DNA microarray: Difference between revisions

Revision as of 22:07, 4 August 2003

Revision as of 20:16, 5 August 2003

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"Microarray" refers not only to GeneChips but also to chips that use much longer probe sequences, such as the entire [[gene]]s that may be contained on [[cDNA]]s. Because, Affymetrix owns a [[patent]] both on the use of oligonucleotide probes as well as on a means to affix them to chips, microarrays not made by Affymetrix are manufactured by a different technique that is non-proprietary.

Typically arrays are used to detect the presence of [[mRNA]]s that may have been [[transcription|transcribed]] from different genes and which encode different proteins. The RNA is extracted from many cells of a single type, then converted to cDNA and "amplified" in [[concentration]] by [[reverse transcriptase|rt]][[PCR]]. [[Fluorescent tag]]s are chemically attached to the strands of DNA. A cDNA [[molecule]] that contains a sequence complementary to one of the single-stranded probe sequences will stick via base pairing (more at [[DNA]]) to the spot at which the complementary probes are affixed. The spot will then [[fluorescence|fluoresce]] (glow) when examined.

The glow indicates that cells in the sample werehad activelyrecently [[transcription|transcribing]]transcribed a gene that contained the sequence being probed sequence. The intensity of the glow depends on how many moleculescopies of a particular mRNA were present and thus roughly indicates the ''activity'' or ''expression level'' of that gene. So arrays in a sense paint a picture or "profile" of which genes in the [[genome]] are active in a particular genecell type and under a particular condition.

ResearchersBecause usuallymost employproteins microarraysremain forof aunknown comparisonfunction, betweenand twobecause many genes are active all the time in all kinds of cells, researchers usually use microarrays to make close samplescomparisons. For example, an RNA sample from [[brain tumor]] cells, might be compared to a sample from healthy [[neuron]]s or [[glia]]. Probes that bind RNA in the tumor sample but not in the healthy one indicate genes that are uniquely associated with the disease. Typically tagsin ofsuch differenta colorstest, arethe attachedtwo to thesample's cDNAs fromare thetagged with two samplesdistinct colors, enabling comparison on a single chip. Among the various [[protein]]s encoded by disease-associated genes, researchersResearchers hope to find molecules that could be therapeutically targeted with drugs. among the various [[protein]]s encoded by disease-associated genes.

Although the chips detect RNAs and not proteins, many scientists refer to these kinds of analysis as [[gene expression|"expression analysis"]] or [[expression profiling]]. Since there are hundreds of thousands of distinct probes on an array, each can accomplish the equivalent of thousands of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations.

The lack of standardization in non-commercial arrays presents an [[interoperability problem]] in [[bioinformatics]], which hinders the exchange of array data. Many researchers use Affymetrix technology to a large extent because it is popular and standardized. At the same time, various grass-roots [[open source|open-source]] projects are attempting to fascilitate the exchange and analysis of data produced with non-proprietary chips.