scholarly journals Navigating Public Microarray Databases

2004 ◽  
Vol 5 (6-7) ◽  
pp. 471-479 ◽  
Author(s):  
Christopher J. Penkett ◽  
Jürg Bähler
Keyword(s):  
Data Sources ◽  
European Bioinformatics Institute ◽  
Published Data ◽  
Expression Data ◽  
The Public ◽  
Genome Wide ◽  
Public Repositories ◽  
Set Up ◽  
Downstream Analysis ◽  
Microarray Studies

With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources.

scholarly journals Curated compendium of human transcriptional biomarker data

2017 ◽  
Author(s):  
Nathan P. Golightly ◽  
Anna I. Bischoff ◽  
Avery Bell ◽  
Parker D. Hollingsworth ◽  
Stephen R. Piccolo
Keyword(s):  
Machine Learning Algorithms ◽  
Data Reuse ◽  
Clinical Settings ◽  
The Public ◽  
The Past ◽  
Genome Wide ◽  
Gene Level ◽  
Public Repositories ◽  
Reproducible Manner

AbstractGenome-wide transcriptional profiles provide broad insights into cellular activity. One important use of such data isto identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for predicting outcomes in clinical settings. Over the past decades, data from many translational-biomarker studies have been deposited in public repositories, enabling other scientists to reuse the data in follow-up studies. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated a compendium of 45 translational-biomarker datasets from the public domain. To increase the data’s utility, we reprocessed the raw expression data using a standard computational pipeline and standardized the clinical annotations in a fully reproducible manner (see osf.io/ssk3t). We believe these data will be particularly useful to researchers seeking to validate gene-level findings or to perform benchmarking studies—for example, to compare and optimize machine-learning algorithms’ ability to predict biomedical outcomes.

scholarly journals A measure of agreement across numerous conditions: Reproducibility of co-expression networks across tissues

2017 ◽  
Author(s):  
Alejandro Cáceres ◽  
Juan R. González
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Expression Data ◽  
Full Agreement ◽  
Statistical Measures ◽  
Expression Studies ◽  
Genome Wide ◽  
Gene Expression Studies ◽  
Microarray Studies ◽  
Level Of Agreement

AbstractThere is great interest to study how co-expression gene networks change across tissues. However, the reproducibility assessment of these studies is challenged by a lack of fully confirmatory experiments from independent researchers. While an increment in the number of studies with expression data for several tissues is expected, statistical measures are still needed to assess the reproducibility between studies. We identified a gap in the statistical literature concerning the assessment of agreement between studies across numerous conditions. The gap precluded us to test, using standard statistics, the level of agreement between the GTEX (RNAseq) and BRAINEAC (microarray) studies to distinguish the structure of co-expression networks across four brain tissues. We propose a generalization of a classical measure of agreement, Cohen’s κ, derive its distributional characteristics and determine its reliability properties. In the gene expression studies, our generalization of κ showed full agreement for genome-wide networks in BRAINEAC benchmarked against GTEX, and highest agreement for brain specific pathways. Our highly interpretable measure can contribute to anticipated efforts on reproducibility research.

Water Pollution and Its Impact on Environment of Society

2016 ◽  
Vol 3 (5) ◽  
Author(s):  
N. Thyagaraju
Keyword(s):  
Water Pollution ◽  
Pollution Prevention ◽  
Human Beings ◽  
Individual Level ◽  
The Public ◽  
The Government ◽  
Living Organisms ◽  
Set Up ◽  
Biological Entities ◽  
Micro Organisms

The present seminar paper mainly highlight  the concept of  water pollution, causes of water pollution,  Its Effects, Elements of  pollutants, Methods  used to prevent the water pollution in environment  and the mandatory initiatives taken by the concerned authorities for prevention of  water pollution. Water   is essential for survival of all living organisms on the earth. Thus for human beings and plants to survive on land, water should be easily accessible. The term “Pollution” is generally refers to addition of any foreign body either living or non – living or deletion of anything that naturally exists. The basic Sources of Water pollution causes due to Culmination into lakes, rivers, ponds, seas, oceans etc. Domestic drainage and sanitary waste, Industrial drainage and sewage, Industrial waste from factories, Dumping of domestic garbage, Immersion of Idols made of plaster of Paris, Excess use of Insecticides , pesticides, fungicides, Chemical fertilizers, Soil erosion during heavy rains and floods, Natural disasters, tsunami etc. General pollutants  which are also caused for water pollution  which include Organic, Inorganic, and Biological entities, Insecticides, Pesticides, Disinfectants ,Detergents, Industrial solvents, Acids, Ammonia fertilizers, heavy metals, Harmful bacteria, Virus, Micro –Organisms and worms, Toxic chemicals. Agricultural lands become infertile and thereby production also drops, Spread of epidemic diseases like Cholera, Dysentery, Typhoid, Diarrhea, Hepatitis, Jaundice etc. The  basic responsibility of the Government, NGOs, National Pioneer scientific Research Institutions may conduct  research oriented programs on control of water pollution by create  awareness among the public through mass media and Environmental Education on recycling units,  and  water treatment plants must be established both at domestic levels and Industry levels, Every citizen must feel responsible to control water pollution. There have been many water pollution prevention acts that have been set up by the governments of the world. But these are not enough for permanent water pollution solutions. Each of us needs to take up the responsibility and do something at an everyday at individual level. Otherwise we can’t survive in a society forever in a future. 

