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thpar / diffany

Diffany is an open-source toolbox for calculating and visualizing differential networks.
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[CLOSED] Calculate diff network from microarray #6

Closed diffany-admin closed 9 years ago

diffany-admin commented 9 years ago

Issue by svlandeg Thu Oct 31 16:52:32 2013

Calculate differential network from microarray data: https://github.ugent.be/BEG/diffnet/wiki/Differential-algorithms#from-2-microarray-datasets

diffany-admin commented 9 years ago

Comment by svlandeg Thu Mar 6 11:04:34 2014

Now working on this with Marieke's osmotic stress data

diffany-admin commented 9 years ago

Comment by svlandeg Fri Jun 20 09:32:43 2014

Example, original network, with DE genes presented by colored nodes: 24_tch3

Differential network: differential_24h

diffany-admin commented 9 years ago

Comment by svlandeg Thu Aug 28 14:29:54 2014

Discussed this with Marieke and Nathalie. The differential network should also include those interactions where only one node is DE (e.g. HY5). Perhaps with the exception of too generic transcription factors, which are sometimes overrepresented in the data because of corpus bias (e.g. AGL 15). For such "hubs" in the data, we can check the proportion of interaction partners that are in the seed set (in our case: DE genes), to determine whether or not the hubs are relevant.

Further, some sort of "fuzzyness" interval would be great for the non-DE genes which only barely didn't make the cut, e.g. between 0.05 and 0.1 -> include them if they have a high FC, or if they are connected to the existing network, etc.

Finally, we agreed on removing unspecified regulatory associations, to avoid pulling in generic TFs with only computational evidence for instance.

diffany-admin commented 9 years ago

Comment by svlandeg Fri Aug 29 14:35:41 2014

Done: filtering unspecified regulatory interactions, thus removing much data from AGL15, GL1/3, SEP3 and HY5. The PPI data probably also contains such hub biases! (cf #192)