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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/28209126/a-meta-analysis-reveals-complex-regulatory-properties-at-taf14-repressed-genes
#1
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
#2
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-oxidase-1
#3
Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan D Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Véronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry J Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq
Plants sense and integrate a variety of signals from the environment through various interacting signal transduction pathways that involve hormones and signaling molecules. Using the ALTERNATIVE OXIDASE 1a (AOX1a) gene expression as a model system of retrograde or stress signaling between mitochondria and the nucleus, the MYB DOMAIN PROTEIN 29 (MYB29) was identified as a negative regulator (rao7 mutant) in a genetic screen of Arabidopsis thaliana. rao7/myb29 mutants have increased levels of AOX1a at a transcript and protein level after induction with antimycin A...
February 6, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28158590/a-whole-blood-transcriptome-meta-analysis-identifies-gene-expression-signatures-of-cigarette-smoking
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28108623/tumor-induced-stromal-stat1-accelerates-breast-cancer-via-deregulating-tissue-homeostasis
#10
Victoria R Zellmer, Patricia M Schnepp, Sarah L Fracci, Xuejuan Tan, Erin N Howe, Siyuan Zhang
: The tumor microenvironment (TME) is a dynamic tissue space in which the tumor exists, plays a significant role in tumor initiation, and is a key contributor in cancer progression; however, little is known about tumor-induced changes in the adjacent tissue stroma. Herein, tumor-induced changes in the TME were explored at the morphological and molecular level to further understand cancer progression. Tumor-adjacent mammary glands (TAGs) displayed altered branching morphology, expansion of myofibroblasts, and increased mammosphere formation, broadly suggesting a tumor-induced field effect...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28099854/single-cell-transcriptomic-analysis-defines-heterogeneity-and-transcriptional-dynamics-in-the-adult-neural-stem-cell-lineage
#11
Ben W Dulken, Dena S Leeman, Stéphane C Boutet, Katja Hebestreit, Anne Brunet
Neural stem cells (NSCs) in the adult mammalian brain serve as a reservoir for the generation of new neurons, oligodendrocytes, and astrocytes. Here, we use single-cell RNA sequencing to characterize adult NSC populations and examine the molecular identities and heterogeneity of in vivo NSC populations. We find that cells in the NSC lineage exist on a continuum through the processes of activation and differentiation. Interestingly, rare intermediate states with distinct molecular profiles can be identified and experimentally validated, and our analysis identifies putative surface markers and key intracellular regulators for these subpopulations of NSCs...
January 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/28090760/expression-patterns-of-cardiac-aging-in-drosophila
#12
Leah Cannon, Alexander C Zambon, Anthony Cammarato, Zhi Zhang, Georg Vogler, Matthew Munoz, Erika Taylor, Jérôme Cartry, Sanford I Bernstein, Simon Melov, Rolf Bodmer
Aging causes cardiac dysfunction, often leading to heart failure and death. The molecular basis of age-associated changes in cardiac structure and function is largely unknown. The fruit fly, Drosophila melanogaster, is well-suited to investigate the genetics of cardiac aging. Flies age rapidly over the course of weeks, benefit from many tools to easily manipulate their genome, and their heart has significant genetic and phenotypic similarities to the human heart. Here, we performed a cardiac-specific gene expression study on aging Drosophila and carried out a comparative meta-analysis with published rodent data...
February 2017: Aging Cell
https://www.readbyqxmd.com/read/28056781/meta-analysis-reveals-conserved-cell-cycle-transcriptional-network-across-multiple-human-cell-types
#13
Bruno Giotti, Anagha Joshi, Tom C Freeman
BACKGROUND: Cell division is central to the physiology and pathology of all eukaryotic organisms. The molecular machinery underpinning the cell cycle has been studied extensively in a number of species and core aspects of it have been found to be highly conserved. Similarly, the transcriptional changes associated with this pathway have been studied in different organisms and different cell types. In each case hundreds of genes have been reported to be regulated, however there seems to be little consensus in the genes identified across different studies...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049134/mirandb-a-resource-of-online-services-for-mirna-research
#14
Seyed Hamid Aghaee-Bakhtiari, Ehsan Arefian, Pierre Lau
Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available. However, the increasing number and diversity of bioinformatics tools, each covering a specific and specialized area, as well as their redundancies, represent potential sources of complication for end users...
