I have the data for a gene network obtained from HumanNet but I am unable to interpret the scores been given from HumanNet. I would like to know on what basis these scores have been calculated.
Also I am unable to find out the exact cutoff value associated with the HumanNet score.
HumanNet scores were designed to indicate pairs of genes that are more or less likely to share the same GO functional annotation (GO "biological process"). For an example of construction of one of the individual features: for CX, or co-expression, lots of microarray experiments in different conditions, calculating the pearson correlation between all pairs of genes for their expression over different conditions, and using regression to get a score from those correlation values related to GO functional annotation. The individual features were integrated based on their power in predicting GO functional annotation, resulting in an "integrated" score, the last column in the dataset.
There's a better explanation of the derivation methods in the WormNet (2008) paper: http://www.nature.com/ng/journal/v40/n2/abs/ng.2007.70.html
>>Also I am unable to find out the exact cutoff value associated with the HumanNet score.
Not sure what you mean by this. Glad to try to answer if you could clarify.
[Context: I'm not an author of HumanNet, but it's from my lab (http://marcottelab.org), and I've used it a lot.]
thank u Raksha for putting up this question... and thank you Sir for your response.
This is what need to be clarify the most...
As I am using HumanNet for my gene network studies,, and what i have seen is that,,the "Report" been obtained on imputing seed genes in HumanNet, are associated with some "SCORE" for the "Linked seed genes" as well as for "Predicted genes". So what should be the cutoff/reference value (highest and lowest) associated with these scores" . [For example: I have also used STRING 9.0, for networking and in that, some confidence score cutoff values are mentioned and n this basis the genes are ranked in associated network].
and on what basis the "linked genes and predicted genes" are ranked by "total connectivity".
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