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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/29355066/circadian-and-light-driven-metabolic-rhythms-in-drosophila-melanogaster
#1
Seth D Rhoades, Katrina Nayak, Shirley Zhang, Amita Sehgal, Aalim M Weljie
Complex interactions of environmental cues and transcriptional clocks drive rhythmicity in organismal physiology. Light directly affects the circadian clock; however, little is known about its relative role in controlling metabolic variations in vivo. Here we used high time-resolution sampling in Drosophila at every 2 h to measure metabolite outputs using a liquid-chromatography tandem mass spectrometry (LC-MS/MS) approach. Over 14% of detected metabolites oscillated with circadian periodicity under light-dark (LD) cycles...
January 1, 2018: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#2
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29303513/in-vitro-modeling-of-hepatocellular-carcinoma-molecular-subtypes-for-anti-cancer-drug-assessment
#3
Hadassa Hirschfield, C Billie Bian, Takaaki Higashi, Shigeki Nakagawa, Tizita Z Zeleke, Venugopalan D Nair, Bryan C Fuchs, Yujin Hoshida
Tractable experimental model that accounts for inter-tumor molecular heterogeneity is a key element of anti-cancer drug development. Hepatocellular carcinoma is known to exhibit highly heterogeneous molecular aberrations across the tumors, including somatic genetic and epigenetic alterations. Previous studies showed that molecular tumor subtypes determined by transcriptome, as a comprehensive functional readout, are reproducibly observed across global patient populations irrespective of geographic and etiological variations...
January 5, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29302075/foxo1-a2m-and-tgf-%C3%AE-1-three-novel-genes-predicting-depression-in-gene-x-environment-interactions-are-identified-using-cross-species-and-cross-tissues-transcriptomic-and-mirnomic-analyses
#4
Annamaria Cattaneo, Nadia Cattane, Chiara Malpighi, Darina Czamara, Anna Suarez, Nicole Mariani, Eero Kajantie, Alessia Luoni, Johan G Eriksson, Jari Lahti, Valeria Mondelli, Paola Dazzan, Katri Räikkönen, Elisabeth B Binder, Marco A Riva, Carmine M Pariante
To date, gene-environment (GxE) interaction studies in depression have been limited to hypothesis-based candidate genes, since genome-wide (GWAS)-based GxE interaction studies would require enormous datasets with genetics, environmental, and clinical variables. We used a novel, cross-species and cross-tissues "omics" approach to identify genes predicting depression in response to stress in GxE interactions. We integrated the transcriptome and miRNome profiles from the hippocampus of adult rats exposed to prenatal stress (PNS) with transcriptome data obtained from blood mRNA of adult humans exposed to early life trauma, using a stringent statistical analyses pathway...
January 4, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29300726/regulation-of-circadian-clock-transcriptional-output-by-clock-bmal1
#5
Alexandra J Trott, Jerome S Menet
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions. The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously to all of its target genes, its transcriptional output is highly heterogeneous. By performing a meta-analysis of several independent genome-wide datasets, we found that the binding of other transcription factors at CLOCK:BMAL1 enhancers likely contribute to the heterogeneity of CLOCK:BMAL1 transcriptional output...
January 4, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29291225/application-of-viromics-a-new-approach-to-the-understanding-of-viral-infections-in-humans
#6
REVIEW
Mageshbabu Ramamurthy, Sathish Sankar, Rajesh Kannangai, Balaji Nandagopal, Gopalan Sridharan
This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes...
December 2017: Virusdisease
https://www.readbyqxmd.com/read/29285217/identification-of-novel-gene-expression-signature-in-lung-adenocarcinoma-by-using-next-generation-sequencing-data-and-bioinformatics-analysis
#7
Ya-Ling Hsu, Jen-Yu Hung, Yen-Lung Lee, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Ying-Ming Tsai, Inn-Wen Chong, Po-Lin Kuo
Lung adenocarcinoma is one of the leading causes of cancer-related death worldwide. We showed transcriptomic profiles in three pairs of tumors and adjacent non-tumor lung tissues using next-generation sequencing (NGS) to screen protein-coding RNAs and microRNAs. Combined with meta-analysis from the Oncomine and Gene Expression Omnibus (GEO) databases, we identified a representative genetic expression signature in lung adenocarcinoma. There were 9 upregulated genes, and 8 downregulated genes in lung adenocarcinoma...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29280245/systematic-genetic-analyses-of-genome-wide-association-study-data-reveal-an-association-between-the-key-nucleosome-remodeling-and-deacetylase-complex-and-bipolar-disorder-development
#8
Bo Xiang, Kezhi Liu, Minglan Yu, Xuemei Liang, Jin Zhang, Wei Lei, Chaohua Huang, Jing Chen, Xiaochu Gu, Nian Li, Guoying Wu, Yan Wang, Wenying He, Jinhua Tan, Tao Zhang
BACKGROUND: Genome-wide association studies (GWASs) are used to identify genetic variants for association with bipolar disorder (BD) risk; however, each GWAS can only reveal a small fraction of this association. This study systematically analyzed multiple GWAS data sets to provide further insights into potential causal BD processes by integrating the results of Psychiatric Genomics Consortium Phase I (PGC-I) for BD with core human pathways and functional networks. METHODS: The i-Gsea4GwasV2 program was used to analyze data from the PGC-I GWAS for BD (the pathways came from Reactome), as well as the nominally significant pathways...
