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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/28718821/tick-haller-s-organ-a-new-paradigm-for-arthropod-olfaction-how-ticks-differ-from-insects
#1
Ann L Carr, Robert D Mitchell Iii, Anirudh Dhammi, Brooke W Bissinger, Daniel E Sonenshine, R Michael Roe
Ticks are the vector of many human and animal diseases; and host detection is critical to this process. Ticks have a unique sensory structure located exclusively on the 1st pairs of legs; the fore-tarsal Haller's organ, not found in any other animals, presumed to function like the insect antennae in chemosensation but morphologically very different. The mechanism of tick chemoreception is unknown. Utilizing next-generation sequencing and comparative transcriptomics between the 1st and 4th legs (the latter without the Haller's organ), we characterized 1st leg specific and putative Haller's organ specific transcripts from adult American dog ticks, Dermacentor variabilis...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28713914/systematic-identification-of-human-housekeeping-genes-possibly-useful-as-references-in-gene-expression-studies
#2
Maria Caracausi, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Lorenza Vitale, Maria Chiara Pelleri
The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28704447/sexual-dimorphisms-of-mrna-and-mirna-in-human-murine-heart-disease
#3
Masato Tsuji, Takanori Kawasaki, Takeru Matsuda, Tomio Arai, Satoshi Gojo, Jun K Takeuchi
BACKGROUND: Sexual dimorphisms are well recognized in various cardiac diseases such as ischemic cardiomyopathy (ICM), hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). Thorough understanding of the underlying genetic programs is crucial to optimize treatment strategies specified for each gender. By performing meta-analysis and microarray analysis, we sought to comprehensively characterize the sexual dimorphisms in the healthy and diseased heart at the level of both mRNA and miRNA transcriptome...
2017: PloS One
https://www.readbyqxmd.com/read/28694494/differential-co-expression-analysis-reveals-a-novel-prognostic-gene-module-in-ovarian-cancer
#4
Esra Gov, Kazim Yalcin Arga
Ovarian cancer is one of the most significant disease among gynecological disorders that women suffered from over the centuries. However, disease-specific and effective biomarkers were still not available, since studies have focused on individual genes associated with ovarian cancer, ignoring the interactions and associations among the gene products. Here, ovarian cancer differential co-expression networks were reconstructed via meta-analysis of gene expression data and co-expressed gene modules were identified in epithelial cells from ovarian tumor and healthy ovarian surface epithelial samples to propose ovarian cancer associated genes and their interactions...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28690617/transcriptomic-analysis-of-soil-grown-t-aestivum-cv-root-to-reveal-the-changes-in-expression-of-genes-in-response-to-multiple-nutrients-deficiency
#5
Saurabh Gupta, Brijesh S Yadav, Utkarsh Raj, Shiri Freilich, Pritish K Varadwaj
Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28687728/acinetobacter-sp-dw-1-immobilized-on-polyhedron-hollow-polypropylene-balls-and-analysis-of-transcriptome-and-proteome-of-the-bacterium-during-phenol-biodegradation-process
#6
Qihui Gu, Qingping Wu, Jumei Zhang, Weipeng Guo, Huiqing Wu, Ming Sun
Phenol is a hazardous chemical known to be widely distributed in aquatic environments. Biodegradation is an attractive option for removal of phenol from water sources. Acinetobacter sp. DW-1 isolated from drinking water biofilters can use phenol as a sole carbon and energy source. In this study, we found that Immobilized Acinetobacter sp. DW-1cells were effective in biodegradation of phenol. In addition, we performed proteome and transcriptome analysis of Acinetobacter sp. DW-1 during phenol biodegradation...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679947/interspecies-nash-disease-activity-whole-genome-profiling-identifies-a-fibrogenic-role-of-ppar%C3%AE-regulated-dermatopontin
#7
Philippe Lefebvre, Fanny Lalloyer, Eric Baugé, Michal Pawlak, Céline Gheeraert, Hélène Dehondt, Jonathan Vanhoutte, Eloise Woitrain, Nathalie Hennuyer, Claire Mazuy, Marie Bobowski-Gérard, Francesco Paolo Zummo, Bruno Derudas, Ann Driessen, Guy Hubens, Luisa Vonghia, Wilhelmus J Kwanten, Peter Michielsen, Thomas Vanwolleghem, Jérôme Eeckhoute, An Verrijken, Luc Van Gaal, Sven Francque, Bart Staels
Nonalcoholic fatty liver disease prevalence is soaring with the obesity pandemic, but the pathogenic mechanisms leading to the progression toward active nonalcoholic steatohepatitis (NASH) and fibrosis, major causes of liver-related death, are poorly defined. To identify key components during the progression toward NASH and fibrosis, we investigated the liver transcriptome in a human cohort of NASH patients. The transition from histologically proven fatty liver to NASH and fibrosis was characterized by gene expression patterns that successively reflected altered functions in metabolism, inflammation, and epithelial-mesenchymal transition...
