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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
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Cells respond to many types of information, often through receptor proteins positioned on the membrane. They respond to chemical signals, such as hormones, neurotransmitters, and other signaling molecules, initiating a series of molecular reactions to produce an appropriate response. This is called signal transduction. Cells also coordinate different responses elicited by the same signaling molecule via mediators, allowing molecular cross-talk.
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Optogenetic Signaling Activation in Zebrafish Embryos
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BowTieBuilder: modeling signal transduction pathways.

Jochen Supper1, Lucía Spangenberg, Hannes Planatscher

  • 1Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Sand 1, 72076 Tübingen, Germany. jochen@supper.de

BMC Systems Biology
|July 2, 2009
PubMed
Summary
This summary is machine-generated.

BowTieBuilder infers cellular signaling pathways using protein-protein interaction data. This tool accurately identifies core proteins in pathways, aiding biological discovery.

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Area of Science:

  • Cellular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Cells process environmental signals via protein interactions, forming "bow tie" pathways.
  • Understanding these signaling cascades, from sensory to transcription factors (TFs), is crucial but often incomplete.
  • Many signaling pathways remain uncharacterized, limiting our understanding of cellular responses.

Purpose of the Study:

  • To introduce BowTieBuilder, a novel computational tool for inferring signal transduction pathways.
  • To reconstruct pathways using protein-protein interaction (PPI) data without prior knowledge of intermediate proteins.
  • To assess the performance of BowTieBuilder against existing methods and known biological pathways.

Main Methods:

  • BowTieBuilder assembles signaling pathways by maximizing pathway probability from PPI data.
  • Inferred pathways are compared to reference pathways from KEGG for quality assessment.
  • The tool is applied to human innate immune response and gene regulatory network pathways.

Main Results:

  • BowTieBuilder successfully infers signal transduction pathways from multiple source and target proteins.
  • The method demonstrates satisfactory recall and precision rates in pathway reconstruction.
  • Core proteins within signaling pathways are effectively identified by the algorithm.

Conclusions:

  • BowTieBuilder provides a robust method for discovering unknown signaling pathways.
  • The tool accurately identifies key signaling proteins, enhancing biological pathway comprehension.
  • This approach facilitates the study of complex cellular processes, including immune responses and gene regulation.