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transcriptome and meta-analysis

Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S Wishart, Jianguo Xia
We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four new key features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a Biomarker Meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data...
May 14, 2018: Nucleic Acids Research
R Ayana, Shailja Singh, Soumya Pati
Microglial cells form a context-dependent network of brain immunoeffector cells. Despite their indispensable roles, unresolved questions exist around biomarker discovery relevant to their cellular localization, self-renewing potential, and brain developmental dynamics. To resolve the existent gap in the annotation of candidate biomarkers, we conducted a meta-analysis of brain cells using available high-throughput data sets for deciphering microglia-specific expression profiles. We have identified 3,290 significant genes specific to microglia and further selected the top 20 dysregulated genes on the basis of p -value and log2 FC...
2018: Frontiers in Neurology
Maria Chiara Pelleri, Chiara Cattani, Lorenza Vitale, Francesca Antonaros, Pierluigi Strippoli, Chiara Locatelli, Guido Cocchi, Allison Piovesan, Maria Caracausi
Down syndrome (DS) is due to the presence of an extra full or partial chromosome 21 (Hsa21). The identification of genes contributing to DS pathogenesis could be the key to any rational therapy of the associated intellectual disability. We aim at generating quantitative transcriptome maps in DS integrating all gene expression profile datasets available for any cell type or tissue, to obtain a complete model of the transcriptome in terms of both expression values for each gene and segmental trend of gene expression along each chromosome...
2018: Frontiers in Genetics
Kasum Azim, Rainer Akkermann, Martina Cantone, Julio Vera, Janusz J Jadasz, Patrick Küry
In the adult central nervous system (CNS), the subventricular zone (SVZ) of the forebrain is the largest and most active source of neural stem cells (NSCs) that generates mainly neurons and few glial cells lifelong. A large body of evidence has shed light on the distinct families of signaling ligands (i.e., morphogens, growth factors, secreted molecules that alter signaling pathways) in regulating NSC biology. However, most of the research has focused on the mRNA expression of individual or few signaling ligands and their pathway components in specific cell types of the CNS in the context of neurogenesis...
2018: Frontiers in Neuroscience
Xingyi Guo, Weiqiang Lin, Jiandong Bao, Qiuyin Cai, Xiao Pan, Mengqiu Bai, Yuan Yuan, Jiajun Shi, Yaqiong Sun, Mi-Ryung Han, Jing Wang, Qi Liu, Wanqing Wen, Bingshan Li, Jirong Long, Jianghua Chen, Wei Zheng
Genome-wide association studies (GWASs) have identified more than 150 common genetic loci for breast cancer risk. However, the target genes and underlying mechanisms remain largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using normal or tumor breast transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project. We identified a total of 101 genes for 51 lead variants after combing the results of a meta-analysis of METABRIC and TCGA, and the results from GTEx at a Benjamini-Hochberg (BH)-adjusted p < 0...
May 3, 2018: American Journal of Human Genetics
Xuelian Chen, Qin Wen, Andres Stucky, Yunjing Zeng, Shengjia Gao, William G Loudon, Hector W Ho, Mustafa H Kabeer, Shengwen Calvin Li, Xi Zhang, Jiang F Zhong
Glioblastoma multiforme (GBM) remains an incurable brain tumor. The highly malignant behavior of GBM may, in part, be attributed to its intraclonal genetic and phenotypic diversity (subclonal evolution). Identifying the molecular pathways driving GBM relapse may provide novel, actionable targets for personalized diagnosis, characterization of prognosis and improvement of precision therapy. We screened single-cell transcriptomes, namely RNA-seq data of primary and relapsed GBM tumors from a patient, to define the molecular profile of relapse...
April 28, 2018: Carcinogenesis
Carlos Henríquez-Valencia, Anita Arenas-M, Joaquín Medina, Javier Canales
Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response...
2018: Frontiers in Plant Science
Shahid Manzoor, Anna Schnürer, Erik Bongcam-Rudloff, Bettina Müller
Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation...
April 23, 2018: Genes
Hagen Klett, Hannah Fuellgraf, Ella Levit-Zerdoun, Saskia Hussung, Silke Kowar, Simon Küsters, Peter Bronsert, Martin Werner, Uwe Wittel, Ralph Fritsch, Hauke Busch, Melanie Boerries
Late diagnosis and systemic dissemination essentially contribute to the invariably poor prognosis of pancreatic ductal adenocarcinoma (PDAC). Therefore, the development of diagnostic biomarkers for PDAC are urgently needed to improve patient stratification and outcome in the clinic. By studying the transcriptomes of independent PDAC patient cohorts of tumor and non-tumor tissues, we identified 81 robustly regulated genes, through a novel, generally applicable meta-analysis. Using consensus clustering on co-expression values revealed four distinct clusters with genes originating from exocrine/endocrine pancreas, stromal and tumor cells...
2018: Frontiers in Genetics
David A Landry, Marc-André Sirard
In recent years, exciting progress was made to improve the embryo outcome after ovarian stimulation in domestic animals. The practice of follicle-stimulating hormone (FSH) withdrawal, which is defined as the period of time between the last injection of FSH and oocyte retrieval, resulted in embryo yields significantly superior. Since then, specific changes in the transcriptome of granulosa cells were associated with the increase and also the decline in oocyte developmental competence following the FSH decline...
