Background: Sensory proteins react to changing environmental
conditions by transducing signals into the cell. These signals are integrated
into core proteins that activate downstream target proteins such
as transcription factors (TFs). This structure is referred to as
a bow tie, and allows cells to respond appropriately to complex environmental
conditions. Understanding this cellular processing of information,
from sensory proteins (e.g., cell-surface proteins) to target proteins
(e.g., TFs) is important, yet for many processes the signaling pathways
remain unknown.
Results: Here, we present BowTieBuilder for inferring signal transduction
pathways from multiple source and target proteins. Given protein-protein
interaction (PPI) data signaling pathways are assembled without knowledge of
the intermediate signaling proteins while maximizing the overall probability
of the pathway. To assess the inference quality, BowTieBuilder and three
alternative heuristics are applied to several pathways, and the resulting
pathways are compared to reference pathways taken from KEGG. In addition,
BowTieBuilder is used to infer a signaling pathway of the innate immune
response in humans and a signaling pathway that potentially regulates an
underlying gene regulatory network.
Conclusions: We show that BowTieBuilder, given multiple source and/or target
proteins, infers pathways with satisfactory recall and precision rates and
detects the core proteins of each pathway.
@article{Supper2009,
author = {Supper, Jochen and Spangenberg, Luc\'{i}a and Planatscher, Hannes and
Dr\"ager, Andreas and Schr\"oder, Adrian and Zell, Andreas},
title = {{BowTieBuilder: modeling signal transduction pathways}},
journal = {BMC Systems Biology},
year = {2009},
volume = {3},
pages = {67},
number = {1},
month = jun,
abstract = {Background: Sensory proteins react to changing environmental
conditions by transducing signals into the cell. These signals are integrated
into core proteins that activate downstream target proteins such
as transcription factors (TFs). This structure is referred to as
a bow tie, and allows cells to respond appropriately to complex environmental
conditions. Understanding this cellular processing of information,
from sensory proteins (e.g., cell-surface proteins) to target proteins
(e.g., TFs) is important, yet for many processes the signaling pathways
remain unknown.
Results: Here, we present BowTieBuilder for inferring signal transduction
pathways from multiple source and target proteins. Given protein-protein
interaction (PPI) data signaling pathways are assembled without knowledge of
the intermediate signaling proteins while maximizing the overall probability
of the pathway. To assess the inference quality, BowTieBuilder and three
alternative heuristics are applied to several pathways, and the resulting
pathways are compared to reference pathways taken from KEGG. In addition,
BowTieBuilder is used to infer a signaling pathway of the innate immune
response in humans and a signaling pathway that potentially regulates an
underlying gene regulatory network.
Conclusions: We show that BowTieBuilder, given multiple source and/or target
proteins, infers pathways with satisfactory recall and precision rates and
detects the core proteins of each pathway.},
doi = {10.1186/1752-0509-3-67},
pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-3-67.pdf},
url = {http://www.biomedcentral.com/1752-0509/3/67}
}