I am working on two similar proteins, Yap and Taz, and I am trying to find a way to best compile the information as I go. I am attempting to find binding partners or phosphorylation sites that would be worth exploring in my cell type and the data is more overwhelming than putting together a power point with lines and circles. Could someone give a suggestion as to a program that allows a user to write and expand out pathway information from a central protein?
I am thinking about something that works similar to GIANT. You can make connections between two associated molecules and then click on the link and get a pop-up of sources that confirm the link, cell type they used, how they established the link etc. Even better would be a program where you could segregate these interactions based on peptide sequences.
I am new to proteonomics and am hoping that writing this information out will give me a better understanding of the system as a whole and lead to some interesting questions down the line.
If you want to infuse the existing knowledge about how two proteins A and B can interact to a computational protein-protein interaction calculating software then there are plenty of software do the same. ZDOCK, ROSETTA, GRAMM etc. Hopefully I understand you.
Hello Debajyoti, interesting software, but not exactly what I am looking for.
I am less concerned with the computational aspects of the protein interactions and more concerned with developing a network map. Also while I am interested in yap and taz the relationship between the two is not my primary concern, as they both have similar functionality and regulation. Instead I am looking at up and down stream regulators and effectors.
As an example, Yap and Taz are phosphorylated by LATS at specific serine residues and are marked for degradation. Additionally there are links between AMOTL and RhoA in relation to yap and taz. I just want an easy to use interface for making my own notes and map these interactions using something more user friendly than power point.
You could make your annotations as a table of 'nodes' (things that interact) and a table of 'edges' (interactions) in Excel. Give each node a unique identifier, and record what type of node it is, and other relevant details in separate named columns. Record each edge with the IDs of the two nodes which are interacting, the type of interaction, and the direction if it is a one-way interaction, and with other columns for the PUBMED ID of the paper, and other relevant details.
With this structure, you could visualise and explore your network in Cytoscape or Gephi, and other similar graph tools, or if you are building a very large database, you can import your data to something like Neo4J. A structure like this is very generic and frees you to use a variety of tools.
Mindnode is a free and very simple graph building software if you want something quick and easy but you will soon run into limitations that Cytoscape or Gephi will overcome.
I was about to say the Microsoft Access should be your go-to software with database building. Some parts of it work like Excel, but it has more database capability, such as creating information flowcharts and relational tools. Also, you can make your own "app" with it that would have search fields etc...
Try reading this
http://en.wikipedia.org/wiki/Comparison_of_relational_database_management_systems
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