Hello,
I would like to perform Markov cluster (MCL) PPI, is there any tutorial which can show how to perform this? I don't mind about the language but I prefer python, ruby and R or matlab
Thanks
Markov clustering (MCL) is implemented as a stand-alone software written in C but the distribution also contains a perl implementation. See its homepage and in particular the protocol section. If your graph is in the format nodeA\tnodeB\tweight then you can process it with
mcl input.txt --abc -o output.txt -I 2.0
The R implementation is in the MCL package. It is also available in the clusterMaker2 plugin for Cytoscape.
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@Jean-Karim Heriche sorry for stupid question but do you know how the input data should look like? for example, should I have 1 columns of proteins IDs and one column of expression ? or something else ?
@Jean-Karim Heriche it is not what I wanted , as I said I don't know the technique. I must know which information I need to have for making it at first. you tell me about nodeA, nodeB and weight. I have read many papers with different structure of data inputs. if I knew the nodes then I don't need to do MCL to random walk, I can do it in a more easier way. My question is to find a tutorial and not just some websites
Sorry I don't understand what it is you're after. Your initial question read as if you wanted to know how to do Markov clustering.
The input can be structured in several different ways depending on which implementation you use. If using the stand-alone mcl with the --abc option, then you can use the tab-delimited format I described.
@Jean-Karim Heriche Yes wola, that is what I am looking for. I don't care about a written package. I am more looking to find different structure of the inputs, for example, how the edge is calculated , how weight normally is calculated etc. Of course I apologise if my question is not very straight forward :-p such things happen very often to people who rarely sleep :-p
So if I understand correctly, you're actually asking how to build a weighted graph. This then depends on the data you have and the question you're trying to address.
@Jean-Karim Heriche I have found experimentally that few unregulated proteins. So there are two ways in my opinion to see how these proteins are interacting with each other and whether they make a cluster or not which this is out of my question. the second way is to make a physical network. I am asking this one, I have a set of proteins IDs and I want to know how they interact, I know online databases like STIRNG etc which I am not interested in . I want to know if there is any other way to do that (look how far we get from my original question :-p)))