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ELABORATION 1.4 Terms in genomics
ОглавлениеCNA:Many biological organisms have several copies of the same gene (see Figure 1.5). Copy number aberration (CNA) quantifies this (see Example 1.2).Epi-genetics:DNA can be modified chemically thereby regulating expression of the corresponding genes. This chemical modification of the DNA is called epi-genetics (see Figure 1.5).Genetics:Biological organisms have DNA encoding their genetic make-up. Genetics studies this DNA.Methylation:A methyl group can be attached to the DNA, affecting transcription. This is a part of epi-genetics (see Figure 1.5).Mutation:DNA consists of four types of nucleotides (A, T, G, and C) containing the genetic code. Some of these nucleotides may be mutated, e.g., change from A to T. If this happens for a single nucleotide then this is called a single nucleotide polymorphism (SNP, see Figure 1.5).RNAseq:The modern way of measuring gene-expression or the RNA of a biological organism. There are many types of RNA of which messenger-RNA (mRNA) is the most studied one.Transcriptomics:Genes are transcribed to RNA and transcriptomics concerns the analysis of these transcripts.
Figure 1.5 Idea of copy number variation (a), methylation (b), and mutation (c) of the DNA. For (a) and (c): Source: Adapted from Koch et al., 2012.
Genomics is a very active field with many multiblock data analysis challenges due to the rapid development of measuring techniques. Whereas in former days gene-expression was measured with micro-arrays, this technology has been overtaken by next generation sequencing (mRNAseq, miRNAseq, siRNAseq, scRNAseq to name a few). This has led to open-access repositories containing genomics data of very different types, e.g., in cancer research (Tomczak et al., 2015) which is often the basis for generating new multiblock data analysis methods (Aben et al., 2016, 2018; Song et al., 2018). Other examples are combining genomics data with data from non-omics techniques like medical imaging, e.g., for treatment response predictions.