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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#1
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...
November 29, 2016: 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
#2
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...
November 18, 2016: RNA
https://www.readbyqxmd.com/read/27862943/blood-transcriptomic-comparison-of-individuals-with-and-without-autism-spectrum-disorder-a-combined-samples-mega-analysis
#3
Daniel S Tylee, Jonathan L Hess, Thomas P Quinn, Rahul Barve, Hailiang Huang, Yanli Zhang-James, Jeffrey Chang, Boryana S Stamova, Frank R Sharp, Irva Hertz-Picciotto, Stephen V Faraone, Sek Won Kong, Stephen J Glatt
Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms...
November 11, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/27842596/integrative-analysis-of-genetic-data-sets-reveals-a-shared-innate-immune-component-in-autism-spectrum-disorder-and-its-co-morbidities
#4
Sumaiya Nazeen, Nathan P Palmer, Bonnie Berger, Isaac S Kohane
BACKGROUND: Autism spectrum disorder (ASD) is a common neurodevelopmental disorder that tends to co-occur with other diseases, including asthma, inflammatory bowel disease, infections, cerebral palsy, dilated cardiomyopathy, muscular dystrophy, and schizophrenia. However, the molecular basis of this co-occurrence, and whether it is due to a shared component that influences both pathophysiology and environmental triggering of illness, has not been elucidated. To address this, we deploy a three-tiered transcriptomic meta-analysis that functions at the gene, pathway, and disease levels across ASD and its co-morbidities...
November 14, 2016: Genome Biology
https://www.readbyqxmd.com/read/27835655/a-transcriptome-meta-analysis-proposes-novel-biological-roles-for-the-antifungal-protein-anafp-in-aspergillus-niger
#5
Norman Paege, Sascha Jung, Paul Schäpe, Dirk Müller-Hagen, Jean-Paul Ouedraogo, Caroline Heiderich, Johanna Jedamzick, Benjamin M Nitsche, Cees A van den Hondel, Arthur F Ram, Vera Meyer
Understanding the genetic, molecular and evolutionary basis of cysteine-stabilized antifungal proteins (AFPs) from fungi is important for understanding whether their function is mainly defensive or associated with fungal growth and development. In the current study, a transcriptome meta-analysis of the Aspergillus niger γ-core protein AnAFP was performed to explore co-expressed genes and pathways, based on independent expression profiling microarrays covering 155 distinct cultivation conditions. This analysis uncovered that anafp displays a highly coordinated temporal and spatial transcriptional profile which is concomitant with key nutritional and developmental processes...
2016: PloS One
https://www.readbyqxmd.com/read/27803687/emerging-putative-associations-between-non-coding-rnas-and-protein-coding-genes-in-neuropathic-pain-added-value-from-reusing-microarray-data
#6
Hemalatha B Raju, Nicholas F Tsinoremas, Enrico Capobianco
Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27802351/an-integrative-analysis-of-preeclampsia-based-on-the-construction-of-an-extended-composite-network-featuring-protein-protein-physical-interactions-and-transcriptional-relationships
#7
Daniel Vaiman, Francisco Miralles
Preeclampsia (PE) is a pregnancy disorder defined by hypertension and proteinuria. This disease remains a major cause of maternal and fetal morbidity and mortality. Defective placentation is generally described as being at the root of the disease. The characterization of the transcriptome signature of the preeclamptic placenta has allowed to identify differentially expressed genes (DEGs). However, we still lack a detailed knowledge on how these DEGs impact the function of the placenta. The tools of network biology offer a methodology to explore complex diseases at a systems level...
