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https://www.readbyqxmd.com/read/28321948/gene-networks-show-associations-with-seed-region-connectivity
#1
Marie Forest, Yasser Iturria-Medina, Jennifer S Goldman, Claudia L Kleinman, Amanda Lovato, Kathleen Oros Klein, Alan Evans, Antonio Ciampi, Aurélie Labbe, Celia M T Greenwood
Primary patterns in adult brain connectivity are established during development by coordinated networks of transiently expressed genes; however, neural networks remain malleable throughout life. The present study hypothesizes that structural connectivity from key seed regions may induce effects on their connected targets, which are reflected in gene expression at those targeted regions. To test this hypothesis, analyses were performed on data from two brains from the Allen Human Brain Atlas, for which both gene expression and DW-MRI were available...
March 21, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28287180/functional-interactors-of-three-genome-wide-association-study-genes-are-differentially-expressed-in-severe-chronic-obstructive-pulmonary-disease-lung-tissue
#2
Jarrett D Morrow, Xiaobo Zhou, Taotao Lao, Zhiqiang Jiang, Dawn L DeMeo, Michael H Cho, Weiliang Qiu, Suzanne Cloonan, Victor Pinto-Plata, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Augustine M K Choi, Edwin K Silverman, Craig P Hersh
In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28283027/integrated-analysis-of-genetic-behavioral-and-biochemical-data-implicates-neural-stem-cell-induced-changes-in-immunity-neurotransmission-and-mitochondrial-function-in-dementia-with-lewy-body-mice
#3
Anita Lakatos, Natalie R S Goldberg, Mathew Blurton-Jones
We previously demonstrated that transplantation of murine neural stem cells (NSCs) can improve motor and cognitive function in a transgenic model of Dementia with Lewy Bodies (DLB). These benefits occurred without changes in human α-synuclein pathology and were mediated in part by stem cell-induced elevation of brain-derived neurotrophic factor (BDNF). However, instrastriatal NSC transplantation likely alters the brain microenvironment via multiple mechanisms that may synergize to promote cognitive and motor recovery...
March 10, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28266556/integrative-diffusion-weighted-imaging-and-radiogenomic-network-analysis-of-glioblastoma-multiforme
#4
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/28260099/identification-of-prognostic-genes-in-kidney-renal-clear-cell-carcinoma-by-rna%C3%A2-seq-data-analysis
#5
Yanqin Gu, Linfeng Lu, Lingfeng Wu, Hao Chen, Wei Zhu, Yi He
The present study aimed to analyze RNA-seq data of kidney renal clear cell carcinoma (KIRC) to identify prognostic genes. RNA‑seq data were downloaded from The Cancer Genome Atlas. Feature genes with a coefficient of variation (CV) >0.5 were selected using the genefilter package in R. Gene co‑expression networks were constructed with the WGCNA package. Cox regression analysis was performed using the survive package. Furthermore, a functional enrichment analysis was conducted using Database for Annotation, Visualization and Integrated Discovery tools...
February 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28259920/identification-of-the-key-genes-implicated-in-the-transformation-of-olp-to-oscc-using-rna-sequencing
#6
Qiaozhen Yang, Bin Guo, Hongying Sun, Jie Zhang, Shangfeng Liu, Saiyin Hexige, Xuedi Yu, Xiaxia Wang
Oral lichen planus (OLP) is a chronic inflammatory disease that may transform to oral squamous cell carcinoma (OSCC), while its carcinogenesis mechanisms are not entirely clear. This study was designed to identify the important genes involved in the malignant transformation of OLP to OSCC. After RNA-sequencing, the differently expressed genes (DEGs) in OLP vs. normal and OSCC vs. normal groups, respectively, were identified by limma package in R language, and then clustering analysis were conducted by Pheatmap package in R language...
March 2, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28205147/identification-of-candidate-mirna-biomarkers-for-pancreatic-ductal-adenocarcinoma-by-weighted-gene-co-expression-network-analysis
#7
M Giulietti, G Occhipinti, G Principato, F Piva
PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a dismal prognosis which is, among others, due to a lack of suitable biomarkers and therapeutic targets. Previously, basic gene expression analysis methods have been used for their identification, but recently new algorithms have been developed allowing more comprehensive data analyses. Among them, weighted gene co-expression network analysis (WGCNA) has already been applied to several cancer types with promising results...
February 15, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28203405/weighted-gene-co-expression-network-analysis-in-identification-of-metastasis-related-genes-of-lung-squamous-cell-carcinoma-based-on-the-cancer-genome-atlas-database
#8
Feng Tian, Jinlong Zhao, Xinlei Fan, Zhenxing Kang
BACKGROUND: Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. METHODS: We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis...
