Interpreting Genemania weights and filtering based on weights

[nivedas...@gmail.com]

Hi,
I am using the genemania app on Cytoscape to generate a network of gene interactions. My settings for attribute limit and gene limit are both 0. The interaction network generated shows two columns in the edge table for weighing interactions - 1) raw weight: a list of weights 2) normalized weight.

How do I interpret this weight and filter my interaction data based on an arbitrary score? The FAQ page does not answer this, it says 'Coming soon': http://pages.genemania.org/faq/#how-do-i-interpret-the-network-weights

Thanks in advance!

[Gary Bader]

Hello - the weight per network represents how specifically and densely connected your genes are within this network and this is a measure of how useful the network is for predicting function for your query genes. However, this is only useful to identify additional genes that may be related to your query genes.  If you set the attribute and gene limit to zero, you are not using this information to find additional genes and you should instead use equal by network weighting in your query.

Best,

Gary

[nivedas...@gmail.com]

Thanks for the response. I was wondering if the raw weights or the normalized weights can be used as a confidence score to filter the number of interactions retrieved? My goal is to visualize protein-protein interaction network. Since the network is very dense, I would like to limit the number of interactions by showing only those with highest confidence and discard the rest. For example, here is a table I've retrieved from genemania :

SUID	data type	networks	normalized max weight	raw weights
432	Co-expression	Boivin-Vidal-2012	1.25E-04	0.011788654
434	Co-expression	Boivin-Vidal-2012	1.27E-04	0.012002653
436	Co-expression	Hernandez-Novoa-Kovacs-2008|Peng-Stevenson-2013	7.58E-05	0.005101466551423073|0.007797231897711754
438	Co-expression	Anderson-Neville-2007	9.03E-05	0.009969791
439	Co-expression	Lattin-Sweet-2008	9.24E-05	0.00718554
440	Co-localization	Zhang-Hughes-2004	7.25E-05	0.012013779
441	Predicted	Conservation profile-Inparanoid	4.37E-05	0.007320687

 

Should the filtering be done on the basis of raw weights or normalized max weight? How should I interpret the scale of these weights? Is lower weight indication of a more confident interaction or vice versa?