Question: pathway analysis tools
0
gravatar for siyu
5.2 years ago by
siyu130
China
siyu130 wrote:

Does anyone know any tools that can analyze a broken gene's influence on the KEGG pathway?

thanks~!

pathway tool • 1.4k views
ADD COMMENTlink modified 5.2 years ago by pld4.8k • written 5.2 years ago by siyu130
1
gravatar for nilakshafreezon
5.2 years ago by
Sri Lanka
nilakshafreezon110 wrote:

Have you looked at KEGGscape ?

ADD COMMENTlink written 5.2 years ago by nilakshafreezon110

thanks! If I know a gene which is destroy by a stop-codon mutation, I want to know its influence on corresponding pathway. Can the KEGGscape implement it ?

ADD REPLYlink written 5.2 years ago by siyu130

I hope so, Im not quite sure though. That's why I gave it as an option so you could check out for your self.

ADD REPLYlink written 5.1 years ago by nilakshafreezon110
1
gravatar for pld
5.2 years ago by
pld4.8k
United States
pld4.8k wrote:

I'm not sure that any pathway enrichment programs can make that analysis for you. Correct me if I'm wrong, but I don't think Cytoscape/KEGGscape has any sort of simulation capabilities, they're more for annotation/curation/visualization. Your task falls more under topology analysis and other classes modeling approaches.

It looks like someone has a Cytoscape plugin

http://www.cbmc.it/~scardonig/interference/Interference.php

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088938

You could build your pathway up using KEGG and then push this data into the plugin above. That seems like a reasonable approach.

Lastly, you could poke away at it manually, maybe look at the immediate downstream nodes your protein interacts with and try and see if you can understand what happens when your protein fails to exert whatever interactions on these. You could also poke around in pubmed to see if someone has run the wet work on either a knockout of your protein, or mutations to downstream proteins mimicking whatever effects a knockout of your protein would have.

Or see if someone has a kinetic/etc model of the pathway you're interested in and set the concentration of your protein of interest to zero. COPASI is pretty easy to play with once you learn it and someone else has the model already published.

ADD COMMENTlink written 5.2 years ago by pld4.8k

thanks for your help! Cytoscape looks like a software, so I need to do it by hand one by one if I have mangs genes and some KEGG pathways. how can I write a script to work parallelly ?

ADD REPLYlink written 5.1 years ago by siyu130
0
gravatar for siyu
5.2 years ago by
siyu130
China
siyu130 wrote:

thanks! If I know a gene which is destroy by a stop-codon mutation, I want to know its influence on corresponding pathway. Can the KEGGscape implement it ?

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by siyu130
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