January 2017: Journal of Thoracic Disease
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
#9
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/28109426/wgcna-application-to-proteomic-and-metabolomic-data-analysis
#10
G Pei, L Chen, W Zhang
Progresses in mass spectrometric instrumentation and bioinformatics identification algorithms made over the past decades allow quantitative measurements of relative or absolute protein/metabolite amounts in cells in a high-throughput manner, which has significantly expedited the exploration into functions and dynamics of complex biological systems. However, interpretation of high-throughput data is often restricted by the limited availability of suitable computational methods and enough statistical power. While many computational methodologies have been developed in the past decades to address the issue, it becomes clear that network-focused rather than individual gene/protein-focused strategies would be more appropriate to obtain a complete picture of cellular responses...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28104750/gene-networks-in-skeletal-muscle-following-endurance-exercise-are-co-expressed-in-blood-neutrophils-and-linked-with-blood-inflammation-markers
#11
James A Broadbent, Dayle Sampson, Surendran Sabapathy, Luke J Haseler, Karl-Heinz Wagner, Andrew Cameron 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 h, 48 h 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...
January 19, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28098893/systematic-analysis-of-microarray-datasets-to-identify-parkinson-s-disease%C3%A2-associated-pathways-and-genes
#12
Yinling Feng, Xuefeng Wang
In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28018242/network-analysis-based-approach-for-exploring-the-potential-diagnostic-biomarkers-of-acute-myocardial-infarction
#13
Jiaqi Chen, Ling Yu, Siwei Zhang, Xia Chen
Acute myocardial infarction (AMI) is a severe cardiovascular disease that is a serious threat to human life. However, the specific diagnostic biomarkers have not been fully clarified and candidate regulatory targets for AMI have not been identified. In order to explore the potential diagnostic biomarkers and possible regulatory targets of AMI, we used a network analysis-based approach to analyze microarray expression profiling of peripheral blood in patients with AMI. The significant differentially-expressed genes (DEGs) were screened by Limma and constructed a gene function regulatory network (GO-Tree) to obtain the inherent affiliation of significant function terms...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27984699/gene-expression-correlated-to-severe-asthma-characteristics-reveals-heterogeneous-mechanisms-of-severe-disease
#14
Brian D Modena, Eugene R Bleecker, William W Busse, Serpil C Erzurum, Benjamin M Gaston, Nizar N Jarjour, Deborah A Meyers, Jadranka Milosevic, John R Tedrow, Wei Wu, Naftali Kaminski, Sally E Wenzel
RATIONALE: Severe asthma is a heterogeneous disease with multiple molecular mechanisms. Gene expression studies of asthmatic bronchial epithelial cells have provided biological insight and underscored possible mechanistic differences between individuals. OBJECTIVE: Identify networks of genes reflective of underlying biological processes that define severe asthma(SA). METHODS: Airway epithelial cell gene expression from 155 asthmatics and healthy controls(HC) in the Severe Asthma Research Program was analyzed by weighted gene co-expression network analysis (WGCNA) to identify gene networks and profiles associated with severe asthma and its specific characteristics (i...
December 16, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27982099/co-expression-analysis-and-identification-of-fecundity-related-long-non-coding-rnas-in-sheep-ovaries
#15
Xiangyang Miao, Qingmiao Luo, Huijing Zhao, Xiaoyu Qin
Small Tail Han sheep, including the FecB(B)FecB(B) (Han BB) and FecB(+) FecB(+) (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27959337/peripheral-blood-gene-expression-profiles-linked-to-monoamine-metabolite-levels-in-cerebrospinal-fluid
#16
J J Luykx, L M Olde Loohuis, M Neeleman, E Strengman, S C Bakker, E Lentjes, P Borgdorff, E P A van Dongen, P Bruins, R S Kahn, S Horvath, S de Jong, R A Ophoff
The blood-brain barrier separates circulating blood from the central nervous system (CNS). The scope of this barrier is not fully understood which limits our ability to relate biological measurements from peripheral to central phenotypes. For example, it is unknown to what extent gene expression levels in peripheral blood are reflective of CNS metabolism. In this study, we examine links between central monoamine metabolite levels and whole-blood gene expression to better understand the connection between peripheral systems and the CNS...
December 13, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27933543/integrative-analysis-of-genetic-genomic-and-phenotypic-data-for-ethanol-behaviors-a-network-based-pipeline-for-identifying-mechanisms-and-potential-drug-targets
#17
James W Bogenpohl, Kristin M Mignogna, Maren L Smith, Michael F Miles
Complex behavioral traits, such as alcohol abuse, are caused by an interplay of genetic and environmental factors, producing deleterious functional adaptations in the central nervous system. The long-term behavioral consequences of such changes are of substantial cost to both the individual and society. Substantial progress has been made in the last two decades in understanding elements of brain mechanisms underlying responses to ethanol in animal models and risk factors for alcohol use disorder (AUD) in humans...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27907186/inter-tissue-gene-co-expression-networks-between-metabolically-healthy-and-unhealthy-obese-individuals
#18
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
#19
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/27896962/adaptive-testing-of-snp-brain-functional-connectivity-association-via-a-modular-network-analysis
#20
Chen Gao, Junghi Kim, Wei Pan
Due to its high dimensionality and high noise levels, analysis of a large brain functional network may not be powerful and easy to interpret; instead, decomposition of a large network into smaller subcomponents called modules may be more promising as suggested by some empirical evidence. For example, alteration of brain modularity is observed in patients suffering from various types of brain malfunctions. Although several methods exist for estimating brain functional networks, such as the sample correlation matrix or graphical lasso for a sparse precision matrix, it is still difficult to extract modules from such network estimates...
2016: Pacific Symposium on Biocomputing
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