  Motivation: The reconstruction of gene networks from gene expression
microarrays is gaining popularity as methods improve and as more data become
available. The reliability of such networks could be judged by the probability
that a connection between genes is spurious, resulting from chance fluctuations
rather than from a true biological relationship. Results: Unlike the false
discovery rate and positive false discovery rate, the decisive false discovery
rate (dFDR) is exactly equal to a conditional probability without assuming
independence or the randomness of hypothesis truth values. This property is
useful not only in the common application to the detection of differential gene
expression, but also in determining the probability of a spurious connection in
a reconstructed gene network. Estimators of the dFDR can estimate each of three
probabilities: 1. The probability that two genes that appear to be associated
with each other lack such association. 2. The probability that a time ordering
observed for two associated genes is misleading. 3. The probability that a time
ordering observed for two genes is misleading, either because they are not
associated or because they are associated without a lag in time. The first
probability applies to both static and dynamic gene networks, and the other two
only apply to dynamic gene networks. Availability: Cross-platform software for
network reconstruction, probability estimation, and plotting is free from
http://www.davidbickel.com as R functions and a Java application.