2016: PloS One
https://www.readbyqxmd.com/read/27785066/biomarker-discovery-to-improve-prediction-of-breast-cancer-survival-using-gene-expression-profiling-meta-analysis-and-tissue-validation
#8
Liwei Meng, Yingchun Xu, Chaoyang Xu, Wei Zhang
PURPOSE: Breast cancer is the leading cause of cancer death worldwide in women. The molecular mechanism for human breast cancer is unknown. Gene microarray has been widely used in breast cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis survival. So far, the valuable multigene signatures in clinical practice are unclear, and the biological importance of individual genes is difficult to detect, as the described signatures virtually do not overlap...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27777588/a-transcriptomic-signature-of-mouse-liver-progenitor-cells
#9
Adam M Passman, Jasmine Low, Roslyn London, Janina E E Tirnitz-Parker, Atsushi Miyajima, Minoru Tanaka, Helene Strick-Marchand, Gretchen J Darlington, Megan Finch-Edmondson, Scott Ochsner, Cornelia Zhu, James Whelan, Bernard A Callus, George C T Yeoh
Liver progenitor cells (LPCs) can proliferate extensively, are able to differentiate into hepatocytes and cholangiocytes, and contribute to liver regeneration. The presence of LPCs, however, often accompanies liver disease and hepatocellular carcinoma (HCC), indicating that they may be a cancer stem cell. Understanding LPC biology and establishing a sensitive, rapid, and reliable method to detect their presence in the liver will assist diagnosis and facilitate monitoring of treatment outcomes in patients with liver pathologies...
2016: Stem Cells International
https://www.readbyqxmd.com/read/27771009/molecular-and-biochemical-characterization-of-a-benzenoid-phenylpropanoid-meta-para-o-methyltransferase-from-rauwolfia-serpentina-roots
#10
Brent Wiens, Vincenzo De Luca
The monoterpenoid indole alkaloids, reserpine and rescinnamine contain 3, 4, 5-trimethoxybenzoate or 3, 4, 5-trimethoxycinnamate, respectively, within their structures and they accumulate in different plant organs and particularly within roots of Rauwolfia serpentina. This plant also accumulates acylated sugars substituted with 3, 4, 5-trimethoxybenzoate and 3, 4, 5-trimethoxycinnamate. In the present study, transcriptome and metabolome analyses of R. serpentina roots allowed the identification of 7 candidate O-methytransferase (OMT) genes that might be associated with the formation of 3, 4, 5-trimethoxybenzoate and 3, 4, 5-trimethoxycinnamate and led to the molecular cloning of 4 genes for functional expression and analysis...
October 19, 2016: Phytochemistry
https://www.readbyqxmd.com/read/27754866/transcriptomic-analysis-reveals-novel-transcription-factors-associated-with-renin-angiotensin-aldosterone-system-in-human-atheroma
#11
Ali Nehme, Catherine Cerutti, Kazem Zibara
Despite the well-known role of the renin-angiotensin-aldosterone system (RAAS) in atheroma, its global local organization is poorly understood. In this study, we used transcriptomic meta-analysis to reveal the local transcriptional organization and regulation of 37 extended RAAS (extRAAS) genes in atheroma. Expression analysis and hierarchical clustering were done on extRAAS genes in 32 paired early and advanced atherosclerotic lesions. Contrary to receptor-coding transcripts, multiple angiotensin-metabolizing enzymes showed higher expression in advance, in comparison to early lesions...
October 17, 2016: Hypertension
https://www.readbyqxmd.com/read/27752041/interactome-transcriptome-analysis-discovers-signatures-complementary-to-gwas-loci-of-type-2-diabetes
#12
Jing-Woei Li, Heung-Man Lee, Ying Wang, Amy Hin-Yan Tong, Kevin Y Yip, Stephen Kwok-Wing Tsui, Si Lok, Risa Ozaki, Andrea O Luk, Alice P S Kong, Wing-Yee So, Ronald C W Ma, Juliana C N Chan, Ting-Fung Chan
Protein interactions play significant roles in complex diseases. We analyzed peripheral blood mononuclear cells (PBMC) transcriptome using a multi-method strategy. We constructed a tissue-specific interactome (T2Di) and identified 420 molecular signatures associated with T2D-related comorbidity and symptoms, mainly implicated in inflammation, adipogenesis, protein phosphorylation and hormonal secretion. Apart from explaining the residual associations within the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) study, the T2Di signatures were enriched in pathogenic cell type-specific regulatory elements related to fetal development, immunity and expression quantitative trait loci (eQTL)...
