DNA transcription makes tRNA, rRNA, and mRNA {gene expression}|.
purposes
Gene expression studies gene functions, regulation, and interactions. Hybridization measures gene expression for gene discovery, gene identification, biochemical pathways, and disease mechanisms.
probes
Human-genome arrays have probes for all genes. Human-transcriptome arrays have probes for all transcripts. SNP arrays have all SNPs. Arrays can have immune, toxicity, or cancer-gene probes.
RNA or single-strand DNA oligonucleotides {antisense RNA}|, complementary to cell mRNAs, can bind to mRNA and prevent gene expression. Antisense RNAs can be in vectors, or techniques can inject them into cells.
300-base to 500-base sequences {expressed sequence tag} (EST) are specific to expressed gene regions, typically at 3' ends. ESTs map gene chromosomal locations from several tissues, recover corresponding gene sequences by electronic-database similarity searching, and retrieve complete cDNA clones for further analysis. Whole-genome shotgun sequencing using EST assembly reduces redundancy and creates longer consensus sequences.
For gene-probe spots and dyes, software calculates ratios {expression ratio} {gene expression ratio}: normalized expression level divided by normalized expression level for control gene. Average expression ratio is 1. If expression ratio is greater than or equal to 2 {up-regulated, expression} or less than or equal to 0.5 {down-regulated, expression}, genes have significant expression {differentially expressed}. Expression-ratio base-two logarithm averages 0, is +1 if expression ratio is 2, and is -1 if expression ratio is 0.5.
Gene similarity measures can be distances {gene distance} between expression vectors in expression space.
metric
Distances can have metrics {metric distance}. Distance can always be positive. Distance between point and itself can always be 0. Euclidean distance between two points can always be less than or equal to sum of distance from first point to third point and distance from third point to second point {triangle rule}.
metric: Euclidean distance
Euclidean distances can be differences in point coordinates. Euclidean distances are metric.
semi-metric
Distance measures {semi-metric distance} can be always positive and have distance between point and itself always zero, but not obey triangle rule.
To emphasize variation amounts, especially for timed experiments, methods {scaling method} can reduce large expression-ratio values by changing expression-ratio range. Scaling can set average logarithm to zero {mean centering}, by subtracting baseline value. Scaling can adjust logarithm range to -1 to +1. Scaling can normalize expression-vector magnitudes to 1.
Gene-expression technologies can use cell extracts from different tissues, same tissues under different conditions, or same tissues under same conditions, over time sequences {serial analysis of gene expression} (SAGE) {expressed RNA}. From RNA, two cell extracts from same tissues under same conditions can make first-strand cDNA labeled with fluorescent dye, one with Cy3 and one with Cy5. Purified labeled cDNA solution soaks slides at optimum temperatures for times. Robots measure slide-spot probe-DNA and labeled-cDNA hybridization.
Compared to control level, genes can have less expression {down-regulated, gene}. Less expression under same conditions indicates similar biological functions.
Compared to control level, genes can have more expression {up-regulated, gene}. More expression under same conditions indicates similar biological functions.
Artificial situations {experiment} can test hypotheses or answer questions. Genomics experiments use one or more assays, samples, and markers.
Arrays can have random sets of spots with various concentrations and known green-intensity vs. red-intensity ratios {Random Ratio Dilution series test} (RRD). Automated spot finding works at the 85% level. Variation coefficient {coefficient of variance} (CV) is less than 20%.
Lasers can fluoresce microarray to read sample results {reader, microarray} {microarray reader} {scanner, microarray} {microarray scanner}. Displays can zoom, track, and normalize arrays or array sets. Dual red/green lasers need constant laser-spot size and large field depth. Scanning simultaneously minimizes spatial crosstalk. Microarrays are in automatic loaders to maintain positions.
Control samples {standard sample} calibrate instruments or methods.
Oligonucleotides attach to plates {array} in rectangular patterns, to test one sample for hybridization.
plates
Plates can be silicon chips {DNA chip}, plastic blocks with small wells {microarray, plate}, optical-fiber tips {bead array}, or glass slides {planar array}.
process
For example, plastic blocks have wells. Wells have reactive-chemical solutions to assay samples. Array probes samples by hybridizing oligonucleotides to sample RNAs or cDNAs. Reader detects hybridization amount using light. Statistical and comparative calculations follow.
Sample plates {master plate} stored in freezers can make daughter plates.
Master plates supply other plates {daughter plate}.
Arrays {microarray} can have 9x9-spot matrices at hundreds of positions, to test many genes against one or more test oligonucleotides, plus controls and fiducial-probes.
Plates {microtiter plate} can have small wells.
Sample plates contain pits {well, array} that can hold one or more samples.
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Date Modified: 2022.0225