July 6, 2017: JCI Insight
https://www.readbyqxmd.com/read/28676447/profiling-conserved-biological-pathways-in-autosomal-dominant-polycystic-kidney-disorder-adpkd-to-elucidate-key-transcriptomic-alterations-regulating-cystogenesis-a-cross-species-meta-analysis-approach
#8
REVIEW
Shatakshee Chatterjee, Srikant Prasad Verma, Priyanka Pandey
PURPOSE: Initiation and progression of fluid filled cysts mark Autosomal Dominant Polycystic Kidney Disease (ADPKD). Thus, improved therapeutics targeting cystogenesis remains a constant challenge. Microarray studies in single ADPKD animal models species with limited sample sizes tend to provide scattered views on underlying ADPKD pathogenesis. Thus we aim to perform a cross species meta-analysis to profile conserved biological pathways that might be key targets for therapy. METHODS: Nine ADPKD microarray datasets on rat, mice and human fulfilled our study criteria and were chosen...
July 1, 2017: Gene
https://www.readbyqxmd.com/read/28676233/customized-workflow-development-and-data-modularization-concepts-for-rna-sequencing-and-metatranscriptome-experiments
#9
Steffen C Lott, Markus Wolfien, Konstantin Riege, Andrea Bagnacani, Olaf Wolkenhauer, Steve Hoffmann, Wolfgang R Hess
RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses...
July 1, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28667284/a-molecular-hypothesis-to-explain-direct-and-inverse-co-morbidities-between-alzheimer-s-disease-glioblastoma-and-lung-cancer
#10
Jon Sánchez-Valle, Héctor Tejero, Kristina Ibáñez, José Luis Portero, Martin Krallinger, Fátima Al-Shahrour, Rafael Tabarés-Seisdedos, Anaïs Baudot, Alfonso Valencia
Epidemiological studies indicate that patients suffering from Alzheimer's disease have a lower risk of developing lung cancer, and suggest a higher risk of developing glioblastoma. Here we explore the molecular scenarios that might underlie direct and inverse co-morbidities between these diseases. Transcriptomic meta-analyses reveal significant numbers of genes with inverse patterns of expression in Alzheimer's disease and lung cancer, and with similar patterns of expression in Alzheimer's disease and glioblastoma...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28649742/genotranscriptomic-meta-analysis-of-the-chd-family-chromatin-remodelers-in-human-cancers-initial-evidence-of-an-oncogenic-role-for-chd7
#11
Xiaofang Chu, Xuhui Guo, Yuanyuan Jiang, Huimei Yu, Lanxin Liu, Wenqi Shan, Zeng-Quan Yang
Chromodomain helicase DNA binding proteins (CHD) are characterized by N-terminal tandem chromodomains and a central ATP-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer...
