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Omics analysis

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https://www.readbyqxmd.com/read/29666913/comprehensive-lipid-profiling-in-the-mediterranean-mussel-mytilus-galloprovincialis-using-hyphenated-and-multidimensional-chromatography-techniques-coupled-to-mass-spectrometry-detection
#1
Paola Donato, Giuseppe Micalizzi, Marianna Oteri, Francesca Rigano, Danilo Sciarrone, Paola Dugo, Luigi Mondello
The task of lipid analysis and profiling is taking centre stage in many research fields and as a consequence, there has been an intense effort to develop suitable methodologies to discover, identify, and quantify lipids in the systems investigated. Given the high complexity and diversity of the lipidome, researchers have been challenged to afford thorough knowledge of all the lipid species in a given sample, by gathering the data obtained by complementary analytical techniques. In this research, an "omic" approach was developed to quickly fingerprint lipids in the Mediterranean mussel (Mytilus galloprovincialis), by exploiting multidimensional and hyphenated techniques...
April 17, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29666255/digitizing-omics-profiles-by-divergence-from-a-baseline
#2
Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, Anching Lien, Tejasvi Matam, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, Donald Geman
Data collected from omics technologies have revealed pervasive heterogeneity and stochasticity of molecular states within and between phenotypes. A prominent example of such heterogeneity occurs between genome-wide mRNA, microRNA, and methylation profiles from one individual tumor to another, even within a cancer subtype. However, current methods in bioinformatics, such as detecting differentially expressed genes or CpG sites, are population-based and therefore do not effectively model intersample diversity...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665821/plasma-proteomic-analysis-reveals-altered-protein-abundances-in-cardiovascular-disease
#3
Vasiliki Lygirou, Agnieszka Latosinska, Manousos Makridakis, William Mullen, Christian Delles, Joost P Schanstra, Jerome Zoidakis, Burkert Pieske, Harald Mischak, Antonia Vlahou
BACKGROUND: Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis...
April 17, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29661792/using-single-cell-genomics-to-understand-developmental-processes-and-cell-fate-decisions
#4
REVIEW
Jonathan A Griffiths, Antonio Scialdone, John C Marioni
High-throughput -omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision-making is inherently a unicellular process to which "bulk" -omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single-cell methods bridge this gap, allowing high-throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single-cell gene expression data and highlight areas of developmental biology where single-cell techniques have made important contributions...
April 16, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29656515/comparative-cyp-omic-analysis-between-the-ddt-susceptible-and-resistant-drosophila-melanogaster-strains-91-c-and-91-r
#5
Keon Mook Seong, Brad S Coates, May R Berenbaum, John M Clark, Barry R Pittendrigh
BACKGROUND: Cytochrome P450 monooxygenases (P450s) are involved in the biosynthesis of endogenous intracellular compounds and the metabolism of xenobiotics, including chemical insecticides. We investigated the structural and expression level variance across all P450 genes with respect to the evolution of insecticide resistance under multigenerational DDT selection. RESULTS: RNA-seq and reverse transcriptase quantitative PCR indicated that the transcript levels of seven P450 genes were significantly up-regulated and three P450 genes were down-regulated in the DDT-resistant strain 91-R, as compared to the control strain 91-C...
April 15, 2018: Pest Management Science
https://www.readbyqxmd.com/read/29656435/a-multi-omic-study-reveals-btg2-as-a-reliable-prognostic-marker-for-early-stage-non-small-cell-lung-cancer
#6
Sipeng Shen, Ruyang Zhang, Yichen Guo, Elizabeth Loehrer, Yongyue Wei, Ying Zhu, Qianyu Yuan, Sebastian Moran, Thomas Fleischer, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, Li Su, Feng Chen, David C Christiani
B-cell translocation gene 2 (BTG2) is a tumor suppressor protein and is known to be downregulated in several types of cancer. In this study, we investigated a potential role for BTG2 in early-stage non-small cell lung cancer (NSCLC) survival. We analysed BTG2 methylation data from 1,230 early-stage NSCLC patients from five international cohorts, as well as gene expression data from 3,038 lung cancer cases from multiple cohorts. Three CpG probes (cg01798157, cg06373167, cg23371584) that detected BTG2 hypermethylation in tumor tissues were associated with lower overall survival...
