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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/28335819/concordance-analysis-of-microarray-studies-identifies-representative-gene-expression-changes-in-parkinson-s-disease-a-comparison-of-33-human-and-animal-studies
#1
Erin Oerton, Andreas Bender
BACKGROUND: As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. METHODS: In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease...
March 23, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#2
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334340/meta-analytic-framework-for-liquid-association
#3
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28329862/the-transcriptome-of-the-zebrafish-embryo-after-chemical-exposure-a-meta-analysis
#4
Andreas Schüttler, Kristin Reiche, Rolf Altenburger, Wibke Busch
Numerous studies have been published in the past years investigating the transcriptome of the zebrafish embryo (ZFE) upon being subjected to chemical stress. Aiming at a more mechanistic understanding of the results of such studies, knowledge about commonalities of transcript regulation in response to chemical stress is needed. Thus, our goal in this study was to identify and interpret genes and gene sets constituting a general response to chemical exposure. Therefore, we aggregated and reanalyzed published toxicogenomics data obtained with the ZFE...
February 27, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28320322/exploring-the-nature-of-prediagnostic-blood-transcriptome-markers-of-chronic-lymphocytic-leukemia-by-assessing-their-overlap-with-the-transcriptome-at-the-clinical-stage
#5
Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A Kyrtopoulos, Ingvar A Bergdahl, Ann-Sofie Johansson, Dennie D G A J Hebels, Theo M C M de Kok, Paolo Vineis, Roel C H Vermeulen
BACKGROUND: We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched controls. We hypothesized that a large fraction of these markers were likely related to early disease manifestations. Here we aim to gain a better understanding of the natural history of the identified markers by comparing results from our prediagnostic analysis, the only prediagnostic analysis to date, to results obtained from a meta-analysis of a series of publically available transcriptomics profiles obtained in incident CLL cases and controls...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28295046/transcriptomic-immaturity-of-the-hippocampus-and-prefrontal-cortex-in-patients-with-alcoholism
#6
Tomoyuki Murano, Hisatsugu Koshimizu, Hideo Hagihara, Tsuyoshi Miyakawa
Alcoholism, which is defined as the recurring harmful use of alcohol despite its negative consequences, has a lifetime prevalence of 17.8%. Previous studies have shown that chronic alcohol consumption disrupts various brain functions and behaviours. However, the precise mechanisms that underlie alcoholism are currently unclear. Recently, we discovered "pseudo-immature" brain cell states of the dentate gyrus and prefrontal cortex (PFC) in mouse models of psychotic disorders and epileptic seizure. Similar pseudo-immaturity has been observed in patients with psychotic disorders, such as schizophrenia and bipolar disorder...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28250240/atrx-a-novel-progesterone-regulated-biomarker-of-mammalian-oocyte-developmental-potential
#7
Lynne Clare O'Shea, Edward Daly, Carmel Hensey, Trudee Fair
A multi-species meta-analysis of published transcriptomic data from models of oocyte competence identified the chromatin remodelling factor ATRX, as a putative biomarker of oocyte competence. The objective of the current study was to test the hypothesis that ATRX protein expression by cumulus oocyte complexes (COCs) reflects their intrinsic quality and developmental potential. In excess of 10,000 bovine COCs were utilized to test our hypothesis. COCs were in vitro matured (IVM) under conditions associated with reduced developmental potential: IVM in the presence or absence of (1) progesterone synthesis inhibitor (Trilostane); (2) nuclear progesterone receptor inhibitor (Aglepristone) or (3) an inducer of DNA damage (Staurosporine)...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28249569/unity-in-defence-honeybee-workers-exhibit-conserved-molecular-responses-to-diverse-pathogens
#8
Vincent Doublet, Yvonne Poeschl, Andreas Gogol-Döring, Cédric Alaux, Desiderato Annoscia, Christian Aurori, Seth M Barribeau, Oscar C Bedoya-Reina, Mark J F Brown, James C Bull, Michelle L Flenniken, David A Galbraith, Elke Genersch, Sebastian Gisder, Ivo Grosse, Holly L Holt, Dan Hultmark, H Michael G Lattorff, Yves Le Conte, Fabio Manfredini, Dino P McMahon, Robin F A Moritz, Francesco Nazzi, Elina L Niño, Katja Nowick, Ronald P van Rij, Robert J Paxton, Christina M Grozinger
BACKGROUND: Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets...
