Paper Info
Title
Representing and reasoning about signal networks: an illustration using NF\kappaB dependent signaling pathways
Abstract
We propose a formal language to represent and reasonabout signal transduction networks.The existing approachessuch as ones based on Petri nets, and \pi-calculusfall short in many ways and our work suggests that an artificialIntelligence (AI) based approach may be well suitedfor many aspects.We apply a form of action languageto represent and reason about NF/kappaB dependent signalingpathways.Our language supports several essential featuresof reasoning with signal transduction knowledge, such as:reasoning with partial (or incomplete) knowledge, and reasoningabout triggered evolutions of the world and elaborationtolerance.Because of its growing important role incellular functions, we select NF/kappaB dependent signaling tobe our test bed.NF/kappaB is a central mediator of the immuneresponse, and it can regulate stress responses, as well ascell death/survival in several cell types.While many extracellularsignals may lead to the activation of NF/kappaB, fewrelated pathways are elucidated.We study the tasks of representationof pathways, reasoning with pathways, explaining observations, and planning to alter the outcomes; andshow that all of them can be well formulated in our framework.Thus our work shows that our AI based approach isa good candidate for feasible and practical representationof and reasoning about signal networks.
Year
DOI
Venue
2003
10.1109/CSB.2003.1227427
CSB
Keywords
DocType
ISBN
Petri net,signal transduction knowledge,approach isa good candidate,signal network,representationof pathway,kappaB dependent signalingpathways,practical representationof,reasonabout signal transduction network,essential featuresof reasoning,formal language
Conference
0-7695-2000-6
Citations 
PageRank 
References 
1
0.34
1
Authors
4
Name
Order
Citations
PageRank
Chitta Baral12353269.58
Karen Chancellor210.34
Nam Tran31157.51
Nhan Tran4182.88