Table 2 Up-regulated genes in cancer cells grown as a co-culture with CAFs

1

4.18

TRIM6

Tripartite motif-containing protein 6

ubiquitin-protein ligase activity; structural constituent of cytoskeleton; RNA binding; cytoskeletal protein binding

spermatogenesis; neurotransmitter secretion; intracellular protein transport; exocytosis; cell cycle; signal transduction; synaptic transmission; carbohydrate metabolic process; protein metabolic process; cell-cell signaling; dorsal/ventral axis specification; mesoderm development; mammary gland development

2

3.76

PPP1R12A

Protein phosphatase 1 regulatory subunit 12A

protein binding; phosphatase regulator activity

protein metabolic process

3

3.73

TCHHL1

Trichohyalin-like protein 1

4

3.24

QRICH2

Glutamine-rich protein 2

receptor activity

fertilization; cell adhesion

5

3.14

TMEM82

Transmembrane protein 82

6

3.14

ZNF212

Zinc finger protein 212

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

7

3.13

PYROXD1

Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1

oxidoreductase activity

immune system process; respiratory electron transport chain; apoptosis; ferredoxin metabolic process; oxygen and reactive oxygen species metabolic process

8

3.10

PDE5A

cGMP-specific 3',5'-cyclic phosphodiesterase

hydrolase activity, acting on ester bonds

visual perception; sensory perception; signal transduction; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; signal transduction

9

3.02

CHAD

Chondroadherin

receptor activity

immune system process; cell surface receptor linked signal transduction; cell-cell adhesion; mesoderm development; skeletal system development

10

3.00

QSER1

Glutamine and serine-rich protein 1

11

2.96

PRKX

Serine/threonine-protein kinase

kinase activity

muscle contraction; neurological system process; mitosis; intracellular signaling cascade; protein metabolic process; signal transduction;

12

2.90

ZFAND5

AN1-type zinc finger protein 5

nucleic acid binding

sensory perception; respiratory electron transport chain

13

2.86

C2CD3

C2 domain-containing protein 3

14

2.82

CEP110

Centriolin;Centrosomal protein of 110 kDa

15

2.80

FOXQ1

Forkhead box protein Q1

DNA binding; transcription factor activity

visual perception; sensory perception; cell cycle; cell surface receptor linked signal transduction; carbohydrate metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; cellular component morphogenesis; segment specification; anterior/posterior axis specification; ectoderm development; mesoderm development; embryonic development; nervous system development

16

2.80

NUP210L

Nuclear pore membrane glycoprotein 210-like

intracellular protein transport; nuclear transport

17

2.79

SLC22A11

Solute carrier family 22 member 11

ATPase activity, coupled to transmembrane movement of substances; ligase activity; carbohydrate transmembrane transporter activity; cation transmembrane transporter activity

cation transport; anion transport; extracellular transport; carbohydrate transport; carbohydrate metabolic process

18

2.78

HERC2

Probable E3 ubiquitin-protein ligase HERC2

ubiquitin-protein ligase activity

protein metabolic process; ectoderm development; mesoderm development; skeletal system development; nervous system development

19

2.76

PCSK6

Proprotein convertase subtilisin/kexin type 6

peptidase activity

cell surface receptor linked signal transduction; cell-matrix adhesion; protein metabolic process; signal transduction; mesoderm development

20

2.76

UCK2

Uridine-cytidine kinase 2

kinase activity; transferase activity, transferring glycosyl groups

carbohydrate metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

21

2.76

WFDC5

WAP four-disulfide core domain protein 5

protein binding;peptidase inhibitor activity

protein metabolic process

22

2.75

RPS10

40S ribosomal protein S10

structural constituent of ribosome; nucleic acid binding

protein metabolic process

23

2.75

SLC7A14

Probable cationic amino acid transporter

amino acid transmembrane transporter activity; transmembrane transporter activity

amino acid transport; cellular amino acid and derivative metabolic process

24

2.75

UBQLN2

Ubiquilin-2;UBQLN2

protein metabolic process

25

2.70

CLEC7A

C-type lectin domain family 7 member A

receptor activity; receptor binding

B cell mediated immunity; natural killer cell activation; intracellular protein transport; endocytosis; signal transduction; cell-cell adhesion; signal transduction; cellular defense response

