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Microbiome-wide Association Study
A microbiome-wide association study (MWAS), otherwise known as a metagenome-wide association study (MGWAS), is a statistical methodology used to examine the full metagenome of a defined microbiome in various organisms to determine if some feature (as example, gene or species) of the microbiome is associated with a host trait. MWAS has been adopted by the field of metagenomics from the widely used genome-wide association study (GWAS). While MWAS is phonetically and conceptually tied to GWAS there are several key differentiations: * There are roughly 150 times more genes in the microbiome than in the human genome. A GWAS must only find significantly associated genes along the predefined number of chromosomes of the species. On the other hand, the MWAS must analyze however many features are in an undetermined number of microorganisms. As a result, there is a far higher chance of running into the multiple testing problem. * While host populations contain a relatively similar collecti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microbiome
A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps ''et al.'', but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term ''microbiota'' from the term ''microbiome''. The microbiota consists of all ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Host (biology)
In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasite, parasitic, a mutualism (biology), mutualistic, or a commensalism, commensalist ''guest'' (symbiont). The guest is typically provided with nourishment and shelter. Examples include animals playing host to parasitic worms (e.g. nematodes), cell (biology), cells harbouring pathogenic (disease-causing) viruses, a Fabaceae, bean plant hosting mutualistic (helpful) Rhizobia, nitrogen-fixing bacteria. More specifically in botany, a host plant supplies nutrient, food resources to micropredators, which have an evolutionarily stable strategy, evolutionarily stable relationship with their hosts similar to ectoparasitism. The host range is the collection of hosts that an organism can use as a partner. Symbiosis Symbiosis spans a wide variety of possible relationships between organisms, differing in their permanence and their effects on the two parties. If one of the partners in an ass ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome-wide Association Study
In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of Single-nucleotide polymorphism, genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms. When applied to human data, GWA studies compare the DNA of participants having varying phenotypes for a particular trait or disease. These participants may be people with a disease (cases) and similar people without the disease (controls), or they may be people with different phenotypes for a particular trait, for example blood pressure. This approach is known as phenotype-first, in which the participants are classified first by their clinical manifestation(s), as oppose ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Manhattan Plot Of Microbiome Wide Association Plot
Manhattan (), known regionally as the City, is the most densely populated and geographically smallest of the five boroughs of New York City. The borough is also coextensive with New York County, one of the original counties of the U.S. state of New York. Located near the southern tip of New York State, Manhattan is based in the Eastern Time Zone and constitutes both the geographical and demographic center of the Northeast megalopolis and the urban core of the New York metropolitan area, the largest metropolitan area in the world by urban landmass. Over 58 million people live within 250 miles of Manhattan, which serves as New York City’s economic and administrative center, cultural identifier, and the city’s historical birthplace. Manhattan has been described as the cultural, financial, media, and entertainment capital of the world, is considered a safe haven for global real estate investors, and hosts the United Nations headquarters. New York City is the headquarters of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of 'junk' DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The International Human Genome Project reported the sequence of the genome for ''Homo sapiens'' in 200The Human Genome Project although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequenci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Comparisons Problem
In statistics, the multiple comparisons, multiplicity or multiple testing problem occurs when one considers a set of statistical inferences simultaneously or infers a subset of parameters selected based on the observed values. The more inferences are made, the more likely erroneous inferences become. Several statistical techniques have been developed to address that problem, typically by requiring a stricter significance threshold for individual comparisons, so as to compensate for the number of inferences being made. History The problem of multiple comparisons received increased attention in the 1950s with the work of statisticians such as Tukey and Scheffé. Over the ensuing decades, many procedures were developed to address the problem. In 1996, the first international conference on multiple comparison procedures took place in Israel. Definition Multiple comparisons arise when a statistical analysis involves multiple simultaneous statistical tests, each of which has a potent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Euclidean Space
Euclidean space is the fundamental space of geometry, intended to represent physical space. Originally, that is, in Euclid's Elements, Euclid's ''Elements'', it was the three-dimensional space of Euclidean geometry, but in modern mathematics there are Euclidean spaces of any positive integer dimension (mathematics), dimension, including the three-dimensional space and the ''Euclidean plane'' (dimension two). The qualifier "Euclidean" is used to distinguish Euclidean spaces from other spaces that were later considered in physics and modern mathematics. Ancient History of geometry#Greek geometry, Greek geometers introduced Euclidean space for modeling the physical space. Their work was collected by the Greek mathematics, ancient Greek mathematician Euclid in his ''Elements'', with the great innovation of ''mathematical proof, proving'' all properties of the space as theorems, by starting from a few fundamental properties, called ''postulates'', which either were considered as eviden ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Compositional Data
In statistics, compositional data are quantitative descriptions of the parts of some whole, conveying relative information. Mathematically, compositional data is represented by points on a simplex. Measurements involving probabilities, proportions, percentages, and ppm can all be thought of as compositional data. Ternary plot Compositional data in three variables can be plotted via ternary plots. The use of a barycentric plot on three variables graphically depicts the ratios of the three variables as positions in an equilateral triangle. Simplicial sample space In general, John Aitchison defined compositional data to be proportions of some whole in 1982. In particular, a compositional data point (or ''composition'' for short) can be represented by a real vector with positive components. The sample space of compositional data is a simplex: :: \mathcal^D=\left\. \ The only information is given by the ratios between components, so the information of a composition is preserved un ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term ''transcriptome'' is a portmanteau of the words ''transcript'' and ''genome''; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript changes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteome
The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome. Types of proteomes While proteome generally refers to the proteome of an organism, multicellular organisms may have very different proteomes in different cells, hence it is important to distinguish proteomes in cells and organisms. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term ''proteome'' has also been used to refer to the collectio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random Forest
Random forests or random decision forests is an ensemble learning method for classification, regression and other tasks that operates by constructing a multitude of decision trees at training time. For classification tasks, the output of the random forest is the class selected by most trees. For regression tasks, the mean or average prediction of the individual trees is returned. Random decision forests correct for decision trees' habit of overfitting to their training set. Random forests generally outperform decision trees, but their accuracy is lower than gradient boosted trees. However, data characteristics can affect their performance. The first algorithm for random decision forests was created in 1995 by Tin Kam Ho using the random subspace method, which, in Ho's formulation, is a way to implement the "stochastic discrimination" approach to classification proposed by Eugene Kleinberg. An extension of the algorithm was developed by Leo Breiman and Adele Cutler, who reg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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