  Most disorders are caused by a combination of multiple genetic and/or
environmental factors. If two diseases are caused by the same molecular
mechanism, they tend to co-occur in patients. Here we provide a quantitative
method to disentangle how much genetic or environmental risk factors contribute
to the pathogenesis of 358 individual diseases, respectively. We pool data on
genetic, pathway-based, and toxicogenomic disease-causing mechanisms with
disease co-occurrence data obtained from almost two million patients. From this
data we construct a multilayer network where nodes represent disorders that are
connected by links that either represent phenotypic comorbidity of the patients
or the involvement of a certain molecular mechanism. From the similarity of
phenotypic and mechanism-based networks for each disorder we derive measure
that allows us to quantify the relative importance of various molecular
mechanisms for a given disease. We find that most diseases are dominated by
genetic risk factors, while environmental influences prevail for disorders such
as depressions, cancers, or dermatitis. Almost never we find that more than one
type of mechanisms is involved in the pathogenesis of diseases.
