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Table 2 List of 50 largest network clusters and association with particular tissue/cells/pathway.

From: A gene expression atlas of the domestic pig

Cluster ID

Number of transcripts

Profile Description

Class

Sub-class

5

622

Macs-other immune

Immune

Macrophage

18

195

Alveolar macs>>other macs

Immune

Tissue macrophage

32

81

LPS-induced (high in other tissues)

Immune

Immune response (IFN)

35

67

LPS-induced mac-specific

Immune

Immune response (LPS)

34

73

MHC class1-related

Immune

MHC class I

11

293

Thymus>Blood>spleen

Immune

T cell

38

65

Small intestine (jej./ileum)>blood-spleen-LN

Immune

B cell

7

430

Blood>>macs-other immune

Immune

Blood

17

197

Blood>macs>spleen (immune)

Immune

Blood

21

139

Blood-immune organs>GI tract (immune)

Immune

Blood

4

1007

CNS-highest in cortex

CNS

Neuronal

15

213

Cerebellum>>other CNS

CNS

Cerebellum

6

611

CNS-high in spinal cord

CNS

Astrocyte

41

59

Retina

CNS

Retinal epithelium

8

425

Liver (hepatocyte)

GI tract

Liver

16

201

Tongue Esophagus>skin

GI tract

Stratified epithelium

19

168

Kidney cortex>medulla-liver

GI tract

Kidney epithelium

20

155

Small intestine>>kidney-liver

GI tract

SI epithelium (enterocyte)

25

121

GI tract>>gall bladder

GI tract

Epithelial

26

110

GI tract>>others

GI tract

Columnar epithelial

45

53

Pancreas

GI tract

Exocrine pancreas

46

51

Liver>kidney

GI tract

Hepatocyte

47

49

Salivary gland

GI tract

Salivary gland acinar cell

10

333

Skeletal muscle>heart

Musculature-tendon

Musculature

29

98

General-low in macs/CNS

Musculature-tendon

Fibroblast (ECM)

33

75

Heart>upper oesophagus

Musculature-tendon

Musculature

37

66

Smooth muscle (high in many)

Musculature-tendon

Musculature

49

46

Snout tendon>trachea

Musculature-tendon

Cartilage-tendon

23

128

Placenta

Dermal

Placental function

36

67

Skin>>tongue

Dermal

Dermal

22

131

Adrenal gland>>>ovary-placenta-testis

Endocrine

Steroid hormone biosynthesis

31

84

Thyroid gland

Endocrine

Thyroxine biosynthesis

3

1102

Testis-adult

Reproduction

Gamete production

42

59

Testis-adult

Reproduction

Gamete production

9

392

Fallopian tube>adult testis

Reproduction

Female

40

61

Ovary>Testis (juvenile)

Reproduction

Female

44

56

Testis>other

Reproduction

Cell cycle-related

14

218

Many tissues-highly variable

Pathway

Cell cycle

27

108

General but not even

Pathway

Oxidative phosphorylation

48

48

General but not even

Pathway

Histones

50

43

General but not even-highly expressed

Pathway

Ribosomal

24

124

General but not even

House keeping

House keeping

28

108

General but not even

House keeping

House keeping

43

57

General but not even

House keeping

House keeping

1

1309

General, relatively even

House keeping

House keeping (HK1)

2

1193

General, relatively even-low in macs

House keeping

House keeping (HK2)

12

287

General, relatively even

House keeping

House keeping (HK3)

30

87

General, relatively even

House keeping

House keeping (HK4)

39

65

General, relatively even

House keeping

House keeping (HK5)

13

229

Spinal cord 1 rep only (tech artefact)

Tech artefact

 
  1. A list of the 50 largest coexpression clusters evident in the pig gene expression atlas. Listed in the table are the 50 largest clusters of genes originating from our analysis of the pig expression atlas. Clusters are numbered according to their size (the largest being designated cluster 1) but are sorted here according to their grouping within the graph and the biology they represent. The first two columns give the cluster ID and number of transcripts present in the cluster and the following column provides a description of the average expression profile of all transcripts within the cluster. The final two columns aim to group clusters according to the class of tissues in which these genes are predominately expressed and the tissue, cell or pathway we believe they represent.