What are Interaction Networks?
An interaction network is a network of nodes that are connected by specific features of interest (1). These can get to be quite complex as shown in Figure 1, and can be difficult to interpret at first. My specific interest was in proteins, so I used the protein interaction network database STRING to look up what type of proteins FLNB interacts with. With STRING you can choose the depth you want to go into. I choose a smaller scale protein interaction network to easily visualize the proteins directly interacting with FLNB instead of those proteins that don’t directly interact with FLNB. |
Protein Interaction Network of FLNB:
The STRING network proved to be a great tool for looking at proven interacting proteins of the FLNB protein. The FLNB STRING network (Figure 2) was created by entering in “FLNB” into the STRING search engine and selecting the human result that pops up. From seeing the FLNB interaction network, I was able to find that the various interaction networks shared many of the same functions. One of these groups of similar proteins was ubiquitin proteins (Figure 2: green) which are involved in protein degradation. Another group was fibronectin receptors (Figure 2: blue) which are involved in cell migration and determine the patterns of pre-cartilage cell adhesion to the extracellular matrix that’s focused on limb-specific patterns of chondrogenesis, the process in which cartilage is developed (2). There was also one protein, FBLIM1 (Figure 2: pink), which deals with adhesion to the extracellular matrix.
Analysis:
The STRING network provided more information about what type of proteins interact with the FLNB protein, which lead to a greater understanding on how the FLNB protein operates within the human body. When seeing that FLNB interacts with several ubiquitin proteins this told me that FLNB must correlate with protein degradation. When looking further into bone development and the cartilage surrounding the bone of joints this made sense, for the cartilage cells surround these bones degrade over time as well as can condense to form bone tissue by a process known as ossification where FLNB has importance (3). The FLNB protein STRING network also showed FLNB interacting with a group of fibronectin receptor proteins. This made sense as well with what is known about the FLNB proteins criticality in proper cartilage migration and support in the joints of large bones (4). By seeing that the FLNB protein interacts with several proteins from these two groups I became curious how these two groups of proteins change over time. I hypothesized this and how this could begin to be experimentally achieved in my conclusions. Lastly, it was great to see the FBLIM1 protein, involved in adhesion to the extracellular matrix, closely interacting with the FLNB protein for it went along with my gene ontology results and thus supporting those results.
References:
1.) "Wikipedia: Interaction Network". Web. May 16, 2014. http://en.wikipedia.org/wiki/Interaction_network
2.) "Wikipedia: Chondrogenesis". Web. May 16, 2014. http://en.wikipedia.org/wiki/Chondrogenesis
3.) "BCC: The skeleton, bones, and joints". Web. April 15, 2014. http://www.bbc.co.uk/schools/gcsebitesize/pe/appliedanatomy/2_anatomy_skeleton_rev4.shtml
4.) Zhang, D. et. al., (2006) "Mutations Responsible for the Larsen Syndrome Cluster in the FLNB Protein." Journal of Medical Genetics, 43(24), doi: 10.1136/jmg.2005.038695
2.) "Wikipedia: Chondrogenesis". Web. May 16, 2014. http://en.wikipedia.org/wiki/Chondrogenesis
3.) "BCC: The skeleton, bones, and joints". Web. April 15, 2014. http://www.bbc.co.uk/schools/gcsebitesize/pe/appliedanatomy/2_anatomy_skeleton_rev4.shtml
4.) Zhang, D. et. al., (2006) "Mutations Responsible for the Larsen Syndrome Cluster in the FLNB Protein." Journal of Medical Genetics, 43(24), doi: 10.1136/jmg.2005.038695