This section is designed to help readers adapt to the complex terminology associated with contemporary molecular genetics, genomics and systems biology. Fuller descriptions of these terms are available at http://www.wikipedia.org/

• Ab initio prediction

methods used to predict the potential genes encoded in the genome,which are trained on datasets made of known genes, and used computationally to predict coding regions out of genome without the aid of cDNA sequence. Although their performance is improving, these algorithms perform very poorly on non-protein coding genes.

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• Annotation

as applied to proteins, DNA sequences or genes. The storage of data describing these entities (protein/gene identities, DNA motifs, gene ontology categorisation, etc.) within a biological database. Active projects include FlyBase and WormBase. See Gene ontology.

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• Assembly

the process of aligning sequenced fragments of DNA into their correct positions within the chromosome or transcript.

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• cDNA

complementary DNA. This is DNA synthesised from a mature mRNA template by the enzyme reverse transcriptase. cDNA is frequently used as an early part of gene cloning procedures, since it is more robust and less subject to degradation than the mRNA itself.

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• ChIP

chromatin immunoprecipitation assay used to determine which segments of genomic DNA are bound to chromatin proteins, mainly including transcription factors.

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• Chip

see Microarray.

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• ChIP-on-chip

use of a DNA microarray to analyse the DNA generated from chromatin immunoprecipitation experiments(see ChIP).

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• cis-acting

a molecule is described as cis-acting when it affects other genes that are physically adjacent, on the same chromosome, or are genetically linked or in close proximity (for mRNA expression, typically a promoter).

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• Collision-induced dissociation

a mechanism by which molecules (e.g. proteins) are fragmented to form molecular ions in the gas phase. These fragments are then analysed within a mass spectrometer to provide mass determination.

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• Connectivity

a term from graph theory, which indicates the number of connections between nodes or vertices in a network. Greater connectedness between nodes is generally used as a measure of robustness of a network.

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• CpG islands

regions that show high density of C followed by G' dinucleotides and are generally associated with promoter elements; in particular, stretches of DNA of at least 200 bp with a C–G content of 50% and an observed CpG/expected CpG in excess of 0.6. The cytosine residues can be methylated,generally to repress transcription, while demethylated CpGs are a hallmark of transcription. CpG dinucleotides are under-represented outside regulatory regions, such as promoters, because methylated C mutates into T by deamination.

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• Edge

as in networks. Connects two nodes (or vertices) within a system. These concepts arise from graph theory.

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• Enhancer

a short segment of genomic DNA that may be located remotely and that,on binding particular proteins (trans-acting factors), increases the rate of transcription of a specific gene or gene cluster.

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• Epistasis

a phenomenon when the properties of one gene are modified by one or more genes at other loci. Otherwise known as a genetic interaction, but epistasis refers to the statistical properties of the phenomenon.

• eQTL

the combination of conventional QTL analysis with gene expression profiling, typically using microarrays. eQTLs describe regulatory elements controlling the expression of genes involved in specific traits.

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• EST

expressed sequence tag. A short DNA sequence determined for a cloned cDNA representing portions of an expressed gene. The sequence is generally several hundred base pairs from one or both ends of the cloned insert.

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• Exaptation

a biological adaptation where the current function is not that which was originally evolved. Thus, the defining (derived) function might replace or persist with the earlier, evolved adaptation.

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• Exon

any region of DNA that is transcribed to the final (spliced) mRNA molecule. Exons interleave with segments of non-coding DNA (introns) that are removed (spliced out) during processing after transcription.

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• Gene forests

genomic regions for which RNA transcripts, produced from either DNA strand, have been identified without gaps (non-transcribed genomic regions). Conversely, regions in which no transcripts have ever been detected are calledgene deserts'.

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• Gene interaction network

a network of functional interactions between genes. Functional interactions can be inferred from many different data types, including protein–protein interactions, genetic interactions, co-expression relationships, the co-inheritance of genes across genomes and the arrangement of genes in bacterial genomes. The interactions can be represented using network diagrams, with lines connecting the interacting elements, and can be modelled using differential equations.

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• Gene ontology (GO)

an ontology is a controlled vocabulary of terms that have logical relationships with each other and that are amenable to computerised manipulation. The Gene Ontology project has devised terms in three domains:biological process, molecular function and cell compartment. Each gene or DNA sequence can be associated with these annotation terms from each domain, and this enables analysis of microarray data on groups of genes based on descriptive terms so provided. See http://www.geneontology.org

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• Gene set enrichment analysis

a computational method that determines whether a defined set of genes,usually based on their common involvement in a biological process, shows statistically significant differences in transcript expression between two biological states.

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• Gene silencing

the switching-off of a gene by an epigenetic mechanism at the transcriptional or post-transcriptional levels. Includes the mechanism of RNAi.

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• Genetic interaction (network)

a genetic interaction between two genes occurs when the phenotypic consequences of a mutation in one gene are modified by the mutational status at a second locus. Genetic interactions can be aggravating (enhancing) or alleviating (suppressing). To date, most high-throughput studies have focussed on systematically identifying synthetic lethal or sick (aggravating)interactions, which can then be visualised as a network of functional interactions (edges) between genes (nodes).

