ArrayTrack
Encyclopedia
ArrayTrack is a multi-purpose bioinformatics tool primarily used for microarray
data management, analysis, and interpretation. ArrayTrack was developed to support in-house filter array research for the U.S. Food and Drug Administration in 2001 and was made freely available to the public as an integrated research tool for microarrays in 2003. Since then, ArrayTrack has averaged about 5,000 users per year. It is regularly updated by the National Center for Toxicological Research
.
ArrayTrack is directly integrated with a variety of other bioinformatics software, such as pathway analysis tools GeneGo MetaCore and Ingenuity Pathway Analysis.
hosted by the FDA. As a Java-based application, ArrayTrack is compatible with Windows
, Mac
, and Linux
machines.
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
data management, analysis, and interpretation. ArrayTrack was developed to support in-house filter array research for the U.S. Food and Drug Administration in 2001 and was made freely available to the public as an integrated research tool for microarrays in 2003. Since then, ArrayTrack has averaged about 5,000 users per year. It is regularly updated by the National Center for Toxicological Research
National Center for Toxicological Research
The National Center for Toxicological Research is the branch of the United States Food and Drug Administration which conducts research to define biological mechanisms of action underlying the toxicity of products regulated by the FDA....
.
Features
ArrayTrack is composed of three major components: Study Database, Tools, and Libraries, which primarily handle data management, analysis, and interpretation, respectively. Each of these components can be directly accessed from the other two, e.g., analysis Tools can be used directly on experimental data stored in the Study Database, and significant genes discovered from the results can be queried in the Libraries to view additional annotations and associated proteins, pathways, Gene Ontology terms, etc.- Study Database: The Study Database contains user-imported experiment data, including both raw data and annotation data. It is mainly used to manage microarrayDNA microarrayA DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
data, but also supports proteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
and metabolomicsMetabolomicsMetabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles...
data. Imported data are initially private to the owner but can be made available to other users. The Study Database also stores significant gene lists, which can be created directly from data analysis results in ArrayTrack. - Tools: A wide variety of analysis and visualization Tools are available in ArrayTrack, including but are not limited to: statistical analysis Tools including T-Test, ANOVA, and SAM-TestSignificance Analysis of MicroarraysSignificance analysis of microarrays is a statistical technique, established in 2001 by Tusher, Tibshirani and Chu, for determining whether changes in gene expression are statistically significant. With the advent of DNA microarrays it is now possible to measure the expression of thousands of...
; unsupervised pattern discovery Tools including Hierarchical Clustering AnalysisHierarchical clusteringIn statistics, hierarchical clustering is a method of cluster analysis which seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two types:...
and Principal Component Analysis; and model prediction Tools including K-Nearest Neighbors and Linear Discriminant AnalysisLinear discriminant analysisLinear discriminant analysis and the related Fisher's linear discriminant are methods used in statistics, pattern recognition and machine learning to find a linear combination of features which characterizes or separates two or more classes of objects or events...
. Although ArrayTrack's Tools are designed to accommodate imported data, they are also compatible with external data. - Libraries: ArrayTrack hosts a collection of Libraries which store specific annotation data, viewable in a dynamic spreadsheet format. There is a Library specific for genesGeneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
, proteinsProteinProteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, pathways, Gene OntologyGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
terms, chemical compoundsChemical compoundA chemical compound is a pure chemical substance consisting of two or more different chemical elements that can be separated into simpler substances by chemical reactions. Chemical compounds have a unique and defined chemical structure; they consist of a fixed ratio of atoms that are held together...
, SNPs, QTL, chip types, and more. Each Library supports multi-input searching, sorting, filtering, copy-pasting, and exporting. Libraries can be directly queried for the desired contents of stored gene lists, analysis results, and other Libraries. A specific entry in any Library can be linked to the equivalent entry in many popular public knowledge bases, including the original sources of data.
ArrayTrack is directly integrated with a variety of other bioinformatics software, such as pathway analysis tools GeneGo MetaCore and Ingenuity Pathway Analysis.
Accessibility
ArrayTrack is freely available to the public and can be accessed online. It is run on the client's computer using a Java-based interface that connects to an Oracle databaseOracle Database
The Oracle Database is an object-relational database management system produced and marketed by Oracle Corporation....
hosted by the FDA. As a Java-based application, ArrayTrack is compatible with Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Mac
Macintosh
The Macintosh , or Mac, is a series of several lines of personal computers designed, developed, and marketed by Apple Inc. The first Macintosh was introduced by Apple's then-chairman Steve Jobs on January 24, 1984; it was the first commercially successful personal computer to feature a mouse and a...
, and Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
machines.