- down-regulation
- An analysis of a statistically significant experiment returned from a
search against a pathway is designated as up-regulated or
down-regulated.
- entrez gene
- Reference sequences for a wide range of species. For details, see
http://www.ncbi.nlm.nih.gov/gene/.
- entrez global
Federated search engine that allows users to search various health
sciences databases at the National Center for Biotechnology Information
(NCBI) website.
See www.ncbi.nlm.nih.gov/Entrez/ for details.
- fold change ratio
- A number describing how much a quantity changes going from an initial to
a final value. An initial value of 50 and a final value of 100
corresponds to a fold change of 2 (a two-fold increase).
- gene
- Stretches of DNA and RNA that code for a polypeptide or for an RNA chain.
Contains hereditary molecular information LOL.
- gene chip
- See: Microarray
- gene expression
- The flow of genetic information from gene to protein; the process, or
the regulation of the process, by which the effects of a gene are
manifested; the manifestation of a heritable trait in an individual
carrying the gene or genes that determine it.
- gene expression omnibus
- GEO is an international public repository that archives and freely
distributes microarray, next-generation sequencing, and other forms of
high-throughput functional genomics data submitted by the research
community. For more information, see http://www.ncbi.nlm.nih.gov/geo.
- gene set enrichment analysis (gsea)
Computational method that determines whether an a priori defined set of
genes shows statistically significant, concordant differences between
two biological states (for example, phenotypes).
See http://www.broadinstitute.org/gsea/index.jsp for details.
- gene signature
- A group of genes whose combined expression pattern is uniquely
characteristic of a medical condition or other clinical outcome of
interest.
- gene symbol
A unique abbreviation of a gene name consisting of italicized uppercase
Latin letters and Arabic numbers. we use Entrez as the full list of
genes (related to but not identical to HUGO)
See http://www.genenames.org/ for details.
- genecards
Database that offers information about human genes (and mouse
homologues).
See http://www.genecards.org for details.
- google scholar
Google application that provides a search of scholarly literature across
multiple disciplines and sources.
See http://scholar.google.com for details.
- gpl platform
- A Platform record is composed of a summary description of the array or
sequencer and, for array-based Platforms, a data table defining the
array template. Each Platform record is assigned a unique and stable GEO
accession number (GPLxxx). A Platform may reference many Samples that
have been submitted by multiple submitters.
- heatmap
- Display of differential expression. Individual values contained in the
matrix are represented by colors.
- hierarchical clustering
- Hierarchical clustering is a type of clustering analysis whose goal is
to organize data so that the objects in the same cluster are more
similar to each other than to those in other clusters.
- high dimensional data
- Datasets where the intersection of a subject and measurement is
comprised of hundreds or thousands of points. For example, in a low
dimensional data measurement such as height, the intersection of subject
and measurement is one number (ex. 180 cm), whereas in a high
dimensional data measurement such as gene expression in a lymph node,
the measurement is 50,000 individual probe expression values.
- histogram
- A visual representation of the distribution of data values within a
dataset.
- homology
- The basis for comparative biology — where organs/structures from one
organism are compared to a similar organ/structure in a different
organism.
- in vitro study
- Those that are conducted using components of an organism that have been
isolated from their usual biological surroundings.
- in vivo studies
- Experimentation using a whole, living organism.
- independent variable
- In an experiment, the independent variable is the variable that is
manipulated.
- job
- In Valhalla, a job refers to a command you have given Analyze to process
or export data. Jobs and job-related events can be found within the
Jobs tab in Analyze.
- kendall correlation
- Kendall’s rank correlation provides a distribution-free test of
independence and a measure of the strength of dependence between two
variables.
- k-means clustering
- The K-Means clustering heatmap clusters genes and/or samples into a
specified number of clusters. The result is k clusters, each centered
around a randomly-selected data point.
- line graph
- Line graphs illustrate the temporal relationship between two major
variables.
- marker selection
- Marker Selection is a display of the top differentially expressed genes
between two specified cohorts.
