Information propagation within the Genetic Network of Saccharomyces cerevisiae.
BACKGROUND
A gene network's capacity to process information, so as to bind past events to future actions, depends on its structure and logic. From previous and new microarray measurements in Saccharomyces cerevisiae following gene deletions and overexpressions, we identify a core gene regulatory network (GRN) of functional interactions between 328 genes and the transfer functions of each gene. Inferred connections are verified by gene enrichment.


RESULTS
We find that this core network has a generalized clustering coefficient that is much higher than chance. The inferred Boolean transfer functions have a mean p-bias of 0.41, and thus similar amounts of activation and repression interactions. However, the distribution of p-biases differs significantly from what is expected by chance that, along with the high mean connectivity, is found to cause the core GRN of S. cerevisiae's to have an overall sensitivity similar to critical Boolean networks. In agreement, we find that the amount of information propagated between nodes in finite time series is much higher in the inferred core GRN of S. cerevisiae than what is expected by chance.


CONCLUSIONS
We suggest that S. cerevisiae is likely to have evolved a core GRN with enhanced information propagation among its genes.
Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Tampere University of Technology, Tampere, Finland.
Sharif
S
Chowdhury
Jason
J
Lloyd-Price
Olli-Pekka
OP
Smolander
Wayne C V
WC
Baici
Timothy R
TR
Hughes
Olli
O
Yli-Harja
Gordon
G
Chua
Andre S
AS
Ribeiro
D053263:Gene Regulatory Networks; D005800:Genes, Fungal / Q000235:genetics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism