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transcriptome and meta-analysis

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https://www.readbyqxmd.com/read/29115927/transcriptomic-responses-to-wounding-meta-analysis-of-gene-expression-microarray-data
#1
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
#2
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
https://www.readbyqxmd.com/read/29106664/proteomicsdb
#3
Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29095491/nitrogen-essential-macronutrient-and-signal-controlling-flowering-time
#4
Konrad Weber, Meike Burow
Nitrogen, as limiting nutrient for plant growth and crop yield, is a main component of fertilizers and heavily used in modern agriculture. Early reports from over-application of fertilizers in crop production have shown to repress the transition from vegetative to reproductive phase. For the model plant Arabidopsis thaliana, there is evidence that low nitrogen conditions promote early flowering, while high nitrogen as well as nitrogen starvation conditions display the opposite effect. To gain a better understanding how nitrogen affects the onset of flowering, we reviewed the existing literature for A...
November 2, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29094313/progress-in-elucidating-biomarkers-of-antidepressant-pharmacological-treatment-response-a-systematic-review-and-meta-analysis-of-the-last-15-years
#5
REVIEW
G Voegeli, M L Cléry-Melin, N Ramoz, P Gorwood
BACKGROUND: Antidepressant drugs are widely prescribed, but response rates after 3 months are only around one-third, explaining the importance of the search of objectively measurable markers predicting positive treatment response. These markers are being developed in different fields, with different techniques, sample sizes, costs, and efficiency. It is therefore difficult to know which ones are the most promising. OBJECTIVE: Our purpose was to compute comparable (i...
November 2, 2017: Drugs
https://www.readbyqxmd.com/read/29089372/quantitative-rna-seq-meta-analysis-of-alternative-exon-usage-in-c-elegans
#6
Nicolas J Tourasse, Jonathan R M Millet, Denis Dupuy
Almost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated. Here we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event...
October 31, 2017: Genome Research
https://www.readbyqxmd.com/read/29068110/a-review-of-genome-wide-transcriptomics-studies-in-parkinson-s-disease
#7
REVIEW
Genevie Borrageiro, William Haylett, Soraya Seedat, Helena Kuivaniemi, Soraya Bardien
Parkinson's disease (PD) is a progressive and incurable neurodegenerative disorder. Although numerous genetic and environmental factors have been linked to the etiology of PD the underlying pathobiology remains poorly understood, hampering the development of improved therapies. Transcriptomics has the potential to reveal significant insights into disease processes. In this review we focused on published transcriptomics studies on PD with the aim of summarizing studies and identifying common biological pathways...
October 25, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29044560/regulating-the-transcriptomes-that-mediate-the-conversion-of-fibroblasts-to-various-nervous-system-neural-cell-types
#8
Niusha Khazaei, Shima Rastegar-Pouyani, Nicholas O'Toole, Ping Wee, Abdulshakour Mohammadnia, Moein Yaqubi
Our understanding of the mechanism of cell fate transition during the direct reprogramming of fibroblasts into various central nervous system (CNS) neural cell types has been limited by the lack of a comprehensive analysis on generated cells, independently and in comparison with other CNS neural cell types. Here, we applied an integrative approach on 18 independent high throughput expression data sets to gain insight into the regulation of the transcriptome during the conversion of fibroblasts into induced neural stem cells, induced neurons, induced astrocytes, and induced oligodendrocyte progenitor cells...
October 17, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29042035/a-systematic-review-of-molecular-responses-to-cancer-therapy-in-normal-human-mucosa
#9
REVIEW
Mette Marcussen, Conni Skrubbeltrang, Julie Støve Bødker, Ilse Christiansen, Martin Bøgsted, Karen Dybkær, Olav Jonas Bergmann, Hans Erik Johnsen
OBJECTIVE: Cancer therapy-induced inflammation of oral and gastrointestinal mucosae affects patients nonuniformly. Preventive strategies are limited; no biomarker exists for pretreatment identification of patients likely to be severely affected. Animal models are preferred for studying molecular responses in mucosae during chemotherapy, but translation into clinical practice is difficult. We performed a systematic review to retrieve articles that described molecular changes in human mucosae during cancer therapy...
October 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/29032502/gut-microbiota-changes-in-the-extreme-decades-of-human-life-a-focus-on-centenarians
#10
REVIEW
Aurelia Santoro, Rita Ostan, Marco Candela, Elena Biagi, Patrizia Brigidi, Miriam Capri, Claudio Franceschi
The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age...
October 14, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28981577/-multi-omic-data-analysis-using-o-miner
#11
Ajanthah Sangaralingam, Abu Z Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, Ai Nagano, Helen Ross-Adams, Jun Wang, Nicholas R Lemoine, Claude Chelala
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies...
August 4, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28977969/a-meta-analysis-of-transcriptomic-characterization-revealed-extracellular-matrix-pathway-involved-in-the-h5n1-and-h7n9-infections
#12
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...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28973476/meta-analysis-of-transcriptomic-datasets-identifies-genes-enriched-in-the-mammalian-circadian-pacemaker
#13
Laurence A Brown, John Williams, Lewis Taylor, Ross J Thomson, Patrick M Nolan, Russell G Foster, Stuart N Peirson
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968784/microscope-an-integrated-resource-for-community-expertise-of-gene-functions-and-comparative-analysis-of-microbial-genomic-and-metabolic-data
#14
Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau, Adrien Josso, Aurélie Lajus, Jordan Langlois, Hugo Pereira, Rémi Planel, David Roche, Johan Rollin, Zoe Rouy, David Vallenet
The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. 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. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes...
September 12, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28955361/gaining-insight-into-exclusive-and-common-transcriptomic-features-linked-with-biotic-stress-responses-in-malus
#15
Bipin Balan, Tiziano Caruso, Federico Martinelli
Identifying key information in transcriptomic data is very important, especially when the "omic" study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28939077/genomic-characterization-of-tobacco-nut-chewing-hpv-negative-early-stage-tongue-tumors-identify-mmp10-asa-candidate-to-predict-metastases
#16
Pawan Upadhyay, Nilesh Gardi, Sanket Desai, Pratik Chandrani, Asim Joshi, Bhaskar Dharavath, Priyanca Arora, Munita Bal, Sudhir Nair, Amit Dutt
OBJECTIVES: Nodal metastases status among early stage tongue squamous cell cancer patients plays a decisive role in the choice of treatment, wherein about 70% patients can be spared from surgery with an accurate prediction of negative pathological lymph node status. This underscores an unmet need for prognostic biomarkers to stratify the patients who are likely to develop metastases. MATERIALS AND METHODS: We performed high throughput sequencing of fifty four samples derived from HPV negative early stage tongue cancer patients habitual of chewing betel nuts, areca nuts, lime or tobacco using whole exome (n=47) and transcriptome (n=17) sequencing that were analyzed using in-house computational tools...
October 2017: Oral Oncology
https://www.readbyqxmd.com/read/28923001/a-molecular-view-of-the-normal-human-thyroid-structure-and-function-reconstructed-from-its-reference-transcriptome-map
#17
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
#18
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
#19
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
#20
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
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