Hi. I would like to know how to work with a set of gene ontology terms that I have. I really need to know how can I make a graph or a conceptual map, with all my GO-terms obtained, and make all relation between them. I hope there is some tools with R programming or something. Thanks!
A good software representing a network between GO terms is Bingo. It's a Cytoscape plugin that you can specify your desired gene list and receive the network of GO terms that are significantly linked to your gene list. Although it does not match exactly with your question, but I think is one of the best choices for you.
You can see several tools for GO term visualization here. I would recommend to use Ontologizer 2.0 and integrated function to do both your enrichment and generate a graph (directed acyclic graph of GO terms) as you required.
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Could you be a little more clear about what type of data you have and how you are hoping to communicate that data? There are many ways to use R, so it's hard to provide you an answer based on the amount of information you have provided us.
I have a lot of IDs.. like:
GO:0043768 GO:0008152
I want to make a network between all this data of GO ids, and classify according to biological process, molecular function and cellular compartment. I tried using RamiGO, but it generates the entire tree with GO ids I do not want. I just want a tree that relates my data, and separated according to the above, and the levels of ontology, or something.
You want to "make a network"--does that mean draw a diagram of related GO terms? You want to classify--classify what? What is "my data"? Separated according to the above--what is the "above"? What are the data you are working with and what biological question are you trying to answer?
I dont speak english, so there are some words that may be wrong. I developed an algorithm that allows me to get information of crystallized proteins of a particular organism. Among all this information gives me ontology ids for the proteins found. My main target of research is finding potential therapeutic targets based on the action of these proteins, or if they are in some particular metabolic pathway. For that I need to make a tree that tells me both ontology ids like protein with which its related. This establishes a relationship between the chosen therapeutic target and because of this election, based on which it acts. And that information will get from the tree of the ontology, or network.
You still haven't provided any information on what you are trying to accomplish with your data, so it's a little hard to point you in the right direction. What is your overall goal of the research -- are you trying to compare different samples or treatments?
Have you tried to use Cytoscape? I'm still taking in the new 3.0 version, but I have been impressed. You may want to show your network data as a hive plot as it might be less visually overwhelming than a network.