26

2.70

SH3BP1

SH3 domain-binding protein 1

protein binding; small GTPase regulator activity

cell surface receptor linked signal transduction; signal transduction; cellular component morphogenesis

27

2.68

HMGB2

High mobility group protein B2

DNA binding; chromatin binding; receptor binding; transcription factor activity

intracellular signaling cascade; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; signal transduction; organelle organization; establishment or maintenance of chromatin architecture

28

2.68

TMSB10

Thymosin beta-10

29

2.67

NEFM

Neurofilament medium polypeptide

structural constituent of cytoskeleton

cellular component morphogenesis; ectoderm development

30

2.67

ZNF274

Zinc finger protein 274

DNA binding;transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

31

2.66

PCDH19

Protocadherin-19

G-protein coupled receptor activity; calcium ion binding

cell surface receptor linked signal transduction; cell-cell adhesion; cell motion; signal transduction; cellular component morphogenesis; ectoderm development; mesoderm development; embryonic development; nervous system development; heart development; muscle organ development

32

2.61

KCMF1

E3 ubiquitin-protein ligase KCMF1

33

2.60

PIP4K2B

Phosphatidylinositol-5-phosphate 4-kinase type-2 beta

kinase activity

cell surface receptor linked signal transduction; lipid metabolic process; signal transduction

34

2.57

GNAT3

Guanine nucleotide-binding protein G(t) subunit alpha-3

GTPase activity; protein binding

cell surface receptor linked signal transduction; signal transduction

35

2.56

LPCAT1

1-acylglycerophosphocholine O-acyltransferase 1

acyltransferase activity; calcium ion binding; calmodulin binding; calcium-dependent phospholipid binding

metabolic process

36

2.56

XPR1

Xenotropic and polytropic retrovirus receptor 1

G-protein coupled receptor activity

cell surface receptor linked signal transduction; signal transduction; embryonic development

37

2.54

LPHN2

Latrophilin-2

G-protein coupled receptor activity

immune system process; neurotransmitter secretion; intracellular protein transport; exocytosis; cell surface receptor linked signal transduction; synaptic transmission; cell adhesion; cell-cell signaling; mesoderm development; angiogenesis; heart development

38

2.54

MPHOSPH6

M-phase phosphoprotein 6

cell cycle

39

2.52

NDUFB10

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

oxidoreductase activity

oxidative phosphorylation; respiratory electron transport chain

40

2.51

DSP

Desmoplakin

structural constituent of cytoskeleton; cytoskeletal protein binding

cell adhesion; cellular component morphogenesis; ectoderm development

41

2.51

EXOC3L2

Exocyst complex component 3-like protein 2

spermatogenesis; immune response; macrophage activation; intracellular protein transport; exocytosis; mesoderm development; angiogenesis; hemopoiesis; response to stimulus

42

2.50

UBXN1

UBX domain-containing protein 1

43

2.49

MYOT

Myotilin;

44

2.49

SHPRH

E3 ubiquitin-protein ligase

DNA helicase activity; nucleic acid binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; organelle organization; establishment or maintenance of chromatin architecture

45

2.49

SMYD1

SET and MYND domain-containing protein 1

DNA binding; transcription factor activity; transcription cofactor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

46

2.48

KTN1

Kinectin

structural constituent of cytoskeleton

intracellular protein transport; cellular component morphogenesis

47

2.48

PJA2

E3 ubiquitin-protein ligase Praja2

DNA binding; transcription factor activity

48

2.48

SRPK1

Serine/threonine-protein kinase SRPK1

kinase activity

immune system process; mitosis; cell surface receptor linked signal transduction; intracellular signaling cascade; carbohydrate metabolic process; protein metabolic process; cell motion; mitosis; signal transduction; segment specification; ectoderm development; mesoderm development; embryonic development; nervous system development; response to stress

49

2.47

ANKS3

Ankyrin repeat and SAM domain-containing protein 3

50

2.47

C20orf26

Uncharacterized protein C20orf26

51

2.47

TREML2

Trem-like transcript 2 protein

52

2.46

TAB2

Mitogen-activated protein kinase kinase kinase 7-interacting protein 2

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

53

2.45

C19orf6

Membralin

structural molecule activity

54

2.45

EPB41L2

Band 4.1-like protein 2

55

2.44

CCDC71

Coiled-coil domain-containing protein 71

56

2.44