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• Genome

a portmanteau of gene and chromosome, the entire hereditary information for an organism that is embedded in the DNA (or, for some viruses, in RNA). Includes protein-coding and non-coding sequences.

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• Heritability

phenotypic variation within a population is attributable to the genetic variation between individuals and to environmental factors. Heritability is the proportion due to genetic variation usually expressed as a percentage.

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• Heterologous hybridization

the use of a cDNA or oligonucleotide microarray of probes designed for one species with target cRNA/cDNAs from a different species.

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• Homeotic

the transformation of one body part to another due to mutation of specific developmentally related genes, notably the Hox genes in animals and MADS-box genes in plants.

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• Hub

as in networks. A node with high connectivity, and thus which interacts with many other nodes in the network. A hub protein interacts with many other proteins in a cell.

• Hybridisation

the process of joining (annealing) two complementary single-stranded DNAs into a single double-stranded molecule. In microarray analysis, the target RNA/DNA from the subject under investigation is denatured and hybridised to probes that are immobilised on a solid phase (i.e. glass microscope slide).

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• Hypomorph

in genetics, a loss-of-function mutation in a gene, but which shows only a partial reduction in the activity it influences rather than a complete loss (cf. hypermorph, antimorph, neomorph, etc).

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• Imprinting

a phenomenon where two inherited copies of a gene are regulated in opposite ways, one being expressed and the other being repressed.

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• Indel

insertion and deletion of DNA, referring to two types of genetic mutation. To be distinguished from a point mutation', which refers to the substitution of a single base.

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• Interactome

a more or less comprehensive set of interactions between elements within cells. Usually applied to genes or proteins as defined by transcriptomic, proteomic or protein–protein interaction data.

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• Intron

see Exon.

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• KEGG

The Kyoto Encyclopedia of Genes and Genomes is a database of metabolic and other pathways collected from a variety of organisms. See http://www.genome.jp/kegg

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• Metabolomics

the systematic qualitative and quantitative analysis of small chemical metabolite profiles. The metabolome represents the collection of metabolites within a biological sample.

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• Metagenomics

the application of genomic techniques to characterise complex communities of microbial organisms obtained directly from environmental samples. Typically, genomic tags are sequence characterised as markers of each species to inform on the range and abundance of species in the community.

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• Microarray

an arrayed set of probes for detecting molecularly specific analytes or targets. Typically, the probes are composed of DNA segments that are immobilised onto the solid surface, each of which can hybridise with a specific DNA present in the target preparation. DNA microarrays are used for profiling of gene transcripts.

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• Model species

a species used to study particular biological phenomena, the outcome offering insights into the workings of other species. Usually, the selection is based on experimental tractability, particularly ease of genetic manipulation. For the geneticist, it is an organism with inbred lines where sibs will be >98% identical (i.e. Drosophila, Caenorhabditis elegans and mice). For genomic science, it refers to a species for which the genomic DNA has been sequenced.

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• miRNA

a category of novel, very short, non-coding RNAs, generated by the cleavage of larger precursors (pri-miRNA). These short RNAs are included in the RNA-induced silencing complex (RISC) and pair to the 3′ ends of target RNA, blocking its translation into proteins (in animals) or promoting RNA cleavage and degradation (in plants).

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• mRNA

a protein-coding mRNA containing a protein-coding region (CDS),preceded by a 5′ and followed by a 3′ untranslated region(5′ UTR and 3′ UTR). The UTRs contain regulatory elements. A full-length cDNA contains the complete sequence of the original mRNA,including both UTRs. However, it is often difficult to assign the starting–termination positions for protein synthesis unambiguously. A cDNA containing the entire CDS is often considered acceptable for bioinformatic and experimental studies requiring full-length cDNAs.

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• ncRNA

non-coding RNA is any RNA molecule with no obvious protein-coding potential for at least 80 or 100 amino acids, as determined by scanning full-length cDNA sequences. It includes ribosomal (rRNA) and transfer RNAs(tRNA) and is now known to include various sub-classes of RNA, including snoRNA, siRNA and piRNA. Just like the coding mRNAs, a large proportion of ncRNAs are transcribed by RNA polymerase II and are large transcripts. A description of the many forms of ncRNA can be found at http://en.wikipedia.org/wiki/Non-coding_RNA.

• Node

as in networks. Objects linked by edges to create a network.

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• PCR

polymerase chain reaction. A molecular biology technique for replicating DNA in vitro. The DNA is thus amplified, sometimes from very small amounts. PCR can be adapted to perform a wide variety of genetic manipulations.

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• piRNA

Piwi-interacting RNA. A class of RNA molecules (29–30 nt long)that complex with Piwi proteins (a class of the Argonaute family of proteins)and are involved in transcriptional gene silencing.

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• PMF

peptide mass fingerprinting. An analytical technique for protein identification in which a protein is fragmented using proteases. The resulting peptides are analysed by mass spectrometry and these masses compared against a database of predicted or measured masses to generate a protein identity.

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the covalent addition of multiple A bases to the 3′ tail of an mRNA molecule. This occurs during the processing of transcripts to form the mature, spliced molecule and is important for regulation of turnover,trafficking and translation.

