Generation and analysis of transcriptomics data.
Transcript profiling ("Transcriptomics") is a widely used technique that obtains information on the abundance of multiple mRNA transcripts within a biological sample simultaneously. Therefore, when a number of such samples are analysed, as in a scientific experiment, large and complex data sets are gene-rated. Here, we describe the use of one method commonly used to generate transcriptomics data, namely the use of Affymetrix GeneChip microarrays. Data generated in transcriptomics experiments can be analysed using a multitude of approaches, but a common goal is to identify those transcripts whose abundance is altered by the experimental conditions, or which differ between sets of samples. Here, we describe a simple approach, the calculation of the volcano score, which identifies transcripts with altered abundance, taking into account both the magnitude of the alteration and its statistical significance.
Molecular Toxicology Group, Safety Assessment Department, AstraZeneca Pharmaceuticals Ltd, Macclesfield, Cheshire, UK.
Philip D
PD
Glaves
Jonathan D
JD
Tugwood
D001710:Biotin / Q000378:metabolism; D002478:Cells, Cultured; D018076:DNA, Complementary / Q000096:biosynthesis / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011786:Quality Control; D018075:RNA, Complementary / Q000096:biosynthesis / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D012984:Software; D013053:Spectrophotometry; D013223:Statistics as Topic / Q000379:methods*
D018076:DNA, Complementary; D018075:RNA, Complementary; D001710:Biotin