Cytoscape 2.8.3 sessions containing the results of network analysis,
described in Lages et al., "Inferring hidden causal relations between 
pathway members using reduced Google matrix of directed biological networks".

Three protein selections have been analyzed : aktmtor, cit7, E2F.
Their analysis is described in GRN_[network_name].cys file correspondingly.

Each session contains 

1) merged transcriptional (TN) and signaling (SN) networks:

GM_SIGNOR (TN from a normal lymphocyte GM12878 cell line and SN from SIGNOR database)
K562_SIGNOR (TN from a leukimea cell line K562 and SN from SIGNOR database)

2) networks of direct interactions between proteins in the sets extracted
from GM_SIGNOR and K562_SIGNOR

GM_SIGNOR_[network_name]_direct
K562_SIGNOR_[network_name]_direct

3) networks of both direct and hidden interactions between proteins in the sets
with emergent and dissapearing hidden interactions shown

K562_SIGNOR_[network_name]_hidden*

Several specific subnetworks shown corresponding to the manuscript figures.