Table 2

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

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


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.

Freeman et al. BMC Biology 2012 10:90   doi:10.1186/1741-7007-10-90

Open Data