analysis of interaction networks - mass of data =) (Dec/20/2006 )
Hi all out there 
Does somebody know a algorithm or tool to analyze protein-protein-interactions?
I'am a total newbie in analyzing interactiondata and so I decided to ask for some advice 
At the moment I'm using Cytoscape, which is an excellent tool for viewing pp-interactions. However my interaction-network looks like a big mass of interactions and I didn't get any clue about interesting proteins. So I'm asking me, isn't there any algorithm or software which can filter important data. For example those interaction partners with more than 2 interactionpartners, or which is the protein with the most interactions, etc.
To get an idea about my problem:
regards Markus
Does somebody know a algorithm or tool to analyze protein-protein-interactions?
I'am a total newbie in analyzing interactiondata and so I decided to ask for some advice
At the moment I'm using Cytoscape, which is an excellent tool for viewing pp-interactions. However my interaction-network looks like a big mass of interactions and I didn't get any clue about interesting proteins. So I'm asking me, isn't there any algorithm or software which can filter important data. For example those interaction partners with more than 2 interactionpartners, or which is the protein with the most interactions, etc.
To get an idea about my problem:
regards Markus
Markus,
1. Can you post the input flat file format (just a portion), maybe we can write a simple parser to extract those data.
2. If Cytoscape is a software just for pp interaction visulization, I would be surprised if they don't offer a filter function. Maybe you should check their manual more closely.
Hi Cyberpostdoc 
I uploaded three files to cytoscape, the mainfile (a *.sif file) contains the interaction relationships. Here is a clipping:
291 nn 4792
291 nn 5581
291 nn 367
291 nn 581
291 nn 10105
291 nn 5481
2230 nn 2230
2230 nn 2232
2230 nn 54205
2232 nn 5451
133 nn 133 --> self interacion is allowed
133 nn 4311
133 nn 3075
133 nn 1906
133 nn 10203
213 tn 348
213 tn 1409
213 tn 5004
213 tn 6927
213 tn 5444
213 tn 259
213 tn 5552
213 tn 5950
213 tn 4036
213 tn 2217
213 tn 8029
213 tn 7532
213 tn 51631
124 nn 124
128 nn 128
128 nn 1107
126 nn 126
10327 nn 54512
The first and third columns contain the interactionpartners represented by the NCBI entrezgene ID. The middle supports the information about the interaction type; in my special case, that could be nn, tn, nt and tt (normal-normal, tumor-normal, normal-tumor, tumor-tumor).
Cyberpostdoc, you are right! Cytoscape supports several filter mechanisms , however manual filtering and collecting 'maybe significant' by visual evaluation seem for me very clumsy
I uploaded three files to cytoscape, the mainfile (a *.sif file) contains the interaction relationships. Here is a clipping:
291 nn 4792
291 nn 5581
291 nn 367
2230 nn 2232
2230 nn 54205
2232 nn 5451
133 nn 133 --> self interacion is allowed
133 nn 4311
133 nn 3075
133 nn 1906
The first and third columns contain the interactionpartners represented by the NCBI entrezgene ID. The middle supports the information about the interaction type; in my special case, that could be nn, tn, nt and tt (normal-normal, tumor-normal, normal-tumor, tumor-tumor).
Cyberpostdoc, you are right! Cytoscape supports several filter mechanisms , however manual filtering and collecting 'maybe significant' by visual evaluation seem for me very clumsy
Let's first figure out what we want:
1. a statistics for each G1, by decending order, it will look like this:
------ ----- ----- ----------
250 45 56 678 67
133 456 345 455 67
...
2. same format for G2 (if G1 nn/nt/tn/tt G2 is different from G2 interacts with G1 in your case, direction effect)
3. if #2 is not true, then G1 and G2 can be pooled and only build #1 result file (interaction is bidirectional)
4. then you can output the top N genes based on any of those interaction type or by total number of interaction types.
So the input is the file you showed above, the output is the file we just specified. Is this correct?
Hi Postdoc and my best wishes for the new year!!!
Thanks a lot for your advice!
I will adopd your ideas and have a look at the result.
Sorry for the late reply, I was skiing
Thanks a lot for your advice!
I will adopd your ideas and have a look at the result.
Sorry for the late reply, I was skiing
Skiing is great!
Let me know if you need any help.