Measuring Consequences of Protein Misfolding and Cellular Stress Using OMICS Techniques - Protein Misfolding and Cellular Stress in Disease and Aging - page 128

genes, which promote formation of a-synuclein inclusions and genes,
which appear to counteract inclusion formation. Consistent with
previous findings, quality control genes were overrepresented among
aggregation suppressing genes and aging-associated genes were
prominent among the genes that promote inclusion formation. The
list of factors identified included both known and new factors which
now may be further investigated and possibly targeted by therapeutic
strategies.
7. Bioinformatics
A maybe not fully satisfactory, but simple and valid definition of
bioinformatics is “ using computers to manage, organize, and ana-
lyze large amounts of biological information ” as stated in ( 1 ).
Bioinformatics comes in three different flavors mainly performed
by differently trained researchers: (1) highly specialized computer
professionals, who develop databases and analysis tools allowing
researchers to query with their datasets and often also to upload
their datasets to contribute to the growth of the databases,
(2) Janus-headed specialists, who are computer specialists as well
as trained in the instruments used in the specific molecular biol-
ogy field and work at the interface of front-line development of
software for running the instruments and converting primary
data to manageable and structured data sets, and (3) “ordinary”
molecular biologists, who are clients to the former two and are
able to take the output from database queries and software to
produce meaningful and illustrative presentations of their com-
plex experimental data as well as extract the information, which
gives the rationale for experimental follow-up. The last group of
researchers is steadily growing as seasoned molecular biologists
have learned bioinformatics “by doing” and the younger genera-
tion has got bioinformatics as a natural part of the curriculum.
This is facilitated by a quantum leap in usability and clever entan-
glement of the various databases. Also several meta-databases
exist combining and presenting information in an intuitive man-
ner. The field is very much in development and steady movement,
as can be seen by websites often changing their setup, and favorite
sites disappearing and new ones coming up. Due to this constant
movement and the scope of this chapter we will in the following
only mention some basic databases and a few examples of tools
from our own practical experience as molecular biologist-bioin-
formaticians. These references may give some hints for beginners
on where to start when dealing with large-scale data.
For functional classification of proteins and genes, the Gene
Ontology (GO) terminology has been developed ( http://www.
geneontology.org/ ) giving descriptive terms to genes from many