SPM

SPM (Subtype-specific Pathway Linear Progression Model) is a mathematical model to identify cancer subtypes, associated pathways, and the order of pathway dysregulation within each subtype. The model addresses the challenge of understanding cancer progression in the presence of heterogeneous mutations across individuals.

Key features of SPM:

1. Simultaneously identifies cancer subtypes and pathways specific to each subtype.

2. Determines the order of dysregulation of the identified pathways within each subtype.

3. Robust to problem-specific factors, including noise, compared to existing methods.

Topic

Molecular interactions, pathways and networks;Genetic variation;Oncology;Mathematics

Detail

  • Operation: Pathway or network prediction;Modelling and simulation

  • Software interface: Command-line user interface

  • Language: R,C++

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Sahand Khakabimamaghani sahandk@sfu.ca

  • Collection: -

  • Maturity: -

Publications

  • Uncovering the subtype-specific temporal order of cancer pathway dysregulation.
  • Khakabimamaghani S, et al. Uncovering the subtype-specific temporal order of cancer pathway dysregulation. Uncovering the subtype-specific temporal order of cancer pathway dysregulation. 2019; 15:e1007451. doi: 10.1371/journal.pcbi.1007451
  • https://doi.org/10.1371/JOURNAL.PCBI.1007451
  • PMID: 31710622
  • PMC: PMC6872169

Download and documentation

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