Skip to main content

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.