December 27, 2017: Bipolar Disorders
https://www.readbyqxmd.com/read/29259393/the-retina-rpe-proteome-in-chick-myopia-and-hyperopia-models-commonalities-with-inherited-and-age-related-ocular-pathologies
#9
Nina Riddell, Pierre Faou, Melanie Murphy, Loretta Giummarra, Rachael A Downs, Harinda Rajapaksha, Sheila G Crewther
Purpose: Microarray and RNA sequencing studies in the chick model of early optically induced refractive error have implicated thousands of genes, many of which have also been linked to ocular pathologies in humans, including age-related macular degeneration (AMD), choroidal neovascularization, glaucoma, and cataract. These findings highlight the potential relevance of the chick model to understanding both refractive error development and the progression to secondary pathological complications...
2017: Molecular Vision
https://www.readbyqxmd.com/read/29238347/langerhans-cells-programmed-by-the-epidermis
#10
REVIEW
Kalum Clayton, Andres F Vallejo, James Davies, Sofia Sirvent, Marta E Polak
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels. These cells determine the appropriate adaptive immune response (inflammation or tolerance) by interpreting the microenvironmental context in which they encounter foreign substances. In a normal physiological, "non-dangerous" situation, LCs coordinate a continuous state of immune tolerance, preventing unnecessary and harmful immune activation. Conversely, when they sense a danger signal, for example during infection or when the physical integrity of skin has been compromised as a result of a trauma, they instruct T lymphocytes of the adaptive immune system to mount efficient effector responses...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29194524/functional-sequencing-read-annotation-for-high-precision-microbiome-analysis
#11
Chengsheng Zhu, Maximilian Miller, Srinayani Marpaka, Pavel Vaysberg, Malte C Rühlemann, Guojun Wu, Femke-Anouska Heinsen, Marie Tempel, Liping Zhao, Wolfgang Lieb, Andre Franke, Yana Bromberg
The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities-microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes...
November 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29187960/meta-analysis-of-liver-and-heart-transcriptomic-data-for-functional-annotation-transfer-in-mammalian-orthologs
#12
Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume Devailly
Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from over 1500 experiments with varied treatments. We used a hyper-graph clustering method to identify clusters of orthologous genes co-expressed in both mouse and rat...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29186694/large-scale-cognitive-gwas-meta-analysis-reveals-tissue-specific-neural-expression-and-potential-nootropic-drug-targets
#13
Max Lam, Joey W Trampush, Jin Yu, Emma Knowles, Gail Davies, David C Liewald, John M Starr, Srdjan Djurovic, Ingrid Melle, Kjetil Sundet, Andrea Christoforou, Ivar Reinvang, Pamela DeRosse, Astri J Lundervold, Vidar M Steen, Thomas Espeseth, Katri Räikkönen, Elisabeth Widen, Aarno Palotie, Johan G Eriksson, Ina Giegling, Bettina Konte, Panos Roussos, Stella Giakoumaki, Katherine E Burdick, Antony Payton, William Ollier, Ornit Chiba-Falek, Deborah K Attix, Anna C Need, Elizabeth T Cirulli, Aristotle N Voineskos, Nikos C Stefanis, Dimitrios Avramopoulos, Alex Hatzimanolis, Dan E Arking, Nikolaos Smyrnis, Robert M Bilder, Nelson A Freimer, Tyrone D Cannon, Edythe London, Russell A Poldrack, Fred W Sabb, Eliza Congdon, Emily Drabant Conley, Matthew A Scult, Dwight Dickinson, Richard E Straub, Gary Donohoe, Derek Morris, Aiden Corvin, Michael Gill, Ahmad R Hariri, Daniel R Weinberger, Neil Pendleton, Panos Bitsios, Dan Rujescu, Jari Lahti, Stephanie Le Hellard, Matthew C Keller, Ole A Andreassen, Ian J Deary, David C Glahn, Anil K Malhotra, Todd Lencz
Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability ("g"), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29186328/meta-analytic-principal-component-analysis-in-integrative-omics-application
#14
SungHwan Kim, Dongwan Kang, Zhiguang Huo, Yongseok Park, George C Tseng
