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Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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minepath.org: a free interactive pathway analysis web server.

Lefteris Koumakis1, Panos Roussos2, George Potamias1

  • 1Institute of Computer Science, Foundation for Research & Technology - Hellas (FORTH), Heraklion, Crete 70013, Greece.

Nucleic Acids Research
|April 22, 2017
PubMed
Summary
This summary is machine-generated.

MinePath is a novel web server for identifying differentially expressed sub-paths in molecular pathways. It uniquely visualizes regulatory mechanisms, offering interactive analysis and flexible result sharing for pathway research.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Differential gene expression analysis is crucial for understanding biological phenotypes.
  • Existing pathway analysis tools often focus on individual genes rather than sub-pathway dynamics.
  • Identifying specific, active pathway segments is essential for pinpointing regulatory mechanisms.

Purpose of the Study:

  • To introduce MinePath, a web-based platform for advanced identification and visualization of differentially expressed sub-paths.
  • To extend pathway analysis by incorporating network topology and precise molecular relationships.
  • To provide innovative interactive visualization of pathway regulatory mechanisms.

Main Methods:

  • Decomposition of pathways into all constituent sub-paths.
  • Matching sub-paths with gene expression profiles to identify differential expression.
  • Utilizing exact gene-gene molecular relationships (activation, inhibition) in algorithmic processes.
  • Developing advanced, interactive visualization of active pathway regulatory mechanisms.

Main Results:

  • MinePath successfully identifies and ranks phenotype-inclined sub-paths.
  • The platform offers novel visualization of underlying and active pathway regulatory mechanisms, not just genes.
  • Interactive features allow live exploration, immediate visualization of functional sub-paths, and dynamic annotations.

Conclusions:

  • MinePath represents a significant advancement in pathway analysis by focusing on sub-pathway dynamics and regulatory mechanisms.
  • The web server's interactive visualization and flexible data sharing capabilities enhance the usability and impact of pathway analysis.
  • This tool facilitates a deeper understanding of biological regulation and phenotype-associated pathway alterations.