scholarly journals A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins

2020 ◽  
Vol 14 ◽  
Author(s):  
Mette Soerensen ◽  
Dominika Marzena Hozakowska-Roszkowska ◽  
Marianne Nygaard ◽  
Martin J. Larsen ◽  
Veit Schwämmle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cognitive Functioning ◽  
Association Study ◽  
Gene Expression Data ◽  
Monozygotic Twins ◽  
Later Life ◽  
Expression Data ◽  
Genome Wide ◽  
A Genome

scholarly journals Astronomy to understand a human environment

1998 ◽  
Vol 162 ◽  
pp. 211-213
Author(s):  
S. Isobe
Keyword(s):  
School System ◽  
Environmental Science ◽  
The Other ◽  
Human Environment ◽  
Science Courses ◽  
The Public ◽  
Global Environmental Problems ◽  
Global Environmental ◽  
Set Up ◽  
School Period

Astronomy is an important science in understanding a human environment. However, it is thought by most politicians, economists, and members of the public that astronomy is a pure science having no contribution to daily human activities except a few matters relating to time. The Japanese government is studying a reorganisation of our school system to have 5 school days per week, instead of 6 days per week, and this July its committee made a recommendation to reduce school hours for science and set up new courses for practical computers and environmental science. I currently made a proposal. It is very difficult for most of the school pupils, who will have non-scientific jobs, to understand science courses currently taught in school, because each science is taught independently from the other sciences. Therefore, their knowledge of sciences obtained during their school period does not greatly help their understanding of global environmental problems.

scholarly journals Identification of unique venous thromboembolism-susceptibility variants in African-Americans

2017 ◽  
Vol 117 (04) ◽  
pp. 758-768 ◽  
Author(s):  
Sebastian Armasu ◽  
Bryan McCauley ◽  
Iftikhar Kullo ◽  
Hugues Sicotte ◽  
Jyotishman Pathak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Venous Thromboembolism ◽  
African Americans ◽  
Differential Expression ◽  
White Women ◽  
Genome Wide Association Study ◽  
Expression Data ◽  
Significant Differential Expression ◽  
Genome Wide ◽  
A Genome

SummaryTo identify novel single nucleotide polymorphisms (SNPs) associated with venous thromboembolism (VTE) in African-Americans (AAs), we performed a genome-wide association study (GWAS) of VTE in AAs using the Electronic Medical Records and Genomics (eMERGE) Network, comprised of seven sites each with DNA biobanks (total ~39,200 unique DNA samples) with genome-wide SNP data (imputed to 1000 Genomes Project cosmopolitan reference panel) and linked to electronic health records (EHRs). Using a validated EHR-driven phenotype extraction algorithm, we identified VTE cases and controls and tested for an association between each SNP and VTE using unconditional logistic regression, adjusted for age, sex, stroke, site-platform combination and sickle cell risk genotype. Among 393 AA VTE cases and 4,941 AA controls, three intragenic SNPs reached genome-wide significance: LEMD3 rs138916004 (OR=3.2; p=1.3E-08), LY86 rs3804476 (OR=1.8; p=2E-08) and LOC100130298 rs142143628 (OR=4.5; p=4.4E-08); all three SNPs validated using internal cross-validation, parametric bootstrap and meta-analysis methods. LEMD3 rs138916004 and LOC100130298 rs142143628 are only present in Africans (1000G data). LEMD3 showed a significant differential expression in both NCBI Gene Expression Omnibus (GEO) and the Mayo Clinic gene expression data, LOC100130298 showed a significant differential expression only in the GEO expression data, and LY86 showed a significant differential expression only in the Mayo expression data. LEMD3 encodes for an antagonist of TGF-β-induced cell proliferation arrest. LY86 encodes for MD-1 which down-regulates the pro-inflammatory response to lipopolysaccharide; LY86 variation was previously associated with VTE in white women; LOC100130298 is a non-coding RNA gene with unknown regulatory activity in gene expression and epigenetics.Supplementary Material to this article is available online at www.thrombosis-online.com.

Showcasing Science

2019 ◽  
Author(s):  
Martin Weiss
Keyword(s):  
Nineteenth Century ◽  
Art Museum ◽  
Scientific Instrument ◽  
The Public ◽  
Public Role ◽  
Electrostatic Generator ◽  
History Of ◽  
World Class ◽  
Hendrik Antoon Lorentz ◽  
Set Up

Teylers Museum was founded in 1784 and soon thereafter became one of the most important centres of Dutch science. The Museum’s first director, Martinus van Marum, famously had the world’s largest electrostatic generator built and set up in Haarlem. This subsequently became the most prominent item in the Museum’s world-class, publicly accessible, and constantly growing collections. These comprised scientific instruments, mineralogical and palaeontological specimens, prints, drawings, paintings, and coins. Van Marum’s successors continued to uphold the institution’s prestige and use the collections for research purposes, while it was increasingly perceived as an art museum by the public. In the early twentieth century, the Nobel Prize laureate Hendrik Antoon Lorentz was appointed head of the scientific instrument collection and conducted experiments on the Museum’s premises. Showcasing Science: A History of Teylers Museum in the Nineteenth Century charts the history of Teylers Museum from its inception until Lorentz’ tenure. From the vantage point of the Museum’s scientific instrument collection, this book gives an analysis of the changing public role of Teylers Museum over the course of the nineteenth century.

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