Read by QxMD icon Read


Martin Sillesen, Theodore Bambakidis, Simone Dekker, Yongqing Li, Hasan B Alam
BACKGROUND: Resuscitation with Fresh Frozen Plasma (FFP) decreases brain lesion size and swelling in a swine model of Traumatic Brain Injury (TBI) and hemorrhagic shock (HS). We hypothesized that brain gene expression profiles following TBI+HS would be modulated by FFP resuscitation. STUDY DESIGN: 15 swine underwent a protocol of TBI and HS, two hours of shock followed by resuscitation with FFP, Normal Saline (NS) or hetastarch (Hextend, HEX, 5/group). After 6 hours, brain RNA was isolated and hybridized onto a Porcine Gene ST 1...
October 7, 2016: Journal of the American College of Surgeons
Amal Al-Garawi, Vincent J Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky-Su, Weiliang Qiu, Nancy Laranjo, Augusto A Litonjua, Scott T Weiss
BACKGROUND: Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. OBJECTIVE: Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels...
2016: PloS One
Xuelin Zhao, Hong Yu, Lingfeng Kong, Qi Li
The Pacific oyster Crassostrea gigas is a dominant aquaculture species in many intertidal zones throughout the Pacific and Atlantic Oceans and can tolerate a wide range of salinity. Studying the gene expression profiles of oyster gills had found differentially expressed genes (DEGs) involved in salinity tolerance. A systematic study of cellular response to salinity stress may provide insights into the mechanism of acquired salinity tolerance. Here, weighted gene co-expression network analysis (WGCNA) was carried out using RNA-seq data from gill transcriptome in response to different salinity...
October 4, 2016: Marine Biotechnology
Dieter Henrik Heiland, Theo Demerath, Elias Kellner, Valerij G Kiselev, Dietmar Pfeifer, Oliver Schnell, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
The purpose of this study was to investigate the molecular background of cerebral blood volume (CBV) and vessel size (VS) of capillaries in glioblastoma multiforme (GBM). Both parameters are derived from extended perfusion MR imaging.A prospective case study including 21 patients (median age 66 years, 10 females) was performed. Before operation, CBV and VS of contrast enhancing tumor were assessed. Tissue was sampled from the assessed areas under neuronavigation control. After RNA extraction, transcriptional data was analyzed by Weighted Gene Co-Expression Network Analysis (WGCNA) and split into modules based on its network affiliations...
August 23, 2016: Oncotarget
Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, Maria L Scattoni, Yuri Bozzi
Autism spectrum disorders (ASD) are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity, and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD; however, a comprehensive approach to identify transcriptional abnormalities in different ASD models has never been performed...
2016: Frontiers in Neuroscience
Marlin Touma, Xuedong Kang, Yan Zhao, Ashley A Cass, Fuying Gao, Reshma Biniwale, Giovanni Coppola, Xinshu Xiao, Brian Reemtsen, Yibin Wang
BACKGROUND: -Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated. METHODS AND RESULTS: -From comprehensive analysis of transcriptomes derived from neonatal mouse heart left and right ventricles, a total of 45,167 unique transcripts were identified, including 21,916 known and 2,033 novel lncRNAs...
September 2, 2016: Circulation. Cardiovascular Genetics
Juan Chen, Hai-Tao Yang, Zhu Li, Ning Xu, Bo Yu, Jun-Ping Xu, Pei-Ge Zhao, Yan Wang, Xiu-Juan Zhang, Dian-Jie Lin
Studies that only assess differentially-expressed (DE) genes do not contain the information required to investigate the mechanisms of diseases. A complete knowledge of all the direct and indirect interactions between proteins may act as a significant benchmark in the process of forming a comprehensive description of cellular mechanisms and functions. The results of protein interaction network studies are often inconsistent and are based on various methods. In the present study, a combined network was constructed using selected gene pairs, following the conversion and combination of the scores of gene pairs that were obtained across multiple approaches by a novel algorithm...
