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Volcano Plot (statistics)
In statistics, a volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. It plots significance versus fold-change on the y and x axes, respectively. These plots are increasingly common in omic experiments such as genomics, proteomics, and metabolomics where one often has a list of many thousands of replicate data points between two conditions and one wishes to quickly identify the most meaningful changes. A volcano plot combines a measure of statistical significance from a statistical test (e.g., a p value from an ANOVA model) with the magnitude of the change, enabling quick visual identification of those data-points (genes, etc.) that display large magnitude changes that are also statistically significant. A volcano plot is constructed by plotting the negative logarithm of the p value on the y axis (usually base 10). This results in data points with low p values (highly significant) appearing toward the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Volcano Eg
A volcano is a rupture in the crust of a planetary-mass object, such as Earth, that allows hot lava, volcanic ash, and gases to escape from a magma chamber below the surface. On Earth, volcanoes are most often found where tectonic plates are diverging or converging, and most are found underwater. For example, a mid-ocean ridge, such as the Mid-Atlantic Ridge, has volcanoes caused by divergent tectonic plates whereas the Pacific Ring of Fire has volcanoes caused by convergent tectonic plates. Volcanoes can also form where there is stretching and thinning of the crust's plates, such as in the East African Rift and the Wells Gray-Clearwater volcanic field and Rio Grande rift in North America. Volcanism away from plate boundaries has been postulated to arise from upwelling diapirs from the core–mantle boundary, deep in the Earth. This results in hotspot volcanism, of which the Hawaiian hotspot is an example. Volcanoes are usually not created where two tectonic plates s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Significance Analysis Of Microarrays
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA (Gene chip analysis), RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome - in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult - if not impossible - to analyze without the help of computer programs. Introduction Microarray data analysis is the final step in reading and processing data produced by a microarray chip. Samples undergo various processes including purification and scanning using the microchip, which then produces a large amount of data that requires processing via computer software. It involves several distinct steps, as outlined in the image below. Changing any one of the steps will change the outcome of the analysis, so t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Normally Distributed
In statistics, a normal distribution or Gaussian distribution is a type of continuous probability distribution for a real-valued random variable. The general form of its probability density function is : f(x) = \frac e^ The parameter \mu is the mean or expectation of the distribution (and also its median and mode), while the parameter \sigma is its standard deviation. The variance of the distribution is \sigma^2. A random variable with a Gaussian distribution is said to be normally distributed, and is called a normal deviate. Normal distributions are important in statistics and are often used in the natural and social sciences to represent real-valued random variables whose distributions are not known. Their importance is partly due to the central limit theorem. It states that, under some conditions, the average of many samples (observations) of a random variable with finite mean and variance is itself a random variable—whose distribution converges to a normal distrib ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology And Chemistry
''Computational Biology and Chemistry'' is a peer-reviewed scientific journal published by Elsevier covering all areas of computational life sciences. The current editor-in-chief are Wentian Li (The Feinstein Institute for Medical Research) and Donald Hamelberg ( Georgia State University). The journal was established in 1976 as ''Computer & Chemistry''. It obtained its current title in 2003 under the editorship of Andrzej K Konopka and James Crabble ( University of Bedfordshire). Abstracting and indexing The journal is abstracted and indexed in: According to the ''Journal Citation Reports'', the journal had a 2011 impact factor The impact factor (IF) or journal impact factor (JIF) of an academic journal is a scientometric index calculated by Clarivate that reflects the yearly mean number of citations of articles published in the last two years in a given journal, as i ... of 1.551, ranking it 42nd out of 85 journals in the category "Biology" and 36th out of 99 journals ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Test Statistic