April 14, 2018: Biology of Reproduction
Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong
BACKGROUND: Transcriptomic datasets often contain undeclared heterogeneity arising from biological variation such as diversity of disease subtypes, treatment subgroups, time-series gene expression, nested experimental conditions, as well as technical variation due to batch effects, platform differences in integrated meta-analyses, etc. However, current analysis approaches are primarily designed to handle comparisons between experimental conditions represented by homogeneous samples, thus precluding the discovery of underlying subphenotypes...
March 19, 2018: BMC Systems Biology
Ellen Young, Manus Carey, Andrew A Meharg, Caroline Meharg
BACKGROUND: Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant species with controlled microbiota inoculation treatments, molecular plant-microbiome interactions can be functionally investigated via RNA-Seq. Complex, natural plant-microbiome studies are limited, typically focusing on microbial rRNA and omitting functional microbiome investigations, presenting a fundamental knowledge gap...
March 20, 2018: Microbiome
Saskia Reibe, Marit Hjorth, Mark A Febbraio, Martin Whitham
Exercise stimulates a wide array of biological processes, but the mechanisms involved are incompletely understood. Many previous studies have adopted transcriptomic analyses of skeletal muscle to address particular research questions, a process that ultimately results in the collection of large amounts of publicly available data that has not been fully integrated or interrogated. To maximize the use of these available transcriptomic exercise data sets, we have downloaded and re-analyzed them and formulated the data into a searchable online tool, geneXX...
March 16, 2018: Physiological Genomics
Honglai Tian
BACKGROUND: Osteoarthritis (OA) is the most common chronic disorder of joints; however, the key genes and transcription factors (TFs) associated with OA are still unclear. Through bioinformatics tools, the study aimed to understand the mechanism of genes associated with the development of OA. METHODS: Four gene expression profiling datasets were used to identify differentially expressed genes (DEGs) between OA and healthy control samples by a meta-analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed with Multifaceted Analysis Tool for Human Transcriptome (MATHT)...
March 7, 2018: Journal of Orthopaedic Surgery and Research
Laurence A Brown, Stuart N Peirson
Transcriptomic experiments are often used in neuroscience to identify candidate genes of interest for further study. However, the lists of genes identified from comparable transcriptomic studies often show limited overlap. One approach to addressing this issue of reproducibility is to combine data from multiple studies in the form of a meta-analysis. Here, we discuss recent work in the field of circadian biology, where transcriptomic meta-analyses have been used to improve candidate gene selection. With the increasing availability of microarray and RNA-Seq data due to deposition in public databases, combined with freely available tools and code, transcriptomic meta-analysis provides an ideal example of how open data can benefit neuroscience research...
2018: Journal of Experimental Neuroscience
Marianna Szemes, Alexander Greenhough, Zsombor Melegh, Sally Malik, Aysen Yuksel, Daniel Catchpoole, Kelli Gallacher, Madhu Kollareddy, Ji Hyun Park, Karim Malik
Neuroblastoma is one of the commonest and deadliest solid tumours of childhood, and is thought to result from disrupted differentiation of the developing sympathoadrenergic lineage of the neural crest. Neuroblastoma exhibits intra- and intertumoural heterogeneity, with high risk tumours characterised by poor differentiation, which can be attributable to MYCN-mediated repression of genes involved in neuronal differentiation. MYCN is known to co-operate with oncogenic signalling pathways such as Alk, Akt and MEK/ERK signalling, and, together with c-MYC has been shown to be activated by Wnt signalling in various tissues...
April 2018: Neoplasia: An International Journal for Oncology Research
Eugenia Sanchez, Eliane Küpfer, Daniel J Goedbloed, Arne W Nolte, Tim Lüddecke, Stefan Schulz, Miguel Vences, Sebastian Steinfartz
The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis...
March 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
Manikandan Murugesan, Kumpati Premkumar
Despite, several lines of evidence suggesting the possible role of hypoxia in stem cell development and differentiation its significance in conferring the stemness and pluripotency remains elusive. In the present study we sought to delineate the candidate genes and molecular pathways imposed during hypoxic microenvironment and its physiological relevance in tipping the balance between the niche and cellular differentiation. Integrated meta-analysis was performed between the hypoxia exposed and normal human embryonic stem cells, employing three transcriptomic cohorts (GSE35819, GSE9510 and GSE37761) retrieved from Gene expression omnibus (GEO) database...
April 6, 2018: Biochemical and Biophysical Research Communications
Zhaoming Qi, Zhanguo Zhang, Zhongyu Wang, Jingyao Yu, Hongtao Qin, Xinrui Mao, Hongwei Jiang, Dawei Xin, Zhengong Yin, Rongsheng Zhu, Chunyan Liu, Wei Yu, Zhenbang Hu, Xiaoxia Wu, Jun Liu, Qingshan Chen
Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein...
February 27, 2018: Plant, Cell & Environment
Elizabeth A McAninch, Kumar B Rajan, Denis A Evans, Sungro Jo, Layal Chaker, Robin P Peeters, David A Bennett, Deborah C Mash, Antonio C Bianco
Context: A common single nucleotide polymorphism in DIO2, Thr92AlaD2, has been associated with a transcriptome typically found in neurodegenerative diseases in postmortem human brain tissue. Objective: To determine whether Thr92AlaD2 is associated with incident Alzheimer disease (AD). Design: Population-based study; human brain tissue microarray. Setting: Community-based cohorts from Chicago and northeastern Illinois and religious clergymen from across the United States constituted the primary population...
May 1, 2018: Journal of Clinical Endocrinology and Metabolism
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