March 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28249256/searching-for-a-lifeline-transcriptome-profiling-studies-of-influenza-susceptibility-and-resistance
#9
Lester Kobzik
An excess or dysregulated host inflammatory responses cause much of the morbidity and mortality caused by severe influenza. Given the limitations of vaccines and antiviral drugs, novel therapeutics to modulate host responses and improve outcomes in severe influenza are needed. One strategy is to learn from the direct comparison of high-survivor versus high-mortality animal models. This review surveys the results of lung transcriptome profiling studies in murine models that directly compare susceptible versus resistant hosts challenged with identical influenza infections...
March 1, 2017: Journal of Innate Immunity
https://www.readbyqxmd.com/read/28243609/meta-analysis-of-pulmonary-transcriptomes-from-differently-primed-mice-identifies-molecular-signatures-to-differentiate-immune-responses-following-bordetella-pertussis-challenge
#10
René H M Raeven, Jeroen L A Pennings, Elly van Riet, Gideon F A Kersten, Bernard Metz
Respiratory infection with Bordetella pertussis leads to severe effects in the lungs. The resulting immunity and also immunization with pertussis vaccines protect against disease, but the induced type of immunity and longevity of the response are distinct. In this study the effects of priming, by either vaccination or infection, on a subsequent pathogen encounter were studied. To that end, three postchallenge transcriptome datasets of previously primed mice were combined and compared to the responses in unprimed control mice...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/28218403/unveiling-gene-trait-relationship-by-cross-platform-meta-analysis-on-chinese-hamster-ovary-cell-transcriptome
#11
Liang Zhao, Hsu-Yuan Fu, Ravali Raju, Nandita Vishwanathan, Wei-Shou Hu
In the past few years, transcriptome analysis has been increasingly employed to better understand the physiology of Chinese hamster ovary (CHO) cells at a global level. As more transcriptome data accumulated, meta-analysis on data sets collected from various sources can potentially provide better insights on common properties of those cells. Here, we performed meta-analysis on transcriptome data of different CHO cell lines obtained using NimbleGen or Affymetrix microarray platforms. Hierarchical clustering, non-negative matrix factorization (NMF) analysis, and principal component analysis (PCA) accordantly showed the samples were clustered into two groups: one consists of adherent cells in serum-containing medium, and the other suspension cells in serum-free medium...
February 20, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28209126/a-meta-analysis-reveals-complex-regulatory-properties-at-taf14-repressed-genes
#12
Josipa Nemet, Nikolina Vidan, Mary Sopta
BACKGROUND: Regulation of gene transcription in response to stress is central to a cell's ability to cope with environmental challenges. Taf14 is a YEATS domain protein in S.cerevisiae that physically associates with several transcriptionally relevant multisubunit complexes including the general transcription factors TFIID and TFIIF and the chromatin-modifying complexes SWI/SNF, INO80, RSC and NuA3. TAF14 deletion strains are sensitive to a variety of stresses suggesting that it plays a role in the transcriptional stress response...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199355/transcriptomic-meta-analysis-reveals-up-regulation-of-gene-expression-functional-in-osteoclast-differentiation-in-human-septic-shock
#13
Samanwoy Mukhopadhyay, Pravat K Thatoi, Abhay D Pandey, Bidyut K Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj K Mohapatra
Septic shock is a major medical problem with high morbidity and mortality and incompletely understood biology. Integration of multiple data sets into a single analysis framework empowers discovery of new knowledge about the condition that may have been missed by individual analysis of each of these datasets. Electronic search was performed on medical literature and gene expression databases for selection of transcriptomic studies done in circulating leukocytes from human subjects suffering from septic shock...
2017: PloS One
https://www.readbyqxmd.com/read/28167700/the-transcription-factor-myb29-is-a-regulator-of-alternative-oxidase1a
#14
Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Veronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry James Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq
Plants sense and integrate a variety of signals from the environment through different interacting signal transduction pathways that involve hormones and signaling molecules. Using ALTERNATIVE OXIDASE1a (AOX1a) gene expression as a model system of retrograde or stress signaling between mitochondria and the nucleus, MYB DOMAIN PROTEIN29 (MYB29) was identified as a negative regulator (regulator of alternative oxidase1a 7 [rao7] mutant) in a genetic screen of Arabidopsis (Arabidopsis thaliana). rao7/myb29 mutants have increased levels of AOX1a transcript and protein compared to wild type after induction with antimycin A...
