Network features and pathway analyses of a signal transduction cascade

Ryoji Yanashima, Noriyuki Kitagawa, Yoshiya Matsubara, Robert Weatheritt, Kotaro Oka, Shinichi Kikuchi, Masaru Tomita, Shun Ishizaki

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant differences were found between the original undirected graphs and the graphs in which inactive proteins were eliminated from the gene expression data. We analyzed signaling networks by focusing on those pathways that best reflected cellular function. Therefore, our analysis of pathways started from the ligands and progressed to transcription factors and cytoskeletal proteins. We employed the Python module to assess the target network. This involved comparing the original and restricted signaling cascades as a directed graph using microarray gene expression profi les of late onset Alzheimer's disease. The most commonly used method of shortest-path analysis neglects to consider the influences of alternative pathways that can affect the activation of transcription factors or cytoskeletal proteins. We therefore introduced included k-shortest paths and k-cycles in our network analysis using the Python modules, which allowed us to attain a reasonable computational time and identify k-shortest paths. This technique reflected results found in vivo and identified pathways not found when shortest path or degree analysis was applied. Our module enabled us to comprehensively analyse the characteristics of biomolecular networks and also enabled analysis of the effects of diseases considering the feedback loop and feedforward loop control structures as an alternative path.

Original languageEnglish
Article number13
JournalFrontiers in Neuroinformatics
Volume3
Issue numberMAY
DOIs
Publication statusPublished - 2009 May 29

Fingerprint

Boidae
Signal transduction
Cytoskeletal Proteins
Signal Transduction
Transcription factors
Transcription Factors
Proteins
Gene Expression
Gene expression
Small-world networks
Alzheimer Disease
Directed graphs
Microarrays
Electric network analysis
Ligands
Chemical activation
Feedback

Keywords

  • Alzheimer's disease
  • Graph theory
  • Hippocampal CA1
  • K-shortest path analysis
  • Network analysis
  • Network robustness
  • Python
  • Signal transduction

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications

Cite this

Yanashima, R., Kitagawa, N., Matsubara, Y., Weatheritt, R., Oka, K., Kikuchi, S., ... Ishizaki, S. (2009). Network features and pathway analyses of a signal transduction cascade. Frontiers in Neuroinformatics, 3(MAY), [13]. https://doi.org/10.3389/neuro.11.013.2009

Network features and pathway analyses of a signal transduction cascade. / Yanashima, Ryoji; Kitagawa, Noriyuki; Matsubara, Yoshiya; Weatheritt, Robert; Oka, Kotaro; Kikuchi, Shinichi; Tomita, Masaru; Ishizaki, Shun.

In: Frontiers in Neuroinformatics, Vol. 3, No. MAY, 13, 29.05.2009.

Research output: Contribution to journalArticle

Yanashima, R, Kitagawa, N, Matsubara, Y, Weatheritt, R, Oka, K, Kikuchi, S, Tomita, M & Ishizaki, S 2009, 'Network features and pathway analyses of a signal transduction cascade', Frontiers in Neuroinformatics, vol. 3, no. MAY, 13. https://doi.org/10.3389/neuro.11.013.2009
Yanashima, Ryoji ; Kitagawa, Noriyuki ; Matsubara, Yoshiya ; Weatheritt, Robert ; Oka, Kotaro ; Kikuchi, Shinichi ; Tomita, Masaru ; Ishizaki, Shun. / Network features and pathway analyses of a signal transduction cascade. In: Frontiers in Neuroinformatics. 2009 ; Vol. 3, No. MAY.
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