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).
| 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 |
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.
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.
2 No effect on function provided by IPA.