PECPI-GO

A novel methodology and software package to analyze pathway enrichment/clustering and protein interaction network associated with Gene Ontology (GO) functional annotation for molecular mechanism reconstruction. Users must be registered first for software download (PECPI-GO is under manuscript reviewing, registration for PECPI-GO is currently unavailable). PECPI-GO can be operated in three OS systems: Windows, Linux, and macOS.

PECPI-GO contains five-step machine-learning methods to decipher complicated relationships among genes, pathways, GO hierarchical structure, and functional annotation in an automatic manner:
gui_control_panel
control panel
  1. Pathway enrichment analysis
    2. gui_pathway_enrichment
  2. Pathway clustering based on graph theory
    3. gui_dendrogram
  3. GO functional annotation of each pathway cluster
    4. gui_pathway_annotation_table gui_pathway_annotation_table
  4. Protein interaction network analysis
    5. gui_ppi
  5. Integration of transcriptome and interactome analysis
    6. gui_ppi