January 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28038934/emerging-cardiac-non-coding-landscape-the-importance-of-meta-analysis
#15
REVIEW
K Shanmugha Rajan, Subbiah Ramasamy, J N George-William, Jeyaprakash Rajendhran
The invention of transcriptome-wide deep sequencing technology has fundamentally changed our understanding of the complex networks that mediate cardiac functions. Since its inception, researchers have uncovered various novel pathways and transcripts that could be one day used for therapeutics and diagnostics. The characterization of various non-protein coding RNAs (ncRNAs) has aided the study of cardiac manifestation in more detail. Although numerous studies have unearthed the importance of miRNA and lncRNA, the existence and importance of other ncRNAs have been neglected due to their unusual behaviors and outdated ideologies...
February 2017: Biochimie
https://www.readbyqxmd.com/read/28031185/metadcn-meta-analysis-framework-for-differential-co-expression-network-detection-with-an-application-in-breast-cancer
#16
Li Zhu, Ying Ding, Cho-Yi Chen, Lin Wang, Zhiguang Huo, SungHwan Kim, Christos Sotiriou, Steffi Oesterreich, George C Tseng
MOTIVATION: Gene co-expression network analysis from transcriptomic studies can elucidate genegene interactions and regulatory mechanisms. Differential co-expression analysis helps further detect alterations of regulatory activities in case/control comparison. Co-expression networks estimated from single transcriptomic study is often unstable and not generalizable due to cohort bias and limited sample size. With the rapid accumulation of publicly available transcriptomic studies, co-expression analysis combining multiple transcriptomic studies can provide more accurate and robust results...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27983601/transcriptome-of-cultured-lung-fibroblasts-in-idiopathic-pulmonary-fibrosis-meta-analysis-of-publically-available-microarray-datasets-reveals-repression-of-inflammation-and-immunity-pathways
#17
Laurent Plantier, Hélène Renaud, Renaud Respaud, Sylvain Marchand-Adam, Bruno Crestani
Heritable profibrotic differentiation of lung fibroblasts is a key mechanism of idiopathic pulmonary fibrosis (IPF). Its mechanisms are yet to be fully understood. In this study, individual data from four independent microarray studies comparing the transcriptome of fibroblasts cultured in vitro from normal (total n = 20) and IPF (total n = 20) human lung were compiled for meta-analysis following normalization to z-scores. One hundred and thirteen transcripts were upregulated and 115 were downregulated in IPF fibroblasts using the Significance Analysis of Microrrays algorithm with a false discovery rate of 5%...
December 13, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27960085/molecular-liver-cancer-prevention-in-cirrhosis-by-organ-transcriptome-analysis-and-lysophosphatidic-acid-pathway-inhibition
#18
Shigeki Nakagawa, Lan Wei, Won Min Song, Takaaki Higashi, Sarani Ghoshal, Rosa S Kim, C Billie Bian, Suguru Yamada, Xiaochen Sun, Anu Venkatesh, Nicolas Goossens, Gretchen Bain, Gregory Y Lauwers, Anna P Koh, Mohamed El-Abtah, Noor B Ahmad, Hiroki Hoshida, Derek J Erstad, Ganesh Gunasekaran, Youngmin Lee, Ming-Lung Yu, Wan-Long Chuang, Chia-Yen Dai, Masahiro Kobayashi, Hiromitsu Kumada, Toru Beppu, Hideo Baba, Milind Mahajan, Venugopalan D Nair, Michael Lanuti, Augusto Villanueva, Angelo Sangiovanni, Massimo Iavarone, Massimo Colombo, Josep M Llovet, Aravind Subramanian, Andrew M Tager, Scott L Friedman, Thomas F Baumert, Myron E Schwarz, Raymond T Chung, Kenneth K Tanabe, Bin Zhang, Bryan C Fuchs, Yujin Hoshida
Cirrhosis is a milieu that develops hepatocellular carcinoma (HCC), the second most lethal cancer worldwide. HCC prediction and prevention in cirrhosis are key unmet medical needs. Here we have established an HCC risk gene signature applicable to all major HCC etiologies: hepatitis B/C, alcohol, and non-alcoholic steatohepatitis. A transcriptome meta-analysis of >500 human cirrhotics revealed global regulatory gene modules driving HCC risk and the lysophosphatidic acid pathway as a central chemoprevention target...
December 12, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#19
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli, Claudine Médigue
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27864472/transcriptome-wide-identification-of-nmd-targeted-human-mrnas-reveals-extensive-redundancy-between-smg6-and-smg7-mediated-degradation-pathways
#20
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
February 2017: RNA
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