Table 4 : IPA outputs of top canonical pathways and top associated network functions for different stages.

  Top Canonical Pathway -log( B-H p-value)

  DCIS-T1 ER+   Retinoic acid Mediated Apoptosis Signaling 1.68
    B Cell Development 1.16
    Autoimmune Thyroid Disease Signalling 1.16
    Allograft Rejection Signaling 1.16
    Graft-versus-Host Disease Signaling 1.16

  T1-T2 ER+   Oxidative Phosphorylation 2.37 *
    Notch Signaling 1.89 *
    Natural Killer Cell Signaling 1.88 *
    E1F2 Signaling 1.47 *
    Ubiquinone Biosynthesis 1.19 *

  T2-T3 ER+   G-Protein Coupled Receptor Signaling 0.515
    Riboflavin Metabolism 0.515
    Pantothenate and CoA Biosynthesis 0.515
    Propanoate Metabolism 0.515

  T2-T3   ERProtein Ubiquitination Pathway 1.63
    Aldosterone Signaling in Epithelial Cells 1.03
    NRF2-mediated Oxidative Stress Response 1.03

  Top Associated Network Function Score

  DCIS-T1 ER+   Hematological System development and Function, Tissue Morphology,
Cellular Growth and Proliferation
    Cellular Function and Maintenance, DNA Replication, Recombination,
and Repair, Cell Signaling
    Molecular Transport, Dematological Disease and Conditions, Developmental 23

  T1-T2 ER+   Gene Expression, RNA Post-Transcriptional Modification, Protein Synthesis 41
    RNA Post-Transcriptional Modification, Dermatological Diseases
and conditions, Infectious Disease
    Cell Death, Cellular Function and Maintenance, Hematological System
Development and Function
    Cellular Assembly and Organization,Cellular Function and Maintenance, Dematological Diseases and Conditions 32
    Cellular Development, Reproductive System Development and Function,
Connective Tissue Disorders

  T2-T3 ER+   Carbohydra Metabolism, Immunological Disease, Lipid Metabolism 30
    Cancer, Connective Tissue Development and Function, Tissue Morphology 25
    Neurological Disease, Developmental Disorder, Embryonic Development 10
    Cancer Reproductive System Disease, Gene Expression 2
    Reproductive System Disease 2

  T2-T3 ER-   Reproductive System Disease, Cellular Development, Lipid Metabolism 31

The terms with* indicate –log (p-value) by Fisher's exact test because these were insignificant after applying multiple testing correction.

Solvang et al.Journal of Medical Statistics and Informatics  2014 2:10DOI : 10.7243/2053-7662-2-10