Biology Reference
In-Depth Information
Table 1.
(
Continued
)
Online Resources
References
VisANT
Combines predicted interactions and
58
experimental data; has an interactive
network visualization front-end.
iHOP
Main focus is on automated literature
59
searches, augmented with imported
interaction data; the retrieved relations
can be grouped into networks.
interaction is termed an “interolog”,
49
and its validity depends on the
evolutionary distance between the two organisms and on the degree of
sequence conservation.
These online resources can serve as a starting point for in-depth
analysis of a certain pathway or protein complex. They can also provide
proteome-wide background information to better understand a given
functional genomics dataset, allowing the following questions, for exam-
ple, to be raised: Does my set of genetically defined loci cluster on the
network? Are certain types of protein modifications found in certain parts
of the functional landcape? Can I use the network to reduce complexity
in my genotyping data? These and other questions are best addressed by
using the powerful information integration provided by organism-wide
protein networks.
References
1. Alberts B. (1998) The cell as a collection of protein machines: preparing the next
generation of molecular biologists
. Cell
92
(3): 291-4.
2. Sharan R, Ulitsky I, Shamir R. (2007) Network-based prediction of protein
function.
Mol Syst Biol
3
: 88.
3. Barabási AL, Oltvai ZN. (2004) Network biology: understanding the cell's func-
tional organization
. Nat Rev Genet
5
(2): 101-13.
4. Skrabanek L, Saini HK, Bader GD, Enright AJ. (2008) Computational predic-
tion of protein-protein interactions.
Mol Biotechnol
38
(1): 1-17.
5. Bader GD, Hogue CW. (2002) Analyzing yeast protein-protein interaction data
obtained from different sources.
Nat Biotechnol
20
(10): 991-7.
