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numerous other protein interaction databases). Similarly, RNA molecules control each

other. For this, TargetScan and miRanda indicate possible binding sites between mRNAs

and miRNAs (small RNAs that regulate mRNAs). Finally, cell compartments through

membranes control that certain reactions take place in specific cell regions. This can be

easily reconstructed using biochemical databases, e.g. KEGG or Roche Biochemical

Pathways. It is also of interest to look at the interaction between a drug and its target. The

STITCH database or the DrumPID database developed by us are helpful for this.

Regulation, in particular through control of gene expression, is thus an important design

principle that is bioinformatically analysed through analyses of RNA and statistical analy­

ses of gene expression, on which network analyses are then based.

How Cells Localize, Transport and Secrete Proteins

11.1

Modern imaging techniques now even achieve optical resolution down to 1 nm (Stefan

Hell, Nobel Prize winner for superresolution microscopy): Using clever tricks, namely

combining flashing (with the DSTORM technique down to 10 nm) and quenching fluores­

cence signals (also goes down to 10 nm), where integrating over time is critical, one can

actually resolve structures much smaller than half the wavelength of visible light

(400–800 nm), which was the classical lowest resolution limit of optical microscopy. In

these techniques, software is indispensable for high resolution. Further bioinformatics

software is required for localization. For example, one can use common microscopy image

processing software such as ImageJ and write scripts for it (called macros) that allow one

to filter out individual features of the image from large amounts of data, for example for

the detection of synaptic vesicles. An introduction to such techniques is provided by

Kaltdorf et al. (2017), including a tutorial on how to learn the software.

It is also important to classify all cellular processes by analyzing the gene ontology.

Combined with information about the protein-protein interactome, the resulting cellular

network can be traced using software such as CellDesigner or Cytoscape. For example,

motor proteins and the actin-myosin cytoskeleton are crucial for cell movement.

The Gene Ontology Consortium has hierarchically classified all processes in the cell

according to three criteria (https://www.geneontology.org): molecular function (e.g.

enzyme and which enzyme), cellular compartment (such as in the cytoplasm or in an organ­

elle) and cell biological process (e.g. a signalling cascade such as apoptosis). Thus, with an

analysis of the gene ontology of the proteins involved, an overview of the design of a pro­

tein network can be quickly obtained by bioinformatics. For example, one can easily evalu­

ate the proportions of the proteins involved in the processes determined with the help of the

Gene Ontology (as also described in Chap. 5, Task 5.9 BiNGO analysis and Task 5.10).

11.2  Bioinformatics Provides Detailed Insights into the Molecular Biology of the Cell