April 15, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29650893/-towards-development-of-innovative-cancer-therapies-trans-omics-approach
#7
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29650557/sputum-proteomics-and-airway-cell-transcripts-of-current-and-ex-smokers-with-severe-asthma-in-u-biopred-an-exploratory-analysis
#8
Kentaro Takahashi, Stelios Pavlidis, Francois Ng Kee Kwong, Uruj Hoda, Christos Rossios, Kai Sun, Matthew Loza, Fred Baribaud, Pascal Chanez, Steve J Fowler, Ildiko Horvath, Paolo Montuschi, Florian Singer, Jacek Musial, Barbro Dahlen, Sven-Eric Dahlen, N Krug, Thomas Sandstrom, Dominic E Shaw, Rene Lutter, Per Bakke, Louise J Fleming, Peter H Howarth, Massimo Caruso, Ana R Sousa, Julie Corfield, Charles Auffray, Bertrand De Meulder, Diane Lefaudeux, Ratko Djukanovic, Peter J Sterk, Yike Guo, Ian M Adcock, Kian Fan Chung
Background: Severe asthma patients with a significant smoking history have airflow obstruction with reported neutrophilia. We hypothesise that multi-omic analysis will enable the definition of smoking and ex-smoking severe asthma molecular phenotypes. Methods: The U-BIOPRED severe asthma patients containing current-smokers (CSA), ex-smokers (ESA), non-smokers (NSA) and healthy non-smokers (NH) was examined. Blood and sputum cell counts, fractional exhaled nitric oxide and spirometry were obtained. Exploratory proteomic analysis of sputum supernatants and transcriptomic analysis of bronchial brushings, biopsies and sputum cells was performed...
April 12, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29649387/multi-omics-research-trends-in-sepsis-a-bibliometric-comparative-analysis-between-the-united-states-the-european-union-28-member-states-and-china
#9
Nikolaos Evangelatos, Kapaettu Satyamoorthy, Georgia Levidou, Pia Bauer, Helmut Brand, Christina Kouskouti, Hans Lehrach, Angela Brand
"-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China...
March 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29643545/-necessity-and-feasibility-of-data-sharing-of-cohort-studies
#10
Y Yang, H Y Zhao, S Y Zhan
Cohort study is one of the important epidemiological methods which plays an irreplaceable status and role in etiological study. Using cohort study design, we can accurately and continuously collect genetic and environmental information, and identify and validate omics biomarkers to provide evidences for precision public health and medicine. However, results from a new cohort would not be available for at least ten years, as five years would be needed for funding, planning and enrolment, and another five for following up even the earliest analyses of the most common diseases; results for most cancers would take longer, with an unaffordable budget for many research investigators or institutions...
April 18, 2018: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/29627729/biomedical-analysis-of-formalin-fixed-paraffin-embedded-tissue-samples-the-holy-grail-for-molecular-diagnostics
#11
REVIEW
Boglarka Donczo, Andras Guttman
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics...
April 2, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29625844/who-iuis-allergen-nomenclature-providing-a-common-language
#12
Anna Pomés, Janet M Davies, Gabriele Gadermaier, Christiane Hilger, Thomas Holzhauser, Jonas Lidholm, Andreas L Lopata, Geoffrey A Mueller, Andreas Nandy, Christian Radauer, Sanny K Chan, Uta Jappe, Jörg Kleine-Tebbe, Wayne R Thomas, Martin D Chapman, Marianne van Hage, Ronald van Ree, Stefan Vieths, Monika Raulf, Richard E Goodman
A systematic nomenclature for allergens originated in the early 1980s, when few protein allergens had been described. A group of scientists led by Dr. David G. Marsh developed a nomenclature based on the Linnaean taxonomy, and further established the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee in 1986. Its stated aim was to standardize the names given to the antigens (allergens) that caused IgE-mediated allergies in humans. The Sub-Committee first published a revised list of allergen names in 1986, which continued to grow with rare publications until 1994...
April 3, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/29624711/lessons-learnt-on-the-analysis-of-large-sequence-data-in-animal-genomics
#13
REVIEW
F Biscarini, P Cozzi, P Orozco-Ter Wengel
The 'omics revolution has made a large amount of sequence data available to researchers and the industry. This has had a profound impact in the field of bioinformatics, stimulating unprecedented advancements in this discipline. Mostly, this is usually looked at from the perspective of human 'omics, in particular human genomics. Plant and animal genomics, however, have also been deeply influenced by next-generation sequencing technologies, with several genomics applications now popular among researchers and the breeding industry...
