5 Cardio-oncology: Network-Based Prediction …
83
Table 5.2 Summary of representative bioinformatics resources and network tools for building
disease modules from the human protein-protein interactome
Name of
databases
Description
Webs
References
Section 1. Systems biology resources
BioGRID
Integrated protein-protein
interaction data
http://thebiogrid.org
[74]
HPRD
Human protein-protein
interaction data
http://www.hprd.org
[108]
Interactome3D Manually curated PPIs with
known three-dimensional
structure information
http://interactome3d.
irbbarcelona.org
[62]
STRING
Functional protein
association networks
database
http://string-db.org
[109]
MINT
Protein-protein interactions
in refereed journals
http://mint.bio.uniroma2.it/
mint
[76]
KinomeNetworkXAn integrative
kinase-substrate database
[65]
PhosphoNetworksA high-resolution
phosphorylation network
connects the specific
phosphorylation sites
present in substrates with
their upstream kinases
http://www.
phosphonetworks.org/
[67, 68]
PhosphositePlus A database and tools for the
study of protein
post-translational
modifications (PTMs)
including phosphorylation,
acetylation, and more
https://www.phosphosite.
org/homeAction.action
[69]
Section 2. Systems biology resources
OMIM
A comprehensive collection
covering literature-curated
human disease genes with
experimental evidence
http://www.omim.org/
[79]
CTD
A database containing
literature-curated
interactions connecting
chemical, genes, and
diseases
http://ctdbase.org/
[80]
ClinVar
A public archive of
relationships among
sequence variation and
various human phenotypes
https://www.ncbi.nlm.nih.
gov/clinvar/
[81]
(continued)
83
Table 5.2 Summary of representative bioinformatics resources and network tools for building
disease modules from the human protein-protein interactome
Name of
databases
Description
Webs
References
Section 1. Systems biology resources
BioGRID
Integrated protein-protein
interaction data
http://thebiogrid.org
[74]
HPRD
Human protein-protein
interaction data
http://www.hprd.org
[108]
Interactome3D Manually curated PPIs with
known three-dimensional
structure information
http://interactome3d.
irbbarcelona.org
[62]
STRING
Functional protein
association networks
database
http://string-db.org
[109]
MINT
Protein-protein interactions
in refereed journals
http://mint.bio.uniroma2.it/
mint
[76]
KinomeNetworkXAn integrative
kinase-substrate database
[65]
PhosphoNetworksA high-resolution
phosphorylation network
connects the specific
phosphorylation sites
present in substrates with
their upstream kinases
http://www.
phosphonetworks.org/
[67, 68]
PhosphositePlus A database and tools for the
study of protein
post-translational
modifications (PTMs)
including phosphorylation,
acetylation, and more
https://www.phosphosite.
org/homeAction.action
[69]
Section 2. Systems biology resources
OMIM
A comprehensive collection
covering literature-curated
human disease genes with
experimental evidence
http://www.omim.org/
[79]
CTD
A database containing
literature-curated
interactions connecting
chemical, genes, and
diseases
http://ctdbase.org/
[80]
ClinVar
A public archive of
relationships among
sequence variation and
various human phenotypes
https://www.ncbi.nlm.nih.
gov/clinvar/
[81]
(continued)