The field of bioinformatics refers to the creation, maintenance, and analysis of biological information such as nucleotide and amino acid sequences. revolves around trying to answer important biological questions by making use of analytical machinery from statistics and computer science, but always being driven by biological understanding.These techniques are used to answer questions such as
- what are the functional roles of different genes and in what cellular processes do they participate;
- how are genes regulated, how do genes and gene products interact, and what are these interaction networks;
- how does gene expression level differ in various cell types and states, how is gene expression changed by various diseases or compound treatments.
Microarrays
Hybridisation is the process of establishing a bond between two of more complementary strands of nucleic acids. The range of technologies involved in hybridising DNA or RNA samples to a large number of oligonucleotide strings arrayed on a solid surface (normally either glass or silicon) is collectively known as oligonucleotide microarray technology, or more commonly as microarrays.
Oligonucleotide strings are short single-stranded DNA or RNA that are used throughout genetic testing, research, and forensics and are usually found as small RNA molecules that function in the regulation of gene expression. A key feature of oligonucleotide strings is that they readily bind to their respective complementary oligonucleotide strings. This binding property makes them effective probes for detecting DNA or RNA.
Oligonucleotide microarrays contain a large number of such oligonucleotide strings arrayed in a known order, where each oligonucleotide string is referred to as a cell of the array. The array is hybridised to a flourescently labelled DNA or RNA sample. Automated laser confocal microscopy is then used to determine if hybridisation has occurred in each cell of the array, indicating that that DNA is being expressed within the sample. More than 10 million different oligonucleotide strings can be arrayed on a 1.28 cm x 1.28 cm glass surface in regular square cells as small as 5 micrometers.
Oligonucleotide strings are short single-stranded DNA or RNA that are used throughout genetic testing, research, and forensics and are usually found as small RNA molecules that function in the regulation of gene expression. A key feature of oligonucleotide strings is that they readily bind to their respective complementary oligonucleotide strings. This binding property makes them effective probes for detecting DNA or RNA.
Oligonucleotide microarrays contain a large number of such oligonucleotide strings arrayed in a known order, where each oligonucleotide string is referred to as a cell of the array. The array is hybridised to a flourescently labelled DNA or RNA sample. Automated laser confocal microscopy is then used to determine if hybridisation has occurred in each cell of the array, indicating that that DNA is being expressed within the sample. More than 10 million different oligonucleotide strings can be arrayed on a 1.28 cm x 1.28 cm glass surface in regular square cells as small as 5 micrometers.
Gene expression
Microarrays completely changed the way hybridisations are inspected by allowing a very large number of hybridisations to be carried out in parallel, a job that would otherwise take years of effort. This makes microarrays very effective when investigating patterns of gene expressions in different tissues. This type of profiling is the most common use of microarray technology.
Arrays in which each probe represents a gene are hybridised to fluorescently labelled DNA prepared from different tissue samples.
The results from any two samples are compared; if hybridisation is stronger in one sample for a specific gene then that gene is said to be differentially expressed in that sample. The knowledge of which tissue a specific gene is expressed in helps to suggest the function of the gene.
Likewise, by looking at a sample from a person with a disease when compared against a control healthy sample, it is possible to see what genes that disease is causing to be over or under expressed. This second technique becomes particularly useful when looking at cancer patients because different cancer types can often be clearly differentiated by their expression profiles.
Nowadays there is a vast amount of this kind of data readily available online from sources such as: Gene Expression Omnibus (GEO), the Cancer Genome Atlas, and Metabric.
Arrays in which each probe represents a gene are hybridised to fluorescently labelled DNA prepared from different tissue samples.
The results from any two samples are compared; if hybridisation is stronger in one sample for a specific gene then that gene is said to be differentially expressed in that sample. The knowledge of which tissue a specific gene is expressed in helps to suggest the function of the gene.
Likewise, by looking at a sample from a person with a disease when compared against a control healthy sample, it is possible to see what genes that disease is causing to be over or under expressed. This second technique becomes particularly useful when looking at cancer patients because different cancer types can often be clearly differentiated by their expression profiles.
Nowadays there is a vast amount of this kind of data readily available online from sources such as: Gene Expression Omnibus (GEO), the Cancer Genome Atlas, and Metabric.
Figure 1: An example of the reading from a microarray. Green represents genes that are over expressed, red those that are under expressed (http://csmbio.csm.jmu.edu/)