This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
Proteing Networks from String
STRING is an online database that finds known and predicted protein interactions and maps them in a network. I searched for SMN1 and found no exact matches, but a search for SMN yielded results for homo sapiens as well as many other species with SMN homologs.
SMN-1
(Figure 1)
SMN-1 in particular was not found using the String program, but ENSP00000348683 was identified as survival of motor neuron protein. The protein sequence that was given is the protein sequence that has been identified for SMN-1. This is the same protein, but the annotation has most likely not been finished. All of the proteins that were discovered to interact with SMN-1 were associated with the production of mRNA. A few Small nuclear ribonucleoprotein-associated proteins and different portions of those proteins were identified to interact with SMN-1. The other proteins identified were gem-associated proteins which also interact with the RNA associated proteins.
(Figure 2)
The protein identified as ENSP00000370083 also had the same amino acid sequence as SMN-1, indicating that it is the same as the protein identified above, but there is a slightly different protein network identified. This only seems to indicate the lack of a complete annotation and adjustment or correlation of all of the data that is available.
D.Melanogaster SMN protein network
(Figure 3)
Many of the same types of proteins were identified as interacting with the D.Melanogaster homolog of SMN. This is what we would expect to see from a homologous protein, it should be performing relatively similar functions and interacting with similar proteins. It seems strange that this homolog was identified with using String, but it was not a top result when the homolog searches were done before.
Osprey Protein Network
(Figure 4)
Yellow - RNA processing
Purple - Cell Organization and Biogenesis
Pink - protein transport
Blue - metabolism
Grey - Unknown
Osprey is a computer program that uses information about protein interactions in order to develop an interaction network of proteins. Although there were initially some difficulties in accessing the information that Osprey uses, I was able to enter SMN1 into the database and the above chart was obtained.
Once again, I discovered that many similar proteins are interacting with SMN-1, that I discovered using SMART. Most of the proteins were involved in RNA processing as I expected and several are involved in cell organization and biogenesis. These proteins most likely interact with the mRNA or proteins that are later formed.
References:
Figure 1. String 8.0 (2009) Protein Search retrieved Apr 26 2009 from: http://string.embl.de/newstring_cgi/show_network_section.pl
Figure 2. String 8.0 (2009) Protein Search retrieved Apr 26 2009 from: http://string.embl.de/newstring_cgi/show_network_section.pl
Figure 3. String 8.0 (2009) Protein Search retrieved Apr 26 2009 from: http://string.embl.de/newstring_cgi/show_network_section.pl
Figure 4. developed using the Osprey program
William Baader
[email protected]
Apr 26 2009
www.gen677.weebly.com
