This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison, Spring 2012.
SOD1 Interaction Network
What is an interaction network?
An interaction network is a model of protein-protein interactions known or predicted to take place in cells. STRING is a database compiling data from genomic context, high-throughput experiments, conserved coexpression and data mining to integrate data from these sources into groups with direct physical and indirect functional associations.
Human SOD1 Interactions
Below is the interaction network of human SOD1 from STRING [1]. Interactions are determined and color-coded by neighborhood, gene fusion, cooccurence, coexpression, experiments, databases, text mining and homology.
(Click to enlarge.)
(Click to enlarge.)
Stitch Network
The network to the left was produced by Stitch, a sister project of String, and includes chemical-protein interactions. This network shows how copper and zinc interact with SOD1 and some of its interacting proteins.
(Click to enlarge.) |
Model Organism Networks
STRING includes interaction networks with SOD1 homologs in many species. Below are the networks from a few model organisms used in ALS research [1]. (Click to enlarge.)
Mouse SOD1 Interaction Network
Zebrafish SOD1 Interaction Network
Fruit Fly SOD Interaction Network
Yeast SOD1p Interaction Network
Analysis
STRING is an easy way to find proteins that have a connection with SOD1 in a variety of organisms. Looking at the networks from human, mouse, zebrafish, fruit fly and yeast SOD1 for conserved interactions shows that there is a core set of proteins associated with SOD1 including SOD2, Catalase, and often CCS (copper chaperone for superoxide dismutase). Another interesting connection is to PARK7 in both humans and zebrafish, which is known to cause Parkinson's disease, highlighting the potential similarities between ALS and other neurodegenerative diseases. The connections with neurofilaments GFAP and NEFL may help explain the neurodegeneration in ALS, as they are critical for the health of neurons.
1. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. (2003). STRING: a database of predicted functional associations between proteins. Nucleic Acid Res 31 (1): 258-61. PMID:12519996