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transcriptome and meta-analysis

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...
March 2, 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 5, 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...
February 28, 2018: Biochemical and Biophysical Research Communications
Qi Zhaoming, Zhang Zhanguo, Wang Zhongyu, Yu Jingyao, Qin Hongtao, Mao Xinrui, Jiang Hongwei, Xin Dawei, Yin Zhengong, Zhu Rongsheng, Liu Chunyan, Wei Yu, Hu Zhenbang, Wu Xiaoxia, Liu Jun, Chen Qingshan
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 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. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their three years of phenotype selection in the field...
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's disease (AD). Design: Population-based study; human brain tissue microarray. Setting: Community-based cohorts from Chicago, Illinois and northeastern Illinois, as well as religious clergymen from across the U...
February 22, 2018: Journal of Clinical Endocrinology and Metabolism
Somayeh Sharifi, Abbas Pakdel, Mansour Ebrahimi, James M Reecy, Samaneh Fazeli Farsani, Esmaeil Ebrahimie
Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of '-omics' data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient way...
2018: PloS One
Wenyi Qin, Hui Lu
Motivation: Detecting differentially expressed (DE) genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don't have a lot of samples, researchers have used meta-analysis to group different datasets for the same disease. Even then, in many cases the statistical power is still not enough. Taking into account the fact that many diseases share the same disease genes, it is desirable to design a statistical framework that can identify diseases' common and specific DE genes simultaneously to improve the identification power...
2018: BioData Mining
Lara P Fernández, Ricardo Ramos-Ruiz, Jesús Herranz, Roberto Martín-Hernández, Teodoro Vargas, Marta Mendiola, Laura Guerra, Guillermo Reglero, Jaime Feliu, Ana Ramírez de Molina
Metabolic alterations encountered in tumors are well recognized and considered as a hallmark of cancer. In addition to Warburg Effect, epidemiological and experimental studies support the crucial role of lipid metabolism in colorectal cancer (CRC). The overexpression of four lipid metabolism-related genes ( ABCA1, ACSL1, AGPAT1 and SCD genes) has been proposed as prognostic marker of stage II CRC (ColoLipidGene signature). In order to explore in depth the transcriptomic and genomic scenarios of ABCA1 , ACSL1 , AGPAT1 and SCD genes, we performed a transcriptomic meta-analysis in more than one thousand CRC individuals...
January 19, 2018: Oncotarget
Vasiliki Pelekanou, Eleftheria Anastasiou, Efstathia Bakogeorgou, George Notas, Marilena Kampa, Rolando Garcia-Milian, Katerina Lavredaki, Eleni Moustou, Georgia Chinari, Petroula Arapantoni, Anthony O'Grady, Vassilios Georgoulias, Andreas Tsapis, Efstathios N Stathopoulos, Elias Castanas
The expression profile of estrogen receptors (ER) in Non-Small Cell Lung Carcinoma (NSCLC) remains contradictory. Here we investigated protein and transcriptome expression of ERα wild type and variants. Tissue Micro-Arrays of 200 cases of NSCLC (paired tumor/non-tumor) were assayed by immunohistochemistry using a panel of ERα antibodies targeting different epitopes (HC20, 6F11, 1D5, ERα36 and ERα17p). ERβ epitopes were also examined for comparison. In parallel we conducted a probe-set mapping (Affymetrix HGU133 plus 2 chip) meta-analysis of 12 NSCLC tumor public transcriptomic studies (1418 cases) and 39 NSCLC cell lines...
February 15, 2018: Steroids
Wei Zhong, Lianzhi Dai, Jing Liu, Song Zhou
Cholangiocarcinoma (CCA) is characterized by delayed diagnosis and poor survival rate. Research efforts have focused on novel diagnostic technologies for this type of cancer. Transcriptomic microarray technology is a useful research strategy for investigating the molecular properties of CCA. The objective of the present study was to identify candidate biomarkers with high potential for clinical application in CCA using a meta‑analysis‑based approach. Gene expression profiles of CCA were downloaded from the Gene Expression Omnibus database for integrated analysis...