April 6, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29620229/mir%C3%A2-22%C3%A2-3p-enhances-multi%C3%A2-chemoresistance-by-targeting-net1-in-bladder-cancer-cells
#14
Jun Xiao, Sanqiang Niu, Jiahong Zhu, Lei Lv, Hui Deng, Daqing Pan, Deyun Shen, Congyun Xu, Zhou Shen, Tao Tao
With the discovery of new chemotherapeutic drugs, chemotherapy becomes increasingly valuable. However, the resistance of tumor cells to chemotherapeutic agents significantly limits the effectiveness and causes chemotherapy failure. MicroRNAs have been shown to regulate drug resistance in many types of cancer. In the present study, we measured the chemosensitivity of five bladder cancer (BCa) cell lines to seven commonly used chemotherapeutic drugs by Vita‑Blue assay. We then identified the most sensitive (5637) and most tolerant cell lines (H‑bc) and conducted a multi‑group test...
April 4, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29617783/a-practical-tool-for-maximal-information-coe_cient-analysis
#15
Davide Albanese, Samantha Riccadonna, Claudio Donati, Pietro Franceschi
Background: The ability of _nding complex associations in large omics datasets, assessing their signi_cance, and prioritizing them according to their strength can be of great help in the data exploration phase. Mutual Information based measures of association are particularly promising, in particular after the recent introduction of the TICe and MICe estimators, which combine computational e_ciency with superior bias/variance properties. An open-source software implementation of these two measures providing a comprehensive procedure to test their signi_cance would be extremely useful...
April 2, 2018: GigaScience
https://www.readbyqxmd.com/read/29617661/integrated-genomic-analysis-of-the-ubiquitin-pathway-across-cancer-types
#16
Zhongqi Ge, Jake S Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang, Jianfang Liu, Craig D Shriver, Hai Hu, Helen Piwnica-Worms, Li Ma, Han Liang
Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29616063/morphdb-prioritizing-genes-for-specialized-metabolism-pathways-and-gene-ontology-categories-in-plants
#17
Arthur Zwaenepoel, Tim Diels, David Amar, Thomas Van Parys, Ron Shamir, Yves Van de Peer, Oren Tzfadia
Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29615613/multi-omics-analysis-reveals-neoantigen-independent-immune-cell-infiltration-in-copy-number-driven-cancers
#18
Daniel J McGrail, Lorenzo Federico, Yongsheng Li, Hui Dai, Yiling Lu, Gordon B Mills, Song Yi, Shiaw-Yih Lin, Nidhi Sahni
To realize the full potential of immunotherapy, it is critical to understand the drivers of tumor infiltration by immune cells. Previous studies have linked immune infiltration with tumor neoantigen levels, but the broad applicability of this concept remains unknown. Here, we find that while this observation is true across cancers characterized by recurrent mutations, it does not hold for cancers driven by recurrent copy number alterations, such as breast and pancreatic tumors. To understand immune invasion in these cancers, we developed an integrative multi-omics framework, identifying the DNA damage response protein ATM as a driver of cytokine production leading to increased immune infiltration...
April 3, 2018: Nature Communications
https://www.readbyqxmd.com/read/29611629/chemometrics-strategies-for-peak-detection-and-profiling-from-multidimensional-chromatography
#19
REVIEW
Meritxell Navarro-Reig, Carmen Bedia, Romà Tauler, Joaquim Jaumot
The increasing complexity of omics research has encouraged the development of new instrumental technologies able to deal with these challenging samples. In this way, the rise of multidimensional separations should be highlighted due to the massive amounts of information that provide with an enhanced analyte determination. Both proteomics and metabolomics benefit from this higher separation capacity achieved when different chromatographic dimensions are combined, either in LC or GC. However, this vast quantity of experimental information requires the application of chemometric data analysis strategies to retrieve this hidden knowledge, especially in the case of non-targeted studies...
April 3, 2018: Proteomics
https://www.readbyqxmd.com/read/29605853/experimental-design-and-bioinformatic-analysis-of-dna-methylation-data
#20
Yulia Medvedeva, Alexander Shershebnev
DNA methylation is a crucial regulatory mechanism of gene expression, affected in many human pathologies. Therefore, it is not surprising that nowadays, in the era of high-throughput methods, a lot of data sets representing DNA methylation in various conditions are available and the amount of such data keeps growing. In this chapter, we discuss those aspects of experiment planning and data analysis, which we consider the most important for reliability and reproducibility of DNA methylation studies: usage of replicates, data quality control at various stages, selection of a statistical model, and incorporation of DNA methylation into the multi-omics analysis...
2018: Methods in Molecular Biology
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