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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/28923001/a-molecular-view-of-the-normal-human-thyroid-structure-and-function-reconstructed-from-its-reference-transcriptome-map
#1
Lorenza Vitale, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Maria Chiara Pelleri, Maria Caracausi
BACKGROUND: The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28918100/transcriptomic-and-epigenomic-biomarkers-of-antidepressant-response
#2
REVIEW
Raoul Belzeaux, Rixing Lin, Chelsey Ju, Marc-Aurele Chay, Laura M Fiori, Pierre-Eric Lutz, Gustavo Turecki
BACKGROUND: Antidepressant treatment is associated with a high rate of poor response, and thus, biomarker development is warranted. METHODS: We aimed to synthesize studies investigating gene expression, small RNAs, and epigenomic biomarkers of antidepressant response. We conducted a narrative review of the literature. RESULTS: Firstly, we detailed the challenges involved, in terms of biological tissues, relevant study time frames, and mandatory statistical tools...
September 8, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28899396/transcriptomic-meta-analysis-identifies-gene-expression-characteristics-in-various-samples-of-hiv-infected-patients-with-nonprogressive-disease
#3
Le-Le Zhang, Zi-Ning Zhang, Xian Wu, Yong-Jun Jiang, Ya-Jing Fu, Hong Shang
BACKGROUND: A small proportion of HIV-infected patients remain clinically and/or immunologically stable for years, including elite controllers (ECs) who have undetectable viremia (<50 copies/ml) and long-term nonprogressors (LTNPs) who maintain normal CD4(+) T cell counts for prolonged periods (>10 years). However, the mechanism of nonprogression needs to be further resolved. In this study, a transcriptome meta-analysis was performed on nonprogressor and progressor microarray data to identify differential transcriptome pathways and potential biomarkers...
September 12, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28874788/comprehensive-transcriptome-mining-of-the-direct-conversion-of-mesodermal-cells
#4
Bijan Akbari, Ping Wee, Moein Yaqubi, Abdulshakour Mohammadnia
The direct reprogramming of somatic cells is a promising approach for regenerative medicine, especially in the production of mesoderm layer-derived cells. Meta-analysis studies provide precise insight into the undergoing processes and help increase the efficiency of reprogramming. Here, using 27 high-throughput expression data sets, we analyzed the direct reprogramming of mesodermal cells in humans and mice. Fibroblast-derived cells showed a common expression pattern of up- and down-regulated genes that were mainly involved in the suppression of the fibroblast-specific gene expression program, and may be used as markers of the initiation of reprogramming...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28855728/meta-signature-of-human-endometrial-receptivity-a-meta-analysis-and-validation-study-of-transcriptomic-biomarkers
#5
Signe Altmäe, Mariann Koel, Urmo Võsa, Priit Adler, Marina Suhorutšenko, Triin Laisk-Podar, Viktorija Kukushkina, Merli Saare, Agne Velthut-Meikas, Kaarel Krjutškov, Lusine Aghajanova, Parameswaran G Lalitkumar, Kristina Gemzell-Danielsson, Linda Giudice, Carlos Simón, Andres Salumets
Previous transcriptome studies of the human endometrium have revealed hundreds of simultaneously up- and down-regulated genes that are involved in endometrial receptivity. However, the overlap between the studies is relatively small, and we are still searching for potential diagnostic biomarkers. Here we perform a meta-analysis of endometrial-receptivity associated genes on 164 endometrial samples (76 from 'pre-receptive' and 88 from mid-secretory, 'receptive' phase endometria) using a robust rank aggregation (RRA) method, followed by enrichment analysis, and regulatory microRNA prediction...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28852117/novel-evidence-for-complement-system-activation-in-chick-myopia-and-hyperopia-models-a-meta-analysis-of-transcriptome-datasets
#6
Nina Riddell, Sheila G Crewther
Myopia (short-sightedness) and hyperopia (long-sightedness) occur when the eye grows too long or short, respectively, for its refractive power. There are currently approximately 1.45 billion myopes worldwide and prevalence is rising dramatically. Although high myopia significantly increases the risk of developing a range of sight-threatening disorders, the molecular mechanisms underlying ocular growth regulation and its relationship to these secondary complications remain poorly understood. Thus, this study meta-analyzed transcriptome datasets collected in the commonly used chick model of optically-induced refractive error...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28845240/human-protein-secretory-pathway-genes-are-expressed-in-a-tissue-specific-pattern-to-match-processing-demands-of-the-secretome
#7
Amir Feizi, Francesco Gatto, Mathias Uhlen, Jens Nielsen
Protein secretory pathway in eukaryal cells is responsible for delivering functional secretory proteins. The dysfunction of this pathway causes a range of important human diseases from congenital disorders to cancer. Despite the piled-up knowledge on the molecular biology and biochemistry level, the tissue-specific expression of the secretory pathway genes has not been analyzed on the transcriptome level. Based on the recent RNA-sequencing studies, the largest fraction of tissue-specific transcriptome encodes for the secretome (secretory proteins)...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28830341/a-regulation-probability-model-based-meta-analysis-of-multiple-transcriptomics-data-sets-for-cancer-biomarker-identification
#8
Xin-Ping Xie, Yu-Feng Xie, Hong-Qiang Wang
BACKGROUND: Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent but subtle gene activity patterns across studies. Study heterogeneity needs to be addressed carefully for this goal. RESULTS: This paper proposes a regulation probability model-based meta-analysis, jGRP, for identifying differentially expressed genes (DEGs)...
