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Computationally predicted functional associations are produced in
CAGT. Most of
experimentally determined interaction data are collected from
MIPS,
BIND,
HPRD etc. and
updated periodically. Some large-scale experimental data, such as
Chip-Chip data
for transcriptional regulatory networks, is collected
independently.
In addition to the computational
predicted interactions produced in our Lab, Predictome database also
collects experimentally determined ones by either directly importing
from literatures, or by synchronizing with existing interaction
databases such as
Biogrid,
MIPS,
BIND,
HPRD
etc. The integration of the interaction is gene-based, meaning that
two protein nodes will be recognized as a single protein, if the
same gene encodes them. This decision not to distinguish gene nodes
from protein nodes was based primarily on the following
observations:
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Independently created interaction databases often use different
naming systems for proteins/genes. For example, MINT uses a
protein's UniProt id in protein-protein interaction for Homo sapiens
which, however, is represented using gene's HGNC (HUGO Gene
Nomenclature Committee) id in Biogrid.
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Genetic associations very often need to be compared to
protein-protein interactions.
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High
throughput gene expression results must often be mapped onto a
protein-protein interaction network or pathway.
Because genes often encode multiple proteins, using gene id to
represent both gene and protein is a natural choice; otherwise,
uncertainty may arise when integrating interaction data. For
example, for a gene with two splice variants, the variant to use
when integrating interactions between the MINT (protein-based) and
Biogrid databases (gene-based) will be ambiguous. The shortcoming of
this solution is that certain splice variants may only share a
subset of interactions. This dilemma can be overcome if alternative
splicing knowledge is represented using a metanode, an undergoing
process of this project.
Detailed information of the interactions in Predictome database can
be found at Interaction
Statistics page. |