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• Post-source decay

in mass spectrometry. The fragmentation of precursor molecular ions as they accelerate away from the ionisation source of the mass spectrometer. All precursor ions leaving the ion source have approximately the same kinetic energy, but fragmentation results in smaller product ions that can be distinguished from precursor ions using a reflectron' by virtue of their lower kinetic energies.

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• Post-translational modification

the chemical modification of a protein after synthesis through translation. Some modifications, notably phosphorylation, affect the properties of the protein, offering a means of regulating function.

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• Principal component analysis (PCA)

a technique for simplifying complex, multi-dimensional datasets to a reduced number of dimensions, the principal components. This procedure retains those characteristics of the data that relate to its variance.

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• Promoter

a regulatory DNA sequence, generally lying upstream of an expressed gene, which in concert with other often distant regulatory elements directs the transcription of a given gene.

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• Proteome

the entire protein complement of an organism, tissue or cell culture at a given time.

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• Quantitative trait

inheritance of a phenotypic property or characteristic that varies continuously between extreme states and can be attributed to interactions between multiple genes and their environment.

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• qPCR

quantitative real-time PCR, sometimes called real-time PCR. A more quantitative form of RT-PCR in which the quantity of amplified product is estimated after each round of amplification.

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• QTL

quantitative trait loci. A region of DNA that contains those genes contributing to the trait under study.

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• RISC

RNA-induced silencing complex. A protein complex that mediates the double-stranded RNA-induced destruction of homologous mRNA.

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• RNAi

RNA interference or RNA-mediated interference. The process by which double-stranded RNA triggers the destruction of homologous mRNA in eukaryotic cells by the RISC.

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• RT-PCR

reverse transcription–polymerase chain reaction. A technique for amplifying a defined piece of RNA that has been converted to its complementary DNA form by the enzyme reverse transcriptase. See qPCR.

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• siRNA

small interfering RNA, or silencing RNA. A class of short (20–25 nt), double-stranded RNA molecules. It is involved in the RNA interference pathway, which alters RNA stability and thus affects RNA concentration and thereby suppresses the normal expression of specific genes. Widely used in biomedical research to ablate specific genes.

• snoRNA

small nucleolar RNA. A sub-class of RNA molecules involved in guiding chemical modification of ribosomal RNA and other RNA genes as part of the regulation of gene expression.

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• SNP

single nucleotide polymorphism. A single base-pair mutation at a specific locus, usually consisting of two alleles. Because SNPs are conserved over evolution, they are frequently used in QTL analysis and in association studies in place of microsatellites, and in genetic fingerprinting analyses.

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• SSH

suppressive subtractive hybridisation. A powerful protocol for enriching cDNA libraries for genes that differ in representation between two or more conditions. It combines normalisation and subtraction in a single procedure and allows the detection of low-abundance, differentially expressed transcripts, such as those involved in signalling and signal transduction.

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• Structural RNAs

a class of non-coding RNA, long known to have a structural role (for instance, the ribosomal RNAs), transcribed by RNA polymerase I or III.

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• Systems biology

treatment of biological entities as systems composed of defined elements interacting in defined ways to enable the observed function and behaviour of that system. The properties of the systems are embedded in a quantitative model that guides further tests of systems behaviour.

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• TATA-boxes

sequences in promoter regions constituted by TATAAA, or similar variants, which were considered the hallmark of Promoters. Recent data show that they are present only in the minority of promoters, where they direct transcription at a single well-defined location some 30 bp downstream of this element.

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• trans-acting

a factor or gene that acts on another unlinked gene, a gene on a separate chromosome or genetically unlinked usually through some diffusible protein product (for mRNA expression, typically a transcription factor).

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• Transcript

an RNA product produced by the action of RNA polymerase reading the sequence of bases in the genomic DNA. Originally limited to protein-coding sequences with flanking UTRs but now known to include large numbers of products that do not code for a protein product.

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• Transcriptome

the full set of mRNA molecules (transcripts) produced by the system under observation. Whilst the genome is fixed for a given organism, the transcriptome varies with context (i.e. tissue source, ontogeny, external conditions or experimental treatment).

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• Transgene

a gene or genetic material that has been transferred between species or between organisms using one of several genetic engineering techniques.

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• Transinduction

generation of transcripts from intergenic regions. At least some such products do not relate to a definable promoter or transcriptional start site.

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• Transposon

sequences of DNA able to move to new positions within the genome of a single cell. This event might cause mutation at the site of insertion. Also called mobile genetic elements' or jumping genes'.

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• Transvection

an epigenetic phenomenon arising from the interaction between one allele and the corresponding allele on the homologous chromosome, leading to gene regulation.

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• TUs

transcriptional units. Used to group all of the overlapping RNA transcripts that are transcribed from the same genomic strand and share exonic sequences.

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• UTR

untranslated region. Regions of the mRNA that lie at either the 3′ or 5′ flanking ends of the molecule (i.e. 3′ UTR and 5′ UTR). They bracket the protein-coding region and contain signals and binding sites that are important for the regulation of both protein translation and RNA degradation.