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Table 1 Summary of the gene coexpression clusters conserved across all datasets studied here

From: Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment

Descriptive class

Cluster description

Cluster ID number

No. of probesets in cluster

No. of genes in cluster

Known markers present in cluster

Gene ontology annotation

Other annotation

Conservation of signature in skin dataset: Cluster number

Conservation of signature in skin dataset: significance of enrichment

* KEGG pathway, ** Curated gene set, *** Swiss-Prot

(p-value for EASE score)

Keywords (p-value)

(Adjusted Fisher’s test)

Immune

Macrophage

7

220

163

CD68, CD14, CD163, CSF1R, Fc Receptors (CD16, CD32, CD64), MHC II molecules

Immune system process (3.96e-32)

 

16

1.3E-120

Defence response (8.79e-22)

T cell

8

181

145

CD2, CD3, CD6, CD7, CD52, TCR

Immune system process (4.99e-35)

TCR signalling pathway (6.1e-25) *

6

3.29E-93

Signal transduction (7.32e-18)

T cell activation (2.58e-19)

Macrophage/T cell interface

13

87

58

 

Immune response (7.20e-06)

 

34

2.6E-13

IFN response

12

115

73

GBP1. IFI27, IFR1, IRF2, OAS1, SP100, STAT1,

Immune response (4.32e-26)

Genes upregulated by IFNB in HT1080 (1.48e-47)**

51

4.06E-56

Response to virus (1.15e-21)

Genes upregulated by IFNA in HT1080 (1.05e-43)**

MHC class I

19

35

16

HLA-A, HLA-B, HLA-C, HLA-E, B2M

Antigen processing and presentation (5.51e-17)

MHC 1 (9.29e-15)***

82

1.2E-58

Ig/ plasma cell

14

85

36

Ig light and heavy chains,

Immune response (7.49e-10)

Ig C region (1.12e-10)

21

2.48E-129

B-cell

79, 142

10, 7

6, 6

CD19, CD20, CD79

B-cell receptor complex (2.31e-06)

BCR signalling (1.28e-09)*

6

6.52E-17

Immune response (1.84e-08)

Mast cell

93

9

4

Tryptase, Fc receptor for IgE

Proteolysis (0.008)

Zymogen (4.77e-04)***

167

2.72E-27

AP1 response

48, 89

13, 9

11, 6

FOS, JUNB,

Sequence specific DNA binding (2.19e-06)

DNA binding (2.75e-09)***

-

-

Regulation of cellular process (1.2e-04)

Stroma

Extracellular matrix

9

163

100

BGN, CALD1, FN1, collagens

Extracellular matrix (1.93e-40)

 

88

5.5E-34

Cell adhesion (1.16e-17)

Adipocyte

27

22

15

ADIPOQ, LPL

Response to wounding (0.004)

PPAR signalling (1.46e-07)*

-

-

Adipocyte vs Fibroblast upregulated (1.49e-15)**

Endothelium

29,38,49

20, 17, 13

17, 13, 11

CD31, CD34, Endomucin, Endoglin, vWF

Cell adhesion (1.3e-08)

Upregulated in glomerul in DM vs normal (8.33e-14)**

58

6.75E-16

Blood vessel development (1.28e-10)

Brentani_Angiogenesis (6.87e-08)**

Endothelium/ECM

59

11

6

COL4A1, COL4A2

Cell adhesion (4.13e-05)

 

215

1.22E-12

Smooth muscle

88, 249

9,6

5, 4

Alpha SMA, calponin

Smooth muscle contraction (4.75e-05)

Muscle protein (3.95e-08)***

907

1.27E-11

Skeletal muscle

46

15

15

Myoglobin, CKm, Myosin

Contractile fibre part (1.53e-17)

 

23

2.55E-31

Muscle development (2.09e-05)

Cell cycle

Cell cycle

6

239

182

AURKA, BUB1, CHEK2, CDC2, MCM2

Cell cycle (3.06e-59)

Serum fibroblast cell cycle (1.17e-117)**

101

1.31E-26

DNA replication (1.48e-39)

Cell cycle related

10, 16, 26

147, 52, 23

125, 44, 19

 

RNA binding (2.29e-11)

RNA binding (2.29e-14)***

-

-

Ribosomal

Ribosomal

54, 60, 64, 97

12, 11, 11, 8

12, 8, 6, 5

RPL38, RPS10, RPS19

Cytosolic ribosome (7.91e-13)

Ribosomal protein (8.44e-11)***

54

4.25E-36

Protein biosynthesis (1.62e-06)***

Other functional classes

Histones

20

30

26

HIST1H1C, HIST1H2AB, HIST1H3H

Nucleosome (9.75e-23)

Nucleosome core (2.61e-21)***

160

9.15E-35

Chromatin assembly (9.24e-21)

Glycolysis

47

13

5

GAPDH, GPI

Glycolysis (1.46e-05)

Gluconeogenesis (9.37e-07)***

151

6E-30

Haemoglobins

91

9

2

HBA1, HBB

  

144

6E-31

Affymetrix controls

Affymetrix controls

23, 28

26, 22

26, 22

   

99

4.57E-59

  1. Each cluster or group of related clusters has been placed into a functional grouping based on the biology from which it is derived. Details of the cluster(s) are provided together with selected pathway/Gene ontology enrichment scores for the genes that make up the clusters. (For a complete list see Additional file 4).