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Dual-flashlight Plot
In statistics, a dual-flashlight plot is a type of scatter-plot in which the standardized mean of a contrast variable ( SMCV) is plotted against the mean of a contrast variable representing a comparison of interest . The commonly used dual-flashlight plot is for the difference between two groups in high-throughput experiments such as microarrays and high-throughput screening studies, in which we plot the SSMD versus average log fold-change on the ''y''- and ''x''-axes, respectively, for all genes or compounds (such as siRNAs or small molecules) investigated in an experiment. As a whole, the points in a dual-flashlight plot look like the beams of a flashlight with two heads, hence the name dual-flashlight plot. With the dual-flashlight plot, we can see how the genes or compounds are distributed into each category in effect sizes, as shown in the figure. Meanwhile, we can also see the average fold-change for each gene or compound. The dual-flashlight plot is similar to the volcan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wiki
A wiki ( ) is a form of hypertext publication on the internet which is collaboratively edited and managed by its audience directly through a web browser. A typical wiki contains multiple pages that can either be edited by the public or limited to use within an organization for maintaining its internal knowledge base. Its name derives from the first user-editable website called " WikiWikiWeb," with "wiki" being a Hawaiian word meaning "quick." Wikis are powered by wiki software, also known as wiki engines. Being a form of content management system, these differ from other web-based systems such as blog software or static site generators in that the content is created without any defined owner or leader. Wikis have little inherent structure, allowing one to emerge according to the needs of the users. Wiki engines usually allow content to be written using a lightweight markup language and sometimes edited with the help of a rich-text editor. There are dozens of differ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SMCV
In statistics, the standardized mean of a contrast variable (SMCV or SMC), is a parameter assessing effect size. The SMCV is defined as mean divided by the standard deviation of a contrast variable. The SMCV was first proposed for one-way ANOVA cases and was then extended to multi-factor ANOVA cases. Background Consistent interpretations for the strength of group comparison, as represented by a contrast, are important. When there are only two groups involved in a comparison, SMCV is the same as the strictly standardized mean difference (SSMD). SSMD belongs to a popular type of effect-size measure called "standardized mean differences" which includes Cohen's d and Glass's \delta. In ANOVA, a similar parameter for measuring the strength of group comparison is standardized effect size (SES). One issue with SES is that its values are incomparable for contrasts with different coefficients. SMCV does not have such an issue. Concept Suppose the random values in t groups ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Contrast Variable
In statistics, particularly in the analysis of variance and linear regression, a contrast is a linear combination of variables (parameters or statistics) whose coefficients add up to zero, allowing comparison of different treatments. Definitions Let \theta_1,\ldots,\theta_t be a set of variables, either parameters or statistics, and a_1,\ldots,a_t be known constants. The quantity \sum_^t a_i \theta_i is a linear combination. It is called a contrast if Casella 2008, p. 11. Furthermore, two contrasts, \sum_^t a_i \theta_i and \sum_^t b_i \theta_i, are orthogonal if Examples Let us imagine that we are comparing four means, \mu_1,\mu_2,\mu_3,\mu_4. The following table describes three possible contrasts: The first contrast allows comparison of the first mean with the second, the second contrast allows comparison of the third mean with the fourth, and the third contrast allows comparison of the average of the first two means with the average of the last two. In a balanced one-way anal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microarray
A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usually a glass slide or silicon thin-film cell—that assays (tests) large amounts of biotic material, biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in antibody microarrays (also referred to as antibody matrix) by Tse Wen Chang in 1983 in a scientific publication and a series of patents. The "gene chip" industry started to grow significantly after the 1995 ''Science Magazine'' article by the Ron Davis and Pat Brown labs at Stanford University. With the establishment of companies, such as Affymetrix, Agilent, Applied Microarrays, Arrayjet, Illumina (company), Illumina, and others, the te ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High-throughput Screening
High-throughput screening (HTS) is a method for scientific discovery especially used in drug discovery and relevant to the fields of biology, materials science and chemistry. Using robotics, data processing/control software, liquid handling devices, and sensitive detectors, high-throughput screening allows a researcher to quickly conduct millions of chemical, genetic, or pharmacological tests. Through this process one can quickly recognize active compounds, antibodies, or genes that modulate a particular biomolecular pathway. The results of these experiments provide starting points for drug design and for understanding the noninteraction or role of a particular location. Assay plate preparation The key labware or testing vessel of HTS is the microtiter plate, which is a small container, usually disposable and made of plastic, that features a grid of small, open divots called ''wells''. In general, microplates for HTS have either 96, 192, 384, 1536, 3456 or 6144 wells. These are a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SSMD
