Table 1

NETGEM Generative process

Require: H {set of functional categories}

Require: G = (V, E) {interaction network graph}

Require: Λ ={λe}eE {prior on functional category mixtures}

Require: Θ ={θh}hH {prior on class transition probability}

1: for all h in H do

2:   Choose Qhh s.t. each row

3: for all e in E do

4:   Choose

5: for t = 1 to T do

6:   for all e in E do

7:      Choose

8:      Choose where

9:      Choose in (5)

10:      Compute

11:   Choose in (1)

Table 1 shows the generative process for the gene expression data for multiple strains s ∈ {1, ..., S} and observation time points t ∈ {1, ..., T} in the NETGEM model. The active functional category controls the change of interaction strength from to in edge e at time t. The interaction strengths affect the observed gene expression data, through the strain damping model and the conditional probability distribution in (1).

Jethava et al. BMC Bioinformatics 2011 12:327   doi:10.1186/1471-2105-12-327

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