Biomedical Engineering Reference
In-Depth Information
PROTOCOL 9.3 Obtaining Protein-Protein Interaction Data
from BioGRID for Function Prediction
Requirements
Internet access to download data and software
•
Programming or scripting language such as C, C++, Perl, Matlab.
•
Method
1 Download the protein-protein interaction data from http://www.thebiogrid.org/
downloads.php.
2 Choose between all interaction data and organism-specific data. Three formats are
available: Excel tab-delimited text, PSI-MI XML version 1 and PSI-MI XML
version 2.5.
3 Each record contains the names of two interacting proteins, the type of experiment
system in which the interaction was observed (e.g. two hybrid) and the PubMed
identifier of the publication from which the interaction was curated.
d
4 Convert protein names to the identifier you desire; for example, RefSeq accession
numbers, SGD or Ensembl identifiers. You would want to use an identifier system that is
consistent with other data, such as GO annotations. This can be done using a tool such
as the Synergizer at http://llama.med.harvard.edu/synergizer/translate/.
Notes
d
The experiment system used in the detection of an interaction reflects the nature and
confidence of the interaction. For example, synthetic lethality detects genetic interactions
while two hybrid detects physical interactions; interactions detected by affinity purification are
more reliable than those detected by two hybrid.
9.2.6.2 Common interacting partners
The above approaches associate proteins through interaction. Some approaches associate
proteins based on their sharing of interaction partners. Samanta and Liang [15] computed
a distance for each pair of proteins
u
and
v
using a hypergeometric score based on each
protein's interaction neighbors defined as
N
m
N
N
−
m
−
n
1
−
−
n
1
m
n
2
m
N
n
1
N
n
2
P (N,u,v,m)
=
where
N
refers to all proteins in the interaction network,
N
u
refers to the neighbors of
protein
u
,
m
=|
N
u
∩
N
v
|
,
n
1
=|
N
u
|
and
n
2
=|
N
v
|
.
