ArrayTrack is a multi-purpose bioinformatics tool primarily used for

microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon t ...

data management, analysis, and interpretation. ArrayTrack was developed to support in-house filter array research for the

U.S. Food and Drug Administration The United States Food and Drug Administration (FDA or US FDA) is a federal agency of the Department of Health and Human Services. The FDA is responsible for protecting and promoting public health through the control and supervision of food ...

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 The National Center for Toxicological Research (NCTR) is a branch of the U.S. Food & Drug Administration (FDA) located in Jefferson, Arkansas. Established in 1971, the Center conducts scientific research to provide reliable data for Food & Dr ...

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

data, but also supports

proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

and

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...

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 A ''t''-test is any statistical hypothesis testing, statistical hypothesis test in which the test statistic follows a Student's t-distribution, Student's ''t''-distribution under the null hypothesis. It is most commonly applied when the test stati ...

ANOVA Analysis of variance (ANOVA) is a collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means. ANOVA was developed by the statistician ...

, and SAM-Test; unsupervised pattern discovery Tools including Hierarchical Clustering Analysis and

Principal Component Analysis Principal component analysis (PCA) is a popular technique for analyzing large datasets containing a high number of dimensions/features per observation, increasing the interpretability of data while preserving the maximum amount of information, and ...

; and model prediction Tools including

K-Nearest Neighbors In statistics, the ''k''-nearest neighbors algorithm (''k''-NN) is a non-parametric supervised learning method first developed by Evelyn Fix and Joseph Hodges in 1951, and later expanded by Thomas Cover. It is used for classification and reg ...

and

Linear Discriminant Analysis Linear discriminant analysis (LDA), normal discriminant analysis (NDA), or discriminant function analysis is a generalization of Fisher's linear discriminant, a method used in statistics and other fields, to find a linear combination of features ...

. 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

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s, pathways,

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

terms,

chemical compound A chemical compound is a chemical substance composed of many identical molecules (or molecular entities) containing atoms from more than one chemical element held together by chemical bonds. A molecule consisting of atoms of only one element ...

SNPs 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 larg ...

QTL A quantitative trait locus (QTL) is a locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) c ...

, 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 Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...

-based interface that connects to an

Oracle database Oracle Database (commonly referred to as Oracle DBMS, Oracle Autonomous Database, or simply as Oracle) is a multi-model database management system produced and marketed by Oracle Corporation. It is a database commonly used for running online t ...

hosted by the FDA. As a Java-based application, ArrayTrack is compatible with

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

, Mac, and

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

machines.

References

{{Reflist

External links

ArrayTrack main page
Bioinformatics software Microarrays