August 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28828699/global-analysis-of-gene-expression-in-maize-leaves-treated-with-low-temperature-ii-combined-effect-of-severe-cold-8%C3%A2-%C3%A2-c-and-circadian-rhythm
#9
M Jończyk, A Sobkowiak, J Trzcinska-Danielewicz, M Skoneczny, D Solecka, J Fronk, P Sowiński
In maize seedlings, severe cold results in dysregulation of circadian pattern of gene expression causing profound modulation of transcription of genes related to photosynthesis and other key biological processes. Plants live highly cyclic life and their response to environmental stresses must allow for underlying biological rhythms. To study the interplay of a stress and a rhythmic cue we investigated transcriptomic response of maize seedlings to low temperature in the context of diurnal gene expression. Severe cold stress had pronounced effect on the circadian rhythm of a substantial proportion of genes...
August 21, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28793203/rna-extraction-from-decaying-wood-for-meta-transcriptomic-analyses
#10
Martino Adamo, Samuele Voyron, Mariangela Girlanda, Roland Marmeisse
Wood decomposition is a key step of the terrestrial carbon cycle and of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating to wood decay we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms...
August 9, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28767422/a-meta-analysis-of-transcriptomic-characterization-revealed-extracellular-matrix-pathway-involved-in-the-h5n1-and-h7n9-infections
#11
Feng Wen, Jinyue Guo, Guangzhi Tong, Dingren Bi, Qi Wang, Xiaomin Liu, Shuaiyong Wang, Tonglin Shan, Wu Tong, Yanjun Zhou, Guoxin Li, Hai Yu
Avian-origin H5N1 and H7N9 influenza A viruses are capable of causing lethal infection in humans, with serious lung pathology and leading to acute respiratory distress syndrome. The contribution of host response associated with the poor prognosis of H5N1 and H7N9 infections remains unclear. The aim of this study was to identify the host factors involved in the high pathogenicity of H5N1 and H7N9 by a systematical meta-analysis. The RNA-seq datasets related to H5N1, H7N9, and H1N1 infections with time series were retrieved from GEO...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28761826/the-inhibitory-effect-of-ginger-extract-on-ovarian-cancer-cell-line-application-of-systems-biology
#12
Roghiyeh Pashaei-Asl, Fatima Pashaei-Asl, Parvin Mostafa Gharabaghi, Khodadad Khodadadi, Mansour Ebrahimi, Esmaeil Ebrahimie, Maryam Pashaiasl
Purpose: Ginger is a natural compound with anti-cancer properties. The effects of ginger and its mechanism on ovarian cancer and its cell line model, SKOV-3, are unclear. In this study, we have evaluated the effect of ginger extract on SKOV-3. Methods: SKOV-3 cells were incubated with ginger extract for 24, 48 and 72 hours. Cell toxicity assay was performed. Different data mining algorithms were applied to highlight the most important features contributing to ginger inhibition on the SKOV-3 cell proliferation...
June 2017: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28754176/genome-wide-gene-by-lead-exposure-interaction-analysis-identifies-unc5d-as-a-candidate-gene-for-neurodevelopment
#13
Zhaoxi Wang, Birgit Claus Henn, Chaolong Wang, Yongyue Wei, Li Su, Ryan Sun, Han Chen, Peter J Wagner, Quan Lu, Xihong Lin, Robert Wright, David Bellinger, Molly Kile, Maitreyi Mazumdar, Martha Maria Tellez-Rojo, Lourdes Schnaas, David C Christiani
BACKGROUND: Neurodevelopment is a complex process involving both genetic and environmental factors. Prenatal exposure to lead (Pb) has been associated with lower performance on neurodevelopmental tests. Adverse neurodevelopmental outcomes are more frequent and/or more severe when toxic exposures interact with genetic susceptibility. METHODS: To explore possible loci associated with increased susceptibility to prenatal Pb exposure, we performed a genome-wide gene-environment interaction study (GWIS) in young children from Mexico (n = 390) and Bangladesh (n = 497)...
July 28, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28718821/tick-haller-s-organ-a-new-paradigm-for-arthropod-olfaction-how-ticks-differ-from-insects
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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