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

Table 3 Significantly (Benjamini-Hochberg FDR ≤ 0.01) enriched functions among differentially expressed genes (DEG) highly-expressed in fat pad relative to parenchyma tissue using Ingenuity Pathways Analysis^® (IPA).

IPA function	P-value	# DEG	Main effect on function¹	Associated functions
Lipid Metabolism	5E-11	95	⇑ Synthesis of lipid, ⇑ Oxidation of lipid	Small Molecule Biochemistry
Molecular Transport	5E-08	67	⇑ Transport of lipid (mostly fatty acids)
Organismal Development	1E-06	79	⇔ Vessel development, ⇓ mass of mammalia
Cellular Movement	2E-04	114	↑ Migration of eukaryotic cells, ⇑ Invasion of cells
Tissue Development	2E-04	120	⇔ Adhesion of cells and remodeling of tissue
Carbohydrate Metabolism	2E-04	63	⇑ Quantity and metabolism of carbohydrates
Connective Tissue Dev. and Funct.	1E-03	46	⇔ Mass of connective tissue	Tissue Morphology
Cellular Growth and Proliferation	3E-03	164	⇓ Growth and proliferation of cells
Cell-To-Cell Signaling and Interaction	4E-03	112	⇑ Activation of cell, ⇔ adhesion of cells
Skeletal/Muscular Sys. Dev. and Funct.	6E-03	34	↑ Proliferation of smooth muscle cells
Nucleic Acid Metabolism	6E-03	24	⇑ Synthesis of Acyl-CoA and cyclic AMP
Organismal Functions	7E-02	32	⇑ Locomotion of rodents

Reported are the number of genes per function (# DEG), the main effect of those genes in 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 (⇑ or ⇓) or minor (↑ or ↓) 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 was greater > 10% compare to those DEG that decrease/increase. When no evident direction of the function was envisaged a ⇔ is reported.

ISSN: 1471-2164