NDLI: Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data

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Molecular BioSystems Vol - 8 Issue - 4

Molecular BioSystems Vol - 8 Issue - 3

Molecular BioSystems Vol - 8 Issue - 2

Molecular BioSystems Vol -7

Molecular BioSystems Vol -6

Molecular BioSystems Vol -5

Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

Molecular BioSystems Vol -2

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data

Content Provider	Royal Society of Chemistry (RSC)
Author	Melas, Ioannis N. Messinis, Dimitris E. Rodriguez, Julio-Saez Mitsos, Alexander Weiss, Thomas S. Alexopoulos, Leonidas G.
Copyright Year	2012
Abstract	Construction of large and cell-specific signaling pathways is essential to understand information processing under normal and pathological conditions. On this front, gene-based approaches offer the advantage of large pathway exploration whereas phosphoproteomic approaches offer a more reliable view of pathway activities but are applicable to small pathway sizes. In this paper, we demonstrate an experimentally adaptive approach to construct large signaling pathways from phosphoproteomic data within a 3-day time frame. Our approach—taking advantage of the fast turnaround time of the xMAP technology—is carried out in four steps: (i) screen optimal pathway inducers, (ii) select the responsive ones, (iii) combine them in a combinatorial fashion to construct a phosphoproteomic dataset, and (iv) optimize a reduced generic pathway via an Integer Linear Programming formulation. As a case study, we uncover novel players and their corresponding pathways in primary human hepatocytes by interrogating the signal transduction downstream of 81 receptors of interest and constructing a detailed model for the responsive part of the network comprising 177 species (of which 14 are measured) and 365 interactions.
Starting Page	1571
Ending Page	1584
Page Count	14
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	8
Issue Number	5
Journal	Molecular BioSystems
DOI	10.1039/c2mb05482e
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Signal transduction Hepatocyte Combinatorial optimization
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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