February 12, 2018: Molecular Medicine Reports
Peter Mu-Hsin Chang, Che-Hong Chen, Chi-Chun Yeh, Hsueh-Ju Lu, Tze-Tze Liu, Ming-Huang Chen, Chun-Yu Liu, Alexander T H Wu, Muh-Hwa Yang, Shyh-Kuan Tai, Daria Mochly-Rosen, Chi-Ying F Huang
Overexpression of ALDH is associated with cancer stem-like features and poor cancer prognosis. High ALDH activity has been observed in cancer stem-like cells. There are a total of 19 human ALDH isoforms, all of which are associated with reducing oxidative stress and protecting cells from damage. However, it is unknown whether all ALDHs are associated with poor cancer prognosis and which ones play a significant role in cancer progression. In this study, we used RNA sequencing data from The Cancer Genome Atlas (TCGA) to evaluate the differential expression of 19 ALDH isoforms in 5 common human cancers...
February 9, 2018: Scientific Reports
Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository...
February 6, 2018: Nucleic Acids Research
Bipin Balan, Francesco Paolo Marra, Tiziano Caruso, Federico Martinelli
RNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network...
January 31, 2018: Scientific Reports
Roberta Ruotolo, Elena Maestri, Luca Pagano, Marta Marmiroli, Jason C White, Nelson Marmiroli
The increasing use of engineered nanomaterials (ENMs) raises questions over their environmental impact. Improving the level of understanding of the genetic and molecular basis of the response to ENM exposure in biota is necessary to accurately assess true risk to sensitive receptors. The aim of this review is to compare the plant response to several metal-based ENMs widely used, such as quantum dots, metal oxides and silver nanoparticles (NPs), integrating available 'omics' data (transcriptomics, miRNAs and proteomics)...
January 29, 2018: Environmental Science & Technology
P Lu, C P Sodhi, Y Yamaguchi, H Jia, T Prindle, W B Fulton, A Vikram, K J Bibby, M J Morowitz, D J Hackam
Little is known about the pathogenesis of metabolic syndrome, although Toll-like receptor 4 (TLR4) has been implicated. We investigated whether TLR4 in the intestinal epithelium regulates metabolic syndrome by coordinating interactions between the luminal microbiota and host genes that regulate metabolism. Mice lacking TLR4 in the intestinal epithelium (TLR4ΔIEC), but not mice lacking TLR4 in myeloid cells nor mice lacking TLR4 globally, developed metabolic syndrome; these features were not observed in TLR4ΔIEC mice given antibiotics...
January 24, 2018: Mucosal Immunology
Filip Vandenbussche, Na Yu, Weidong Li, Lucas Vanhaelewyn, Mohamad Hamshou, Dominique Van Der Straeten, Guy Smagghe
Ultraviolet B light (UV-B, 280-315 nm) is the shortest wavelength of the solar spectrum reaching the surface of the Earth. It has profound effects on plants, ranging from growth regulation to severe metabolic changes. Low level UV-B mainly causes photomorphogenic effects while higher levels can induce stress, yet these effects tend to overlap. Here we identified a condition that allows growth reduction without obvious detrimental stress in wild type Arabidopsis rosette plants. This condition was used to study the effects of a daily UV-B dose on plant characteristics of UV-B adapted plants in detail...
March 2018: Plant Science: An International Journal of Experimental Plant Biology
Marek D Koter, Magdalena Święcicka, Mateusz Matuszkiewicz, Andrzej Pacak, Natalia Derebecka, Marcin Filipecki
Cyst-forming plant-parasitic nematodes are pests threatening many crops. By means of their secretions cyst nematodes induce the developmental and metabolic reprogramming of host cells that lead to the formation of a syncytium, which is the sole food source for growing nematodes. The in depth micro RNA (miRNA) dynamics in the syncytia induced by Globodera rostochiensis in tomato roots was studied. The miRNAomes were obtained from syncytia covering the early and intermediate developmental stages, and were the subject of differential expression analysis...
March 2018: Plant Science: An International Journal of Experimental Plant Biology
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