Microarray analysis

Microarray analysis combines experiments on arrays of immobilized probes with computational methods to measure many biological targets at once. It is used to compare gene expression, genetic variation, and other molecular signals across samples.

DNA microarray: A chip bearing many DNA probes that measure nucleic-acid sequences or abundance through binding and signal detection. Gene-expression studies use these arrays to compare transcript abundance across samples.
Gene expression profiling: The measurement of transcript abundance across genes, samples, or conditions. Expression arrays provide a genome-wide snapshot of transcription in each sample.
Microarray probe: An immobilized molecule on an array that binds or captures a target of interest. Probe sequence and specificity shape which targets an experiment can detect.
RNA sequencing: A sequencing method that measures RNA abundance by converting RNA into a library of sequenceable molecules. It profiles transcripts without restricting measurement to the fixed probes on an array.
Nucleic acid hybridization: The binding of complementary nucleic-acid strands through base pairing. Probe-target binding produces the sequence-specific signals measured by many microarrays.
Single-nucleotide polymorphism array: A microarray designed to genotype selected variants and assess DNA copy number across the genome. These arrays adapt probe-based measurement to inherited variation and chromosomal changes.
Experimental design: The plan for assigning samples, treatments, measurements, and controls in a study. Array comparisons are interpretable only when sample groups and confounders are planned carefully.
Quantitative PCR: A method that quantifies selected DNA or RNA targets through amplification and fluorescence monitoring. It measures a smaller target set with different sensitivity and validation tradeoffs.
Fluorescence: Light emission by a substance after it absorbs light at a different wavelength. Fluorescent labels commonly convert bound targets into measurable array signals.
Comparative genomic hybridization: A method that compares DNA copy number between samples by measuring their hybridization to genomic targets. Array-based comparative genomic hybridization detects gains and losses across chromosomes.

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Multiple comparisons problemRelated: Thousands of gene-level tests create a large multiple-testing burden.