TY  - JOUR
AU  - Porras, Pablo
AU  - Duesbury, Margaret
AU  - Fabregat, Antonio
AU  - Ueffing, Marius
AU  - Orchard, Sandra
AU  - Gloeckner, Christian Johannes
AU  - Hermjakob, Henning
TI  - A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.
JO  - Practical proteomics
VL  - 15
IS  - 8
SN  - 1615-9853
CY  - Weinheim
PB  - Wiley VCH69157
M1  - DZNE-2020-04204
SP  - 1390-1404
PY  - 2015
AB  - Molecular interaction databases are essential resources that enable access to a wealth of information on associations between proteins and other biomolecules. Network graphs generated from these data provide an understanding of the relationships between different proteins in the cell, and network analysis has become a widespread tool supporting -omics analysis. Meaningfully representing this information remains far from trivial and different databases strive to provide users with detailed records capturing the experimental details behind each piece of interaction evidence. A targeted curation approach is necessary to transfer published data generated by primarily low-throughput techniques into interaction databases. In this review we present an example highlighting the value of both targeted curation and the subsequent effective visualization of detailed features of manually curated interaction information. We have curated interactions involving LRRK2, a protein of largely unknown function linked to familial forms of Parkinson's disease, and hosted the data in the IntAct database. This LRRK2-specific dataset was then used to produce different visualization examples highlighting different aspects of the data: the level of confidence in the interaction based on orthogonal evidence, those interactions found under close-to-native conditions, and the enzyme-substrate relationships in different in vitro enzymatic assays. Finally, pathway annotation taken from the Reactome database was overlaid on top of interaction networks to bring biological functional context to interaction maps.
KW  - Animals
KW  - Computer Graphics
KW  - Databases, Protein
KW  - Humans
KW  - Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
KW  - Molecular Sequence Annotation
KW  - Parkinson Disease: metabolism
KW  - Protein Interaction Maps
KW  - Protein-Serine-Threonine Kinases: physiology
KW  - Proteomics: methods
KW  - Software
KW  - LRRK2 protein, human (NLM Chemicals)
KW  - Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 (NLM Chemicals)
KW  - Protein-Serine-Threonine Kinases (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:25648416
C2  - pmc:PMC4415485
DO  - DOI:10.1002/pmic.201400390
UR  - https://pub.dzne.de/record/137882
ER  -