June 26, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28649431/meta-analysis-of-host-response-networks-identifies-a-common-core-in-tuberculosis
#12
Awanti Sambarey, Abhinandan Devaprasad, Priyanka Baloni, Madhulika Mishra, Abhilash Mohan, Priyanka Tyagi, Amit Singh, J S Akshata, Razia Sultana, Shashidhar Buggi, Nagasuma Chandra
Tuberculosis remains a major global health challenge worldwide, causing more than a million deaths annually. To determine newer methods for detecting and combating the disease, it is necessary to characterise global host responses to infection. Several high throughput omics studies have provided a rich resource including a list of several genes differentially regulated in tuberculosis. An integrated analysis of these studies is necessary to identify a unified response to the infection. Such data integration is met with several challenges owing to platform dependency, patient heterogeneity, and variability in the extent of infection, resulting in little overlap among different datasets...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#13
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28640813/identification-of-a-sj%C3%A3-gren-s-syndrome-susceptibility-locus-at-oas1-that-influences-isoform-switching-protein-expression-and-responsiveness-to-type-i-interferons
#14
He Li, Tove Ragna Reksten, John A Ice, Jennifer A Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M Grundahl, Stuart B Glenn, Corinne Miceli-Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija-Leena Eloranta, Johan G Brun, Lasse G Gøransson, Erna Harboe, Joel M Guthridge, Kenneth M Kaufman, Marika Kvarnström, Deborah S Cunninghame Graham, Ketan Patel, Adam J Adler, A Darise Farris, Michael T Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H Weisman, Swamy Venuturupalli, Daniel J Wallace, Kimberly S Hefner, Glen D Houston, Andrew J W Huang, Pamela J Hughes, David M Lewis, Lida Radfar, Evan S Vista, Contessa E Edgar, Michael D Rohrer, Donald U Stone, Timothy J Vyse, John B Harley, Patrick M Gaffney, Judith A James, Sean Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L Rhodus, Barbara M Segal, Courtney G Montgomery, R Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren-Herlenius, Roald Omdal, Roland Jonsson, Wan-Fai Ng, Gunnel Nordmark, Christopher J Lessard, Kathy L Sivils
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28637756/high-resolution-meta-transcriptomics-reveals-the-ecological-dynamics-of-mosquito-associated-rna-viruses-in-western-australia
#15
Mang Shi, Peter Neville, Jay Nicholson, John-Sebastian Eden, Allison Imrie, Edward C Holmes
Mosquitoes harbour a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a meta-transcriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637422/optimal-alpha-reduces-error-rates-in-gene-expression-studies-a-meta-analysis-approach
#16
J F Mudge, C J Martyniuk, J E Houlahan
BACKGROUND: Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the large number of comparisons that are done within an experiment. The result has been a proliferation of techniques aimed at solving the multiple comparisons problem, techniques that have focused primarily on minimizing Type I error with little or no concern about concomitant increases in Type II errors...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28616586/the-autotaxin-lysophosphatidic-acid-pathway-emerges-as-a-therapeutic-target-to-prevent-liver-cancer
#17
Derek J Erstad, Andrew M Tager, Yujin Hoshida, Bryan C Fuchs
Using transcriptome meta-analysis, we recently identified the autotaxin (ATX)-lysophosphatidic acid (LPA) pathway as a regulator of hepatocellular carcinoma (HCC) risk in human cirrhosis patients. Pharmacological targeting of this pathway reduced fibrosis progression and HCC development in animals, identifying ATX-LPA signaling as a novel chemoprevention strategy for cirrhosis and HCC.
2017: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/28610557/integration-of-quantitated-expression-estimates-from-polya-selected-and-rrna-depleted-rna-seq-libraries
#18
Stephen J Bush, Mary E B McCulloch, Kim M Summers, David A Hume, Emily L Clark
BACKGROUND: The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced...
June 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28591656/taming-human-genetic-variability-transcriptomic-meta-analysis-guides-the-experimental-design-and-interpretation-of-ipsc-based-disease-modeling
#19
Pierre-Luc Germain, Giuseppe Testa
Both the promises and pitfalls of the cell reprogramming research platform rest on human genetic variation, making the measurement of its impact one of the most urgent issues in the field. Harnessing large transcriptomics datasets of induced pluripotent stem cells (iPSC), we investigate the implications of this variability for iPSC-based disease modeling. In particular, we show that the widespread use of more than one clone per individual in combination with current analytical practices is detrimental to the robustness of the findings...
June 6, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28587632/meta-analysis-of-cell-specific-transcriptomic-data-using-fuzzy-c-means-clustering-discovers-versatile-viral-responsive-genes
#20
Atif Khan, Dejan Katanic, Juilee Thakar
BACKGROUND: Despite advances in the gene-set enrichment analysis methods; inadequate definitions of gene-sets cause a major limitation in the discovery of novel biological processes from the transcriptomic datasets. Typically, gene-sets are obtained from publicly available pathway databases, which contain generalized definitions frequently derived by manual curation. Recently unsupervised clustering algorithms have been proposed to identify gene-sets from transcriptomics datasets deposited in public domain...
June 6, 2017: BMC Bioinformatics
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