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Table 2 Annotations chart report for over-representation of functional categories.

From: Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity

 

UP & DOWN REGULATED

GO CATEGORY/Term

Gene Count (Ease score P-value)

Cellular compartment

 

Extracellular region

60 (9E-22) ↑, 2 ↓

Endoplasmic reticulum

11 (0.02) ↑

Nuclear

8↑ 6 (0.02) ↓

Organelle

35↑, 18 (0.03) ↓

Mitochondrion

10 (0.04) ↑

Molecular function

 

Catalytic activity

65 (1.4E-5) ↑, 9 ↓

Hydrolase

41 (8.9E-8) ↑, 3 ↓

Peptidase activity

27 (2.9E-10) ↑ 1 ↓

Serine-type peptidase activity

25 (8.3E-19) ↑

Actin binding

15 (8.2E-4) ↑ 7 (0.02) ↓

Calcium binding **

10 (NS) ↑

Vitamin binding

6 (0.0008) ↑

Transferase NO-

3 (0.05) ↑, 3 ↓

Antigen binding**

5 (3.6E-4) ↓

Tissue kallikrein activity

8 (8.5E-12) ↑

Elastase activity

2 (2.5E-2) ↑

Biological process

 

Metabolic process

74 (6.4E-4) ↑, 17 (0.02)

Immune-related process**

68a ↑ 14 (3.6E-6)

Proteolysis

27 (1.5E-11) ↑

Cell structure**

26 (0.02) ↑

Lipid, Fatty acid & steroid metabolism**

15 (1.31E-4) ↑

mRNA transcription regulation**

22(0.09) ↓

Cell communication**

9 (0.05) ↑

Digestion

8 (3.73E-8) ↑

Cellular homeostasis

7 (0.01) ↑

IMMUNE-RELATED PROCESS**

 

B-cell & Antibody-mediated immunity**

9 (1.2E-4) ↓

Response to stress

18 (8.3E-5) ↑ 2.3E-2↓

MHC-I-mediated Immunity**

16 (0.09) ↑

Immunity & Defense**

16 (0.03) ↑ 4 (0.2) ↓

MHC-II-mediated Immunity**

15 (0.002) ↑

Response to external stimulus

14 (4.9E-5) ↑, 6 (0.5) ↓

Response to wounding

10 (5.09E-4) ↑

Inflammatory response

8 (0.001) ↑

Cytokine & chemokine mediated signaling

 

pathway**

7 (0.06) ↑

Other Immune defense**

7 (0.05) ↑

Humoral Immune response

4 (2.2E-3) ↑

Antigen presentation

3 (1.1E-2) ↓

Lymphocyte-mediated immunity

3 (0.008) ↓

Adaptive Immunityb

3 (0.008) ↓

  1. The most relevant GO [23] and PANTHER [38] terms associated with the list of 165 E-IAA modulated genes are shown. Gene counts are the number of genes in the list at the corresponding term and arrows indicate up and down-regulated gene expression. P-value is a modified Fisher exact P-value, Ease score. Graphical representations of functional categories are shown on Figure 4. The list of all genes is available in Additional File 5.
  2. ** PANTHER annotations
  3. a Significance for combined annotation from GO (EASE): 8.35E-5<p < 0.07 and from PANTHER tool: 0.002<p < 0.09.
  4. b Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin super family domains