Biology Reference
In-Depth Information
example, it provides information on the mass of a protein and also generates
amino-acid sequence information (
Dutt and Lee 2000
). Furthermore, mass spec-
trometry can provide data on glycosylation patterns, phosphorylation, and other
posttranslational modifications of proteins.
Proteomics (data on protein expression profiles) can be linked to data on
nucleic-acid sequence. Several software packages are available to compare
multiple protein-expression profiles to identify quantitative changes (
Dutt and
Lee 2000
). For example, proteomics can identify proteins that are associated
with growth control, or responses to high or low temperatures, or to different
chemicals.
Proteomics data are available in databases, including the Protein Information
Resource (PIR) (
Barker et al. 2000
) and SWISS-PROT (
Geisow 1998, Bairoch and
Apweiler 2000
). These sites may contain search engines to compare sequence
similarity and protein function. The SWISS-PROT site provides information on
the function of a protein, its domains structure, its secondary structure (
α
helix,
β
sheet), quaternary structure (homodimer, heterotrimer), similarity to other
proteins, diseases associated with deficiencies in the protein, posttranslational
modifications, and variants. SWISS-PROT has cross-references to additional data-
bases (
Bairoch and Apweiler 2000
). The PIR site provides databases and search
tools (BLAST, FASTA, pattern/peptide, pairwise alignments, multiple alignments,
domain search, global or domain search, and GeneFIND) as well as technical bul-
letins and documentation (
Barker et al. 2000
).
A protein-complex network for
D. melanogaster
was completed in 2011, pro-
viding the largest metazoan protein-complex map to date (
Guruharsha et al.
2011
). It assigns functional links to 586 protein-coding genes that had no previ-
ous functional annotation and linked 2297 proteins in 10,969 interactions. The
goal is to understand how all the functional units in the cell work together to
control development and physiological status.
7.18 Functional Genomics
Functional genomics has been transformed from a concept that was considered
futuristic in the 1980s to an accepted science.
Functional genomics
, the assign-
ment of function to genes, includes understanding the organization and con-
trol of genetic pathways that come together to make up the physiology of an
organism (
Eisenberg et al. 2000
).
Using DNA microarrays or gene chips or transcriptomics, scientists can ana-
lyze complex mixtures of RNA and DNA in a parallel and quantitative fashion.
