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Movements, leaders, victories and the continuing fight for equality.
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Mansa Musa was the ruler of the Mali Empire in West Africa. Details recorded here should be sourced; unknown information is left blank.
MORE →Reflects the personal views, recollections, and perspective of the author, Mike Davis.
This is a personal recollection on the Move fire on May 13, 1985
A microarray database is a repository containing microarray gene expression data. The key uses of a microarray database are to store the measurement data, manage a searchable index, and make the data available to other applications for analysis and interpretation (either directly, or via user downloads).
Microarray databases can fall into two distinct classes:
Some of the most known public, curated microarray databases are:
| Database | Scope | Microarray experiment sets | Sample profiles | As of date |
|---|---|---|---|---|
| ArrayTrack | ArrayTrack hosts both public and private data, including MAQC benchmark data, with integrated analysis tools | 1622 | 50,093 | Feb 2012 |
| NCI mAdb | Hosts NCI data with integrated analysis and statistics tools | ? | 105,000 | Mar 2012 |
| ImmGen database | Open access across all immune system cells; expression data, differential expression, coregulated clusters, regulation | 267 | 1059 | Jan 2012 |
| Genevestigator | Gene expression search engine based on manually curated, well annotated public and proprietary microarray and RNA-seq datasets | 3228 | 232,855 | October 2016 |
| Gene Expression Omnibus - NCBI | any curated MIAME compliant molecular abundance study | 25859 | 641770 | October 28, 2011 |
| ArrayExpress at EBI | Any curated MIAME or MINSEQE compliant transcriptomics data | 24838 | 708914 | October 28, 2011 |
| Stanford Microarray database | private and published microarray and molecule abundance database (now defunct) | 82542 | ? | October 23, 2011 |
| The Cancer Genome Atlas (TCGA) | collection of expression data for different cancers | 21229 | ? | August 30, 2013 |
| GeneNetwork system | Open access standard arrays, exons arrays, and RNA-seq data for genetic analysis (eQTL studies) with analysis suite | ~100 | ~10000 | July, 2010 |
| UNC modENCODE Microarray database | Nimblegen customer 2.1 million array | ~6 | 180 | July 17, 2009 |
| UPSC-BASE | data generated by microarray analysis within Umeå Plant Science Centre (UPSC). | ~100 | ? | November 15, 2007 |
| UPenn RAD database | MIAME compliant public and private studies, associated with ArrayExpress | ~100 | ~2500 | Sept. 1, 2007 |
| UNC Microarray database | provides the service for microarray data storage, retrieval, analysis, and visualization | ~31 | 2093 | April 1, 2007 |
| MUSC database | The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community. | ~45 | 555 | April 1, 2007 |
| caArray at NCI | Cancer data, prepared for analysis on caBIG | 41 | 1741 | November 15, 2006 |
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A microarray database is a repository containing microarray gene expression data. The key uses of a microarray database are to store the measurement data, manage a searchable index, and make the data available to other applications for analysis and interpretation (either directly, or via user downloads). Microarray databases can fall into two distinct classes: A peer reviewed, public repository that adheres to academic or industry standards and is designed to be used by many analysis applications and groups. A good example of this is the Gene Expression Omnibus (GEO) from NCBI or ArrayExpress from EBI. A specialized repository associated primarily with the brand of a particular entity (lab, company, university, consortium, group), an application suite, a topic, or an analysis method, whether it is commercial, non-profit, or academic. These databases might have one or more of the following characteristics: A subscription or license may be needed to gain full access, The content may come primarily from a specific group (e.g. SMD, or UPSC-BASE), the Immunological Genome Project There may be constraints on who can use the data or for what purpose data can be used, Special permission may be required to submit new data, or there may be no obvious process at all, Only certain applications may be equipped to use the data, often also associated with the same entity (for example, caArray at NCI is specialized for the caBIG), Further processing or reformatting of the data may be required for standard applications or analysis, They claim to address the 'urgent need' to have a standard, centralized repository for microarray data. (See YMD, last updated in 2003, for example), There is a claim to an incremental improvement over one of the public repositories, A meta-analysis application, which incorporates studies from one or more public databases (e.g. Gemma primarily uses GEO studies; NextBio uses various sources) Some of the most known public, curated microarray databases are:
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications, predicting certain genetic diseases and in discovering basic relationships among species in the history of life.
A microarray is a 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 solid substrate—usually a glass slide or silicon thin-film cell—that assays (tests) large amounts of 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, and others, the technology of DNA microarrays has become the most sophisticated and the most widely used, while the use of protein, peptide and carbohydrate microarrays is expanding. Types of microarrays include: DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays, BAC microarrays and SNP microarrays MMChips, for surveillance of microRNA populations Protein microarrays Peptide microarrays, for detailed analyses or optimization of protein–protein interactions Tissue microarrays Cellular microarrays (also called transfection microarrays) Chemical compound microarrays Antibody microarrays Glycan arrays (carbohydrate arrays) Phenotype microarrays Reverse phase protein lysate microarrays, microarrays of lysates or serum Interferometric reflectance imaging sensor (IRIS) People in the field of CMOS biotechnology are developing new kinds of microarrays. Once fed magnetic nanoparticles, individual cells can be moved independently and simultaneously on a microarray of magnetic coils. A microarray of nuclear magnetic resonance microcoils is under development.
A DNA microarray (also commonly known as a DNA chip or biochip) 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. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as probes (or reporters or oligos). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.
Before the 1921 destruction of Tulsa’s Greenwood District, Black residents had created a remarkable center of business and community life. The district included stores, professional offices, entertainment venues and homes owned by Black citizens. Understanding Greenwood means learning what was built—not only what was burned.
MORE →Shirley Chisholm, elected in 1968.