by-the-innate-immune-system
#11
Thomas Ulas, Joachim L Schultze, Marc Beyer
Weighted gene co-expression network analysis (WGCNA) allows for the identification and characterization of cell type-specific gene modules in complex transcriptome datasets. Here, we use a microarray dataset of human macrophages comprising 29 conditions and 299 samples generated by differentiation of CD14+ monocytes into macrophages followed by in vitro stimulations to identify stimulation-specific gene modules. These gene modules can be used for experimental validation, as well as further bioinformatic analysis to determine key pathways or upstream transcription factors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29170883/identification-of-key-gene-modules-and-pathways-of-human-breast-cancer-by-co-expression-analysis
#12
Qingnan Zhao, Wenqing Song, Dai Yu He, YanSong Li
BACKGROUND: Breast cancer is the most common and aggressive tumor causing injury to women world wide. Although gene expression analysis had been performed previously, systemic co-expression analysis for this cancer is still lacking to date. We attempted to identify the critical modules of breast cancer. METHODS: Co-expression modules were established with the help of WGCNA and the interactions among them were performed by R language. Biological process and pathways analysis of co-expression genes were figured out by GO and KEGG functional enrichment analysis using DAVID dataset...
November 23, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29170526/driver-pattern-identification-over-the-gene-co-expression-of-drug-response-in-ovarian-cancer-by-integrating-high-throughput-genomics-data
#13
Xinguo Lu, Jibo Lu, Bo Liao, Xing Li, Xin Qian, Keqin Li
Multiple types of high throughput genomics data create a potential opportunity to identify driver patterns in ovarian cancer, which will acquire some novel and clinical biomarkers for appropriate diagnosis and treatment to cancer patients. To identify candidate driver genes and the corresponding driving patterns for resistant and sensitive tumors from the heterogeneous data, we combined gene co-expression modules with mutation modulators and proposed the method to identify driver patterns. Firstly, co-expression network analysis is applied to explore gene modules for gene expression profiles through weighted correlation network analysis (WGCNA)...
November 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29166861/comprehensive-transcriptome-analysis-reveals-distinct-regulatory-programs-during-vernalization-and-floral-bud-development-of-orchardgrass-dactylis-glomerata-l
#14
Guangyan Feng, Linkai Huang, Ji Li, Jianping Wang, Lei Xu, Ling Pan, Xinxin Zhao, Xia Wang, Ting Huang, Xinquan Zhang
BACKGROUND: Vernalization and the transition from vegetative to reproductive growth involve multiple pathways, vital for controlling floral organ formation and flowering time. However, little transcription information is available about the mechanisms behind environmental adaption and growth regulation. Here, we used high-throughput sequencing to analyze the comprehensive transcriptome of Dactylis glomerata L. during six different growth periods. RESULTS: During vernalization, 4689 differentially expressed genes (DEGs) significantly increased in abundance, while 3841 decreased...
November 22, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29151593/gene-expression-profiles-indicate-tissue-specific-obesity-regulation-changes-and-strong-obesity-relevant-tissues
#15
R-H Hao, T-L Yang, Y Rong, S Yao, S-S Dong, H Chen, Y Guo
BACKGROUND: With the growing evidence that other tissues, apart from adipose, could have strong relevance to obesity, it is necessary to comprehensively understand the relationship between obesity and other tissues, and to point out the most relevant tissues. METHODS: There were 549 participants with 20 different tissue types involved in this study. We firstly employed both Spearman's correlation test and weighted correlation network analysis (WGCNA) to identify BMI-related genes...
November 20, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29146547/a-gene-module-associated-with-dysregulated-tcr-signaling-pathways-in-cd4-t-cell-subsets-in-rheumatoid-arthritis
#16
Shuji Sumitomo, Yasuo Nagafuchi, Yumi Tsuchida, Haruka Tsuchiya, Mineto Ota, Kazuyoshi Ishigaki, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Norio Hanata, Shoko Tateishi, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Keishi Fujio, Kazuhiko Yamamoto
We analyzed the transcriptome of detailed CD4(+) T cell subsets including them after abatacept treatment, and examined the difference among CD4(+) T cell subsets and identified gene sets that are closely associated disease activity and abatacept treatment. Seven CD4(+) T cell subsets (naive, Th1, Th17, Th1/17, nonTh1/17, Tfh and Treg) were sorted from PBMCs taken from 10 RA patients and 10 healthy controls, and three RA patients donated samples before and 6 months after abatacept treatment. Paired-end RNA sequencing was performed using HiSeq 2500...
November 13, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29145611/identification-of-novel-potentially-pleiotropic-variants-associated-with-osteoporosis-and-obesity-using-cfdr-method
#17
Yuan Hu, Li-Jun Tan, Xiang-Ding Chen, Zhen Liu, Shi-Shi Min, Qin Zeng, Hui Shen, Hong-Wen Deng
Context: Genome-wide association studies (GWASs) have been successful in identifying loci associated with osteoporosis and obesity. However, the findings just explain a small fraction of the total genetic variance. Objective: The aim of this study was to identify novel pleiotropic genes important in osteoporosis and obesity. Design and Setting: A pleiotropic conditional false discovery rate (cFDR) method was applied to three independent GWAS summary statistics of femoral neck bone mineral density (FN BMD), body mass index (BMI) and waist-hip ratio (WHR)...
November 14, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29145449/estimation-of-the-proteomic-cancer-co-expression-sub-networks-by-using-association-estimators
#18
Cihat Erdoğan, Zeyneb Kurt, Banu Diri
In this study, the association estimators, which have significant influences on the gene network inference methods and used for determining the molecular interactions, were examined within the co-expression network inference concept. By using the proteomic data from five different cancer types, the hub genes/proteins within the disease-associated gene-gene/protein-protein interaction sub networks were identified. Proteomic data from various cancer types is collected from The Cancer Proteome Atlas (TCPA). Correlation and mutual information (MI) based nine association estimators that are commonly used in the literature, were compared in this study...
2017: PloS One
https://www.readbyqxmd.com/read/29145252/identifications-of-potential-therapeutic-targets-and-drugs-in-angiotensin-ii-induced-hypertension
#19
Xiaoli Wu, Ruihua Fan
This study aimed to identify the underlying therapeutic targets of angiotensin II (AngII)-induced hypertension, and screen the related drugs.The gene expression profiles of GSE93579 and GSE75815 were used to identify differentially expressed genes (DEGs) between AngII-induced hypertension and control samples based on meta-analysis. These DEGs were analyzed using Gene-Ontology (GO) function and pathway enrichment methods. Subsequently, the weighed gene coexpression network analysis (WGCNA)-based meta-analysis was applied to determine transcriptional signature with DEGs...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29132311/weighted-gene-co-expression-network-analysis-of-expression-data-of-monozygotic-twins-identifies-specific-modules-and-hub-genes-related-to-bmi
#20
Weijing Wang, Wenjie Jiang, Lin Hou, Haiping Duan, Yili Wu, Chunsheng Xu, Qihua Tan, Shuxia Li, Dongfeng Zhang
BACKGROUND: The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. RESULTS: In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings...
November 13, 2017: BMC Genomics
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