- mesh ontology
- MeSH is the National Library of Medicine’s controlled vocabulary
thesaurus. It consists of sets of terms naming descriptors in a
hierarchical structure that permits searching at various levels of
specificity.
- microarray
- A two-dimensional array on a chip or solid surface that assays large
amounts of DNA material.
- mrna analysis
- Assays that quantify the expression levels of all mRNA molecules in an
experiment.
- navigation tree
- The Window’s Explorer-like, hierarchical representation of study data
that has been loaded into Analyze.
- ncbi
The National Center for Biotechnology Information.
See http:// www.ncbi.nlm.nih.gov/ for
details.
- numeric-node
- Used in Analyze, numeric-nodes are indicated by the (123) symbol,
numeric nodes indicate that the data values associated with the concept
are only numeric (for example, age values, date values, etc.). For more
information, see Continuous Variable.
- ontology
- A hierarchical description of the concepts and relationships that can
exist for an agent or a community of agents.
- orthogonal component
- When performing statistical analysis, independent variables that affect
a particular dependent variable are said to be orthogonal if they are
uncorrelated, since the covariance forms an inner product.
- pathology
- The study of diagnosis and disease.
- pathway
- A group of genes interacting to form an aggregate biological function.
- pearson correlation
- Obtained by dividing the covariance of the two variables by the product
of their standard deviations
- principal component analysis
- A Principal Component Analysis (PCA) is commonly used as a tool in
exploratory data analysis. Data is split into orthogonal components, and
the genes/probes that contribute the most variance to the components are
displayed.
- probe set
- A probe set is a collection of probes designed to interrogate a given
sequence.
- probe set id
A probe set ID is used to refer to a probe set, which looks like the
following:
12345_at or 12345_a_at or 12345_s_at or 12345_x_at
The last three characters (_at) identify the probe set strand.
- p-value
- The number corresponding probability that the occurrences of your
experiment and analysis did not happen by chance. P-value cutoffs are
often 0.05 or 0.01 — when the value is under the threshold, the result
is said to be statistically significant.
- r
R is a language and environment for statistical computing and graphics.
See http://www.r-project.org for details.
- rbm data
- Rules Based Medicine. They provide an array measurement of metabolites
- regression algorithms
- Algorithms that are particularly suited for mining data sets that have
high dimensionality (many attributes), including transactional and
unstructured data.
- rho-value
- Also known as Spearman’s rho, the rho-value is a non-parametric measure
of statistical dependence between two variables. See: Spearman
Correlation.
- r-value
- The value assigned to a correlation coefficient.
- scatter plot
- Type of graph that uses Cartesian coordinates to display values for two
variables for a set of data.
- search filter
- A biomedical concept used to define search criteria in the Search tool.
- search string
- A sequence of biomedical concepts used to define search criteria in the
Search tool.
- slope
- The steepness of the line of best fit in a graph (∆y/∆x).
- snp data
- Single Nucleotide Polymorphism. DNA sequence data marking variation
occurring when a single nucleotide — A, T, C or G — in the genome.
- spearman correlation
- The Spearman’s rank-order correlation is the nonparametric version of
the Pearson product-moment correlation. Spearman’s correlation
coefficient, (, also signified by rho-value) measures the strength of
association between two ranked variables.
- statistical significance
- Results of analyses on data that are statistically significant indicate
a confidence level that the results did not happen by chance.
- subset
- A smaller grouping of participants in a study. See cohort.
- survival analysis
- Assessment of the amount of time that a person or population lives after
a particular intervention or condition.
- t statistic
- Ratio of the departure of an estimated parameter from its notional value
and its standard error.
- table with fisher test
- Examines the significance of associated categorical variables.
- tea analyses
- Target Enrichment Analysis (TEA) measures the enrichment of a gene
signature, gene list, or pathway in a microarray expression experiment.
- tea p-value
- These normalized p‑values are intermediate values in the TEA
calculation. To be considered a statistically significant analysis, an
analysis must have at least one matching biomarker with a TEA p-Value of
less than 0.05.