October 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27729915/a-systematic-view-of-the-mlo-family-in-rice-suggests-their-novel-roles-in-morphological-development-diurnal-responses-the-light-signaling-pathway-and-various-stress-responses
#13
Van N T Nguyen, Kieu T X Vo, Hyon Park, Jong-Seong Jeon, Ki-Hong Jung
The Mildew resistance Locus O (MLO) family is unique to plants, containing genes that were initially identified as a susceptibility factor to powdery mildew pathogens. However, little is known about the roles and functional diversity of this family in rice, a model crop plant. The rice genome has 12 potential MLO family members. To achieve systematic functional assignments, we performed a phylogenomic analysis by integrating meta-expression data obtained from public sources of microarray data and real-time expression data into a phylogenic tree...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27725773/analysis-of-the-brain-mural-cell-transcriptome
#14
Liqun He, Michael Vanlandewijck, Elisabeth Raschperger, Maarja Andaloussi Mäe, Bongnam Jung, Thibaud Lebouvier, Koji Ando, Jennifer Hofmann, Annika Keller, Christer Betsholtz
Pericytes, the mural cells of blood microvessels, regulate microvascular development and function and have been implicated in many brain diseases. However, due to a paucity of defining markers, pericyte identification and functional characterization remain ambiguous and data interpretation problematic. In mice carrying two transgenic reporters, Pdgfrb-eGFP and NG2-DsRed, we found that double-positive cells were vascular mural cells, while the single reporters marked additional, but non-overlapping, neuroglial cells...
October 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27704359/transcriptomic-characterization-of-differential-gene-expression-in-oral-squamous-cell-carcinoma-a-meta-analysis-of-publicly-available-microarray-data-sets
#15
Yang Sun, Zhijian Sang, Qian Jiang, Xiaojun Ding, Youcheng Yu
Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC...
October 4, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/27702671/major-differences-between-human-atopic-dermatitis-and-murine-models-as-determined-by-global-transcriptomic-profiling
#16
David A Ewald, Shinji Noda, Margeaux Oliva, Thomas Litman, Saeko Nakajima, Xuan Li, Hui Xu, Peter Scheipers, Naila Svitacheva, Tord Labuda, James G Krueger, Mayte Suárez-Fariñas, Kenji Kabashima, Emma Guttman-Yassky
BACKGROUND: Atopic dermatitis (AD) is caused by a complex interplay between immune and barrier abnormalities. Murine models of AD are essential for preclinical assessments of new treatments. While many models have been used to simulate AD, their transcriptomic profiles are not fully understood, and a comparison of these models with the human AD transcriptomic fingerprint is lacking. OBJECTIVE: We sought to evaluate the transcriptomic profiles of six common murine models and determine how they relate to human AD skin...
October 1, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27699219/profiling-cancer-testis-antigens-in-non-small-cell-lung-cancer
#17
Dijana Djureinovic, Björn M Hallström, Masafumi Horie, Johanna Sofia Margareta Mattsson, Linnea La Fleur, Linn Fagerberg, Hans Brunnström, Cecilia Lindskog, Katrin Madjar, Jörg Rahnenführer, Simon Ekman, Elisabeth Ståhle, Hirsh Koyi, Eva Brandén, Karolina Edlund, Jan G Hengstler, Mats Lambe, Akira Saito, Johan Botling, Fredrik Pontén, Mathias Uhlén, Patrick Micke
Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small-cell lung cancer (NSCLC), we compared RNAseq data from 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the Caner Testis Database (CTdatabase), 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase, thus representing potential new CTAs...