September 2016: Oncology Letters
Kathleen Oros Klein, Karim Oualkacha, Marie-Hélène Lafond, Sahir Bhatnagar, Patricia N Tonin, Celia M T Greenwood
In a variety of solid cancers, missense mutations in the well-established TP53 tumor suppressor gene may lead to the presence of a partially-functioning protein molecule, whereas mutations affecting the protein encoding reading frame, often referred to as null mutations, result in the absence of p53 protein. Both types of mutations have been observed in the same cancer type. As the resulting tumor biology may be quite different between these two groups, we used RNA-sequencing data from The Cancer Genome Atlas (TCGA) from four different cancers with poor prognosis, namely ovarian, breast, lung and skin cancers, to compare the patterns of coexpression of genes in tumors grouped according to their TP53 missense or null mutation status...
2016: Frontiers in Genetics
Sudharsana Sundarrajan, Mohanapriya Arumugam
Psoriasis is a chronic inflammatory disease of the skin with an unknown aetiology. The disease manifests itself as red and silvery scaly plaques distributed over the scalp, lower back and extensor aspects of the limbs. After receiving scant consideration for quite a few years, psoriasis has now become a prominent focus for new drug development. A group of closely connected and differentially co-expressed genes may act in a network and may serve as molecular signatures for an underlying phenotype. A weighted gene coexpression network analysis (WGCNA), a system biology approach has been utilized for identification of new molecular targets for psoriasis...
November 15, 2016: Gene
Rebecca S G Kong, Guanxiang Liang, Yanhong Chen, Paul Stothard, Le Luo Guan
BACKGROUND: Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach. RESULTS: The rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing...
2016: BMC Genomics
Jihong Hu, Guanglong Chen, Hongyuan Zhang, Qian Qian, Yi Ding
BACKGROUND: Cytoplasmic male sterility (CMS) is an ideal model for investigating the mitochondrial-nuclear interaction and down-regulated genes in CMS lines which might be the candidate genes for pollen development in rice. In this study, a set of rice alloplasmic sporophytic CMS lines was obtained by successive backcrossing of Meixiang B, with three different cytoplasmic types: D62A (D type), ZS97A (WA type) and XQZ-A (DA type). RESULTS: Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expressed genes (DEGs) in each of the three CMS lines compared with the maintainer line Meixiang B...
2016: BMC Plant Biology
David G Brohawn, Laura C O'Brien, James P Bennett
ALS is a rapidly progressive, devastating neurodegenerative illness of adults that produces disabling weakness and spasticity arising from death of lower and upper motor neurons. No meaningful therapies exist to slow ALS progression, and molecular insights into pathogenesis and progression are sorely needed. In that context, we used high-depth, next generation RNA sequencing (RNAseq, Illumina) to define gene network abnormalities in RNA samples depleted of rRNA and isolated from cervical spinal cord sections of 7 ALS and 8 CTL samples...
2016: PloS One
Sally Yepes, Rocío López, Rafael E Andrade, Paula A Rodriguez-Urrego, Liliana López-Kleine, Maria Mercedes Torres
Co-expression networks may provide insights into the patterns of molecular interactions that underlie cellular processes. To obtain a better understanding of miRNA expression patterns in gastric adenocarcinoma and to provide markers that can be associated with histopathological findings, we performed weighted gene correlation network analysis (WGCNA) and compare it with a supervised analysis. Integrative analysis of target predictions and miRNA expression profiles in gastric cancer samples was also performed...
August 2016: Genomics
Ricardo Vallejo, Dana M Tilley, David L Cedeño, Courtney A Kelley, Margaret DeMaegd, Ramsin Benyamin
BACKGROUND: Few studies have evaluated single-gene changes modulated by spinal cord stimulation (SCS), providing a narrow understanding of molecular changes. Genomics allows for a robust analysis of holistic gene changes in response to stimulation. METHODS: Rats were randomized into six groups to determine the effect of continuous SCS in uninjured and spared-nerve injury (SNI) animals. After behavioral assessment, tissues from the dorsal quadrant of the spinal cord (SC) and dorsal root ganglion (DRG) underwent full-genome microarray analyses...