A test statistic is a statistic (a quantity derived from the sample) used in statistical hypothesis testing.Berger, R. L.; Casella, G. (2001). ''Statistical Inference'', Duxbury Press, Second Edition (p.374) A hypothesis test is typically specified in terms of a test statistic, considered as a numerical summary of a data-set that reduces the data to one value that can be used to perform the hypothesis test. In general, a test statistic is selected or defined in such a way as to quantify, within observed data, behaviours that would distinguish the null from the alternative hypothesis, where such an alternative is prescribed, or that would characterize the null hypothesis if there is no explicitly stated alternative hypothesis. An important property of a test statistic is that its sampling distribution under the null hypothesis must be calculable, either exactly or approximately, which allows ''p''-values to be calculated. A ''test statistic'' shares some of the same qualities of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chi-square Test
A chi-squared test (also chi-square or test) is a statistical hypothesis test used in the analysis of contingency tables when the sample sizes are large. In simpler terms, this test is primarily used to examine whether two categorical variables (''two dimensions of the contingency table'') are independent in influencing the test statistic (''values within the table''). The test is valid when the test statistic is chi-squared distributed under the null hypothesis, specifically Pearson's chi-squared test and variants thereof. Pearson's chi-squared test is used to determine whether there is a statistically significant difference between the expected frequencies and the observed frequencies in one or more categories of a contingency table. For contingency tables with smaller sample sizes, a Fisher's exact test is used instead. In the standard applications of this test, the observations are classified into mutually exclusive classes. If the null hypothesis that there are no differ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Odds Ratio
An odds ratio (OR) is a statistic that quantifies the strength of the association between two events, A and B. The odds ratio is defined as the ratio of the odds of A in the presence of B and the odds of A in the absence of B, or equivalently (due to symmetry), the ratio of the odds of B in the presence of A and the odds of B in the absence of A. Two events are independent if and only if the OR equals 1, i.e., the odds of one event are the same in either the presence or absence of the other event. If the OR is greater than 1, then A and B are associated (correlated) in the sense that, compared to the absence of B, the presence of B raises the odds of A, and symmetrically the presence of A raises the odds of B. Conversely, if the OR is less than 1, then A and B are negatively correlated, and the presence of one event reduces the odds of the other event. Note that the odds ratio is symmetric in the two events, and there is no causal direction implied ( correlation does not imply c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single-nucleotide Polymorphism
In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently large fraction of the population (e.g. 1% or more), many publications do not apply such a frequency threshold. For example, at a specific base position in the human genome, the G nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations – G or A – are said to be the alleles for this specific position. SNPs pinpoint differences in our susceptibility to a wide range of diseases, for example age-related macular degeneration (a common SNP in the CFH gene is associated with increased risk of the disease) or nonalcoholic fatty liver disease (a SNP in the PNPLA3 gene is associated with incr ... [...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 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 opposed to genotype-first. Each pers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Association
Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence. Studies of genetic association aim to test whether single-locus alleles or genotype frequencies (or more generally, multilocus haplotype frequencies) differ between two groups of individuals (usually diseased subjects and healthy controls). Genetic association studies today are based on the principle that genotypes can be compared "directly", i.e. with the sequences of the actual genomes or exomes via whole genome sequencing or whole exome sequencing. Before 2010, DNA sequencing methods were used. Description Genetic association can be between phenotypes, such as visible characteristics such as flower color or height, between a phenotype and a genetic polymorphism, such as a single nucleotide polymorphism (SNP), or between two genetic polymorphisms. Association between genetic polymorphisms occurs when there is non-r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Bioinformatics And Computational Biology
The ''Journal of Bioinformatics and Computational Biology'' was founded in 2003 and is published by World Scientific. The journal covers analysis of cellular information, especially in the technical aspect. The managing editor is Limsoon Wong (National University of Singapore). Abstracting and indexing The journal is abstracted and indexed in: * Index Medicus * BIOSIS Previews * Biological Abstracts * MEDLINE * CompuScience * Scopus Scopus is Elsevier's abstract and citation database launched in 2004. Scopus covers nearly 36,377 titles (22,794 active titles and 13,583 inactive titles) from approximately 11,678 publishers, of which 34,346 are peer-reviewed journals in top-l ... * Inspec English-language journals Publications established in 2003 Bioinformatics and computational biology journals World Scientific academic journals ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