Motivation: With the prevalent usage of microarray and massively parallel sequencing, numerous high-throughput omics datasets have become available in the public domain. Integrating abundant information among omics datasets is critical to elucidate biological mechanisms. Due to the high-dimensional nature of the data, methods such as principal component analysis (PCA) have been widely applied, aiming at effective dimension reduction and exploratory visualization. Results: In this paper, we combine multiple omics datasets of identical or similar biological hypothesis and introduce two variations of meta-analytic framework of PCA, namely MetaPCA...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29182646/transcriptome-wide-analysis-of-the-trypanosoma-cruzi-proliferative-cycle-identifies-the-periodically-expressed-mrnas-and-their-multiple-levels-of-control
#15
Santiago Chávez, Guillermo Eastman, Pablo Smircich, Lorena Lourdes Becco, Carolina Oliveira-Rizzo, Rafael Fort, Mariana Potenza, Beatriz Garat, José Roberto Sotelo-Silveira, María Ana Duhagon
Trypanosoma cruzi is the protozoan parasite causing American trypanosomiasis or Chagas disease, a neglected parasitosis with important human health impact in Latin America. The efficacy of current therapy is limited, and its toxicity is high. Since parasite proliferation is a fundamental target for rational drug design, we sought to progress into its understanding by applying a genome-wide approach. Treating a TcI linage strain with hydroxyurea, we isolated epimastigotes in late G1, S and G2/M cell cycle stages at 70% purity...
2017: PloS One
https://www.readbyqxmd.com/read/29167564/whole-transcriptome-sequencing-analyses-reveal-molecular-markers-of-blood-pressure-response-to-thiazide-diuretics
#16
Ana Caroline C Sá, Amy Webb, Yan Gong, Caitrin W McDonough, Somnath Datta, Taimour Y Langaee, Stephen T Turner, Amber L Beitelshees, Arlene B Chapman, Eric Boerwinkle, John G Gums, Steven E Scherer, Rhonda M Cooper-DeHoff, Wolfgang Sadee, Julie A Johnson
Thiazide diuretics (TD) are commonly prescribed anti-hypertensives worldwide. However, <40% of patients treated with thiazide monotherapy achieve BP control. This study uses whole transcriptome sequencing to identify novel molecular markers associated with BP response to TD. We assessed global RNA expression levels in whole blood samples from 150 participants, representing patients in the upper and lower quartile of BP response to TD from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) (50 whites) and from PEAR-2 (50 whites and 50 blacks)...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29166994/biological-phosphorus-recovery-review-of-current-progress-and-future-needs
#17
Yu Yang, Xu Shi, Wendy Ballent, Brooke K Mayer
  This review summarizes the main species of polyphosphate accumulating organisms (PAOs) and algae, illustrates their pathways and key enzymes, discusses biological phosphorous (P) recovery from dilute waters, and identifies research avenues to encourage adoption and implementation. Phylogenic analysis indicates that the Proteobacteria phylum plays an important role in enhanced biological phosphorus removal (EBPR). The use of meta-transcriptome analysis and single cell-based techniques to help overcome the challenges associated with non-PAO competition was discussed...
December 1, 2017: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/29156228/effect-of-abiotic-and-biotic-stress-factors-analysis-using-machine-learning-methods-in-zebrafish
#18
Rajasekar Gutha, Suresh Yarrappagaari, Lavanya Thopireddy, Kesireddy Sathyavelu Reddy, Rajeswara Reddy Saddala
In order to understand the mechanisms underlying stress responses, meta-analysis of transcriptome is made to identify differentially expressed genes (DEGs) and their biological, molecular and cellular mechanisms in response to stressors. The present study is aimed at identifying the effect of abiotic and biotic stress factors, and it is found that several stress responsive genes are common for both abiotic and biotic stress factors in zebrafish. The meta-analysis of micro-array studies revealed that almost 4...
November 11, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29115927/transcriptomic-responses-to-wounding-meta-analysis-of-gene-expression-microarray-data
#19
Piotr Andrzej Sass, Michał Dąbrowski, Agata Charzyńska, Paweł Sachadyn
BACKGROUND: A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. RESULTS: We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29111455/meta-transcriptomics-and-the-evolutionary-biology-of-rna-viruses
#20
REVIEW
Mang Shi, Yong-Zhen Zhang, Edward C Holmes
Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses...
October 27, 2017: Virus Research
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