August 2016: Neuromodulation: Journal of the International Neuromodulation Society
Mohammed Uddin, Giovanna Pellecchia, Bhooma Thiruvahindrapuram, Lia D'Abate, Daniele Merico, Ada Chan, Mehdi Zarrei, Kristiina Tammimies, Susan Walker, Matthew J Gazzellone, Thomas Nalpathamkalam, Ryan K C Yuen, Koenraad Devriendt, Géraldine Mathonnet, Emmanuelle Lemyre, Sonia Nizard, Mary Shago, Ann M Joseph-George, Abdul Noor, Melissa T Carter, Grace Yoon, Peter Kannu, Frédérique Tihy, Erik C Thorland, Christian R Marshall, Janet A Buchanan, Marsha Speevak, Dimitri J Stavropoulos, Stephen W Scherer
A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 × 10(-15)) enrichment of critical-exons within rare CNVs in cases compared to controls...
2016: Scientific Reports
B Ning, D-L Xu, J-H Gao, L-L Wang, S-Y Yan, S Cheng
OBJECTIVE: The objective of this paper is to identify pathway-related modules which are defined as in high-grade osteosarcoma based on topological centralities analysis of networks. MATERIALS AND METHODS: Co-expression network was constructed by weighted gene co-expression network analysis (WGCNA) based on differentially expressed genes (DEGs). Pathway enrichment analysis was conducted by Kyoto Encyclopedia of Genes and Genomes (KEGG) database to detect pathway enriched genes...
June 2016: European Review for Medical and Pharmacological Sciences
Chung-Wei Yang, Chien-Lin Chen, Wei-Chun Chou, Ho-Chen Lin, Yuh-Jyh Jong, Li-Kai Tsai, Chun-Yu Chuang
Spinal muscular atrophy (SMA) is an inherited neuromuscular disease resulting from a recessive mutation in the SMN1 gene. This disease affects multiple organ systems with varying degrees of severity. Exploration of the molecular pathological changes occurring in different cell types in SMA is crucial for developing new therapies. This study collected 39 human microarray datasets from ArrayExpress and GEO databases to build an integrative transcriptomic analysis for recognizing novel SMA targets. The transcriptomic analysis was conducted through combining weighted correlation network analysis (WGCNA) for gene module detection, gene set enrichment analysis (GSEA) for functional categorization and filtration, and Cytoscape (visual interaction gene network analysis) for target gene identification...
2016: PloS One
Jun Jiang, Xian Sun, Wei Wu, Li Li, Hai Wu, Lu Zhang, Guohua Yu, Yao Li
Because of its high pathogenicity and infectivity, tuberculosis is a serious threat to human health. Some information about the functions of the genes in Mycobacterium tuberculosis genome was currently available, but it was not enough to explore transcriptional regulatory mechanisms. Here, we applied the WGCNA (Weighted Gene Correlation Network Analysis) algorithm to mine pooled microarray datasets for the M. tuberculosis H37Rv strain. We constructed a co-expression network that was subdivided into 78 co-expression gene modules...
2016: Scientific Reports
Ji-Yun Huang, Yun Tian, Hui-Juan Wang, Hong Shen, Huan Wang, Sen Long, Mei-Hua Liao, Zhi-Rong Liu, Ze-Ming Wang, Dan Li, Rong-Rong Tao, Tian-Tian Cui, Shigeki Moriguchi, Kohji Fukunaga, Feng Han, Ying-Mei Lu
BACKGROUND: Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopmental disorders that display complicated behavioral symptoms. METHODS: Using gene expressing profiling and the weighted gene co-expression network analysis (WGCNA), we studied genes coregulated by similar factors such as genetic variants or environmental effects in the hippocampus in an animal model of autism. RESULTS: From microarray data, we identified 21,388 robustly expressed genes of which 721 genes were found to be differently expressed in the valproic acid-treated group compared to the control group...
October 2016: CNS Neuroscience & Therapeutics
Sebastián Moschen, Janet Higgins, Julio A Di Rienzo, Ruth A Heinz, Norma Paniego, Paula Fernandez
BACKGROUND: In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables, which has a strong impact on crop yield. Transcription factors (TFs) are key proteins in the regulation of gene expression, regulating different signaling pathways; their function is crucial for triggering and/or regulating different aspects of the leaf senescence process...
2016: BMC Bioinformatics
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"