March 2017: Plant Physiology
https://www.readbyqxmd.com/read/28158590/a-whole-blood-transcriptome-meta-analysis-identifies-gene-expression-signatures-of-cigarette-smoking
#15
Tianxiao Huan, Roby Joehanes, Claudia Schurmann, Katharina Schramm, Luke C Pilling, Marjolein J Peters, Reedik Mägi, Dawn DeMeo, George T O'Connor, Luigi Ferrucci, Alexander Teumer, Georg Homuth, Reiner Biffar, Uwe Völker, Christian Herder, Melanie Waldenberger, Annette Peters, Sonja Zeilinger, Andres Metspalu, Albert Hofman, André G Uitterlinden, Dena G Hernandez, Andrew B Singleton, Stefania Bandinelli, Peter J Munson, Honghuang Lin, Emelia J Benjamin, Tõnu Esko, Hans J Grabe, Holger Prokisch, Joyce B J van Meurs, David Melzer, Daniel Levy
No abstract text is available yet for this article.
November 1, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28158196/transcriptome-wide-co-expression-analysis-identifies-lrrc2-as-a-novel-mediator-of-mitochondrial-and-cardiac-function
#16
Chris McDermott-Roe, Marion Leleu, Glenn C Rowe, Oleg Palygin, John D Bukowy, Judy Kuo, Monika Rech, Steffie Hermans-Beijnsberger, Sebastian Schaefer, Eleonora Adami, Esther E Creemers, Matthias Heinig, Blanche Schroen, Zoltan Arany, Enrico Petretto, Aron M Geurts
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein...
2017: PloS One
https://www.readbyqxmd.com/read/28153032/analyses-of-caspase-1-regulated-transcriptomes-in-various-tissues-lead-to-identification-of-novel-il-1%C3%AE-il-18-and-sirtuin-1-independent-pathways
#17
Ya-Feng Li, Gayani Nanayakkara, Yu Sun, Xinyuan Li, Luqiao Wang, Ramon Cueto, Ying Shao, Hangfei Fu, Candice Johnson, Jiali Cheng, Xiongwen Chen, Wenhui Hu, Jun Yu, Eric T Choi, Hong Wang, Xiao-Feng Yang
BACKGROUND: It is well established that caspase-1 exerts its biological activities through its downstream targets such as IL-1β, IL-18, and Sirt-1. The microarray datasets derived from various caspase-1 knockout tissues indicated that caspase-1 can significantly impact the transcriptome. However, it is not known whether all the effects exerted by caspase-1 on transcriptome are mediated only by its well-known substrates. Therefore, we hypothesized that the effects of caspase-1 on transcriptome may be partially independent from IL-1β, IL-18, and Sirt-1...
February 2, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28152060/expression-quantitative-trait-loci-qtl-in-tumor-adjacent-normal-breast-tissue-and-breast-tumor-tissue
#18
Alejandro Quiroz-Zárate, Benjamin J Harshfield, Rong Hu, Nick Knoblauch, Andrew H Beck, Susan E Hankinson, Vincent Carey, Rulla M Tamimi, David J Hunter, John Quackenbush, Aditi Hazra
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array...
2017: PloS One
https://www.readbyqxmd.com/read/28147342/inhibition-of-cdk8-mediator-kinase-suppresses-estrogen-dependent-transcription-and-the-growth-of-estrogen-receptor-positive-breast-cancer
#19
Martina S J McDermott, Alexander A Chumanevich, Chang-Uk Lim, Jiaxin Liang, Mengqian Chen, Serena Altilia, David Oliver, James M Rae, Michael Shtutman, Hippokratis Kiaris, Balázs Győrffy, Igor B Roninson, Eugenia V Broude
Hormone therapy targeting estrogen receptor (ER) is the principal treatment for ER-positive breast cancers. However, many cancers develop resistance to hormone therapy while retaining ER expression. Identifying new druggable mediators of ER function can help to increase the efficacy of ER-targeting drugs. Cyclin-dependent kinase 8 (CDK8) is a Mediator complex-associated transcriptional regulator with oncogenic activities. Expression of CDK8, its paralog CDK19 and their binding partner Cyclin C are negative prognostic markers in breast cancer...
January 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28118095/multiomics-approach-to-novel-therapeutic-targets-for-cancer-and-aging-related-diseases-role-of-sld7-in-yeast-aging-network
#20
Irem E Dayan, Kazim Yalcin Arga, Kutlu O Ulgen
Genome instability has long been implicated as a salient causal factor in aging and age-related diseases such as cancer and neurodegeneration. However, the molecular mechanisms associated with genome instability remain unclear. Recent studies suggest growth signaling in the organism Saccharomyces cerevisiae and in higher eukaryotes might affect oxidative stress and aging/age-related diseases by activating DNA replication stress that causes DNA damage. In this broader integrative biology and clinical context, MDM two binding protein (MTBP) is a binding protein that has a role in activation of the tumor suppressor protein p53...
February 2017: Omics: a Journal of Integrative Biology
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