July 7, 2016: JCI Insight
https://www.readbyqxmd.com/read/27680512/integrative-transcriptomic-meta-analysis-of-parkinson-s-disease-and-depression-identifies-nampt-as-a-potential-blood-biomarker-for-de-novo-parkinson-s-disease
#18
Jose A Santiago, Alyssa M Littlefield, Judith A Potashkin
Emerging research indicates that depression could be one of the earliest prodromal symptoms or risk factors associated with the pathogenesis of Parkinson's disease (PD), the second most common neurodegenerative disorder worldwide, but the mechanisms underlying the association between both diseases remains unknown. Understanding the molecular networks linking these diseases could facilitate the discovery of novel diagnostic and therapeutics. Transcriptomic meta-analysis and network analysis of blood microarrays from untreated patients with PD and depression identified genes enriched in pathways related to the immune system, metabolism of lipids, glucose, fatty acids, nicotinamide, lysosome, insulin signaling and type 1 diabetes...
September 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27651444/epigenetic-signatures-of-cigarette-smoking
#19
Roby Joehanes, Allan C Just, Riccardo E Marioni, Luke C Pilling, Lindsay M Reynolds, Pooja R Mandaviya, Weihua Guan, Tao Xu, Cathy E Elks, Stella Aslibekyan, Hortensia Moreno-Macias, Jennifer A Smith, Jennifer A Brody, Radhika Dhingra, Paul Yousefi, James S Pankow, Sonja Kunze, Sonia Shah, Allan F McRae, Kurt Lohman, Jin Sha, Devin M Absher, Luigi Ferrucci, Wei Zhao, Ellen W Demerath, Jan Bressler, Megan L Grove, Tianxiao Huan, Chunyu Liu, Michael M Mendelson, Chen Yao, Douglas P Kiel, Annette Peters, Rui Wang-Sattler, Peter M Visscher, Naomi R Wray, John M Starr, Jingzhong Ding, Carlos J Rodriguez, Nicholas J Wareham, Marguerite R Irvin, Degui Zhi, Myrto Barrdahl, Paolo Vineis, Srikant Ambatipudi, André G Uitterlinden, Albert Hofman, Joel Schwartz, Elena Colicino, Lifang Hou, Pantel S Vokonas, Dena G Hernandez, Andrew B Singleton, Stefania Bandinelli, Stephen T Turner, Erin B Ware, Alicia K Smith, Torsten Klengel, Elisabeth B Binder, Bruce M Psaty, Kent D Taylor, Sina A Gharib, Brenton R Swenson, Liming Liang, Dawn L DeMeo, George T O'Connor, Zdenko Herceg, Kerry J Ressler, Karen N Conneely, Nona Sotoodehnia, Sharon L R Kardia, David Melzer, Andrea A Baccarelli, Joyce B J van Meurs, Isabelle Romieu, Donna K Arnett, Ken K Ong, Yongmei Liu, Melanie Waldenberger, Ian J Deary, Myriam Fornage, Daniel Levy, Stephanie J London
BACKGROUND: -DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. METHODS AND RESULTS: -To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation assessed using the Illumina BeadChip 450K array on 15,907 blood derived DNA samples from participants in 16 cohorts (including 2,433 current, 6,518 former, and 6,956 never smokers)...
September 20, 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27651116/transcriptome-meta-analysis-reveals-a-dysregulation-in-extra-cellular-matrix-and-cell-junction-associated-gene-signatures-during-dengue-virus-infection
#20
Sumbul Afroz, Jeevan Giddaluru, Mohd Manzar Abbas, Nooruddin Khan
Dengue Viruses (DENVs) cause one of the most prevalent arthropod-borne viral diseases affecting millions of people worldwide. Identification of genes involved in DENV pathogenesis would help in deciphering molecular mechanisms responsible for the disease progression. Here, we carried out a meta-analysis of publicly available gene expression data of dengue patients and further validated the meta-profile using in-vitro infection in THP-1 cells. Our findings reveal that DENV infection modulates expression of several genes and signalling pathways including interferons, detoxification of ROS and viral assembly...
2016: Scientific Reports
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