In statistics, the strictly standardized mean difference (SSMD) is a measure of effect size. It is the mean divided by the standard deviation of a difference between two random values each from one of two groups. It was initially proposed for quality control and hit selection in high-throughput screening (HTS) and has become a statistical parameter measuring effect sizes for the comparison of any two groups with random values. Background In high-throughput screening (HTS), quality control (QC) is critical. An important QC characteristic in a HTS assay is how much the positive controls, test compounds, and negative controls differ from one another. This QC characteristic can be evaluated using the comparison of two well types in HTS assays. Signal-to-noise ratio (S/N), signal-to-background ratio (S/B), and the Z-factor have been adopted to evaluate the quality of HTS assays through the comparison of two investigated types of wells. However, the S/B does not take into account any ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SiRNA
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded non-coding RNA molecules, typically 20–24 base pairs in length, similar to microRNA (miRNA), and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading messenger RNA (mRNA) after transcription, preventing translation. Text was copied from this source, which is available under Creative Commons Attribution 4.0 International License It was discovered in 1998 by Andrew Fire at the Carnegie Institution for Science in Washington, D.C. and Craig Mello at the University of Massachusetts in Worcester. Structure Naturally occurring siRNAs have a well-defined structure that is a short (usually 20 to 24- bp) double-stranded RNA (dsRNA) with phosphorylated 5' ends and hydroxylated 3' ends with two overhanging nucleotides. The Dicer enzyme catalyzes prod ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small Molecule
In molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; the terms are equivalent in the literature. Larger structures such as nucleic acids and proteins, and many polysaccharides are not small molecules, although their constituent monomers (ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively) are often considered small molecules. Small molecules may be used as research tools to probe biological function as well as leads in the development of new therapeutic agents. Some can inhibit a specific function of a protein or disrupt protein–protein interactions. Pharmacology usually restricts the term "small molecule" to molecules that bind specific biological macromolecules and act as an effector, altering the activity or function of the target. Small molecules can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 a sophisticated data visualization tool used in statistical and genomic analyses to illustrate the relationship between the magnitude of change and statistical significance. It is con ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
P-value
In null-hypothesis significance testing, the ''p''-value is the probability of obtaining test results at least as extreme as the result actually observed, under the assumption that the null hypothesis is correct. A very small ''p''-value means that such an extreme observed outcome would be very unlikely ''under the null hypothesis''. Even though reporting ''p''-values of statistical tests is common practice in academic publications of many quantitative fields, misinterpretation and misuse of p-values is widespread and has been a major topic in mathematics and metascience. In 2016, the American Statistical Association (ASA) made a formal statement that "''p''-values do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone" and that "a ''p''-value, or statistical significance, does not measure the size of an effect or the importance of a result" or "evidence regarding a model or hypothesis". That ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Effect Size
In statistics, an effect size is a value measuring the strength of the relationship between two variables in a population, or a sample-based estimate of that quantity. It can refer to the value of a statistic calculated from a sample of data, the value of one parameter for a hypothetical population, or to the equation that operationalizes how statistics or parameters lead to the effect size value. Examples of effect sizes include the correlation between two variables, the regression coefficient in a regression, the mean difference, or the risk of a particular event (such as a heart attack) happening. Effect sizes are a complement tool for statistical hypothesis testing, and play an important role in power analyses to assess the sample size required for new experiments. Effect size are fundamental in meta-analyses which aim to provide the combined effect size based on data from multiple studies. The cluster of data-analysis methods concerning effect sizes is referred to as estima ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Contrast Variable
In statistics, particularly in the analysis of variance and linear regression, a contrast is a linear combination of variables (parameters or statistics) whose coefficients add up to zero, allowing comparison of different treatments. Definitions Let \theta_1,\ldots,\theta_t be a set of variables, either parameters or statistics, and a_1,\ldots,a_t be known constants. The quantity \sum_^t a_i \theta_i is a linear combination. It is called a contrast if Casella 2008, p. 11. Furthermore, two contrasts, \sum_^t a_i \theta_i and \sum_^t b_i \theta_i, are orthogonal if Examples Let us imagine that we are comparing four means, \mu_1,\mu_2,\mu_3,\mu_4. The following table describes three possible contrasts: The first contrast allows comparison of the first mean with the second, the second contrast allows comparison of the third mean with the fourth, and the third contrast allows comparison of the average of the first two means with the average of the last two. In a balanced one-way anal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
