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Table 2 Significantly (Benjamini-Hochberg FDR ≤ 0.01) enriched functions among differentially expressed genes (DEG) highly-expressed in parenchyma relative to fat pad using Ingenuity Pathways Analysis® (IPA).

From: Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development

IPA function P-value # DEG Main effect on function1 Associated functions
Cell Death 3E-13 203 Apoptosis  
Cellular Growth and Proliferation 2E-11 237 Proliferation, Growth Tissue Morphology
Cellular Movement 3E-11 137 Movement of eukaryotic cells  
Cell-To-Cell Signaling and Interaction 2E-09 118 Adhesion of cells Tissue Development
Cellular Development 2E-06 146 Development of eukaryotic cells, lymphatic cells, and blood cells  
Cell Morphology 3E-06 130 Morphogenesis and shaping of cells  
Cell Cycle 1E-05 107 Mitosis  
Gene Expression 2E-05 119 Transcription  
Cardiovascular Sys. Dev. and Funct. 3E-05 57 Angiogenesis Organismal Development
Cellular Assembly and Organization 5E-05 116 Formation of plasma membrane projection  
Hematological Sys. Dev. and Funct. 1E-04 102 Proliferation of immune cells (leukocytes) Immune and Lymphatic Sys. Dev. and Funct., Immune response
Nervous Sys. Dev. and Funct. 2E-04 69 Growth of neurites; Migration of Neurons  
Organ Development 2E-04 84 N/A2  
Cellular Function and Maintenance 1E-03 21 ↑ Cytoskeleton organization; Release of Intracellular Store  
Connective Tissue Dev. and Funct. 2E-03 46 Proliferation and Movement of fibroblasts  
Cell Signaling 2E-03 36 Quantity of intracellular Ca2+ Molecular Transport, Vitamin and mineral metabolism
DNA Replication, Recombination, and Repair 3E-03 76 DNA synthesis and metabolism; Chromatin remodeling  
Hair and Skin Dev. and Funct. 3E-03 25 Growth of epithelial cells  
Organismal Survival 3E-03 81 Death and survival of mammalia  
Skeletal/Muscular Sys. Dev. and Funct. 5E-03 14 Differentiation of bone cells  
RNA Post-Transcriptional Modification 7E-03 5 Binding of RNA  
  1. Reported also are the number of genes per function (# DEG), the main effect of those genes within functions (annotation of function from IPA) with the direction of the effect, and other significantly-associated functions (based on effect on function). Details of the analysis are reported in Additional file 2.
  2. 1 Major (increase or decrease ) or minor (increase ↑ or decrease ↓) effects on function are obtained by the IPA "effect on function" and was considered major if the number of DEG in the specific effect on function denoted as increase/decrease is >10% compared to those DEG that decrease/increase. When no evident direction of the function could be envisaged a is reported.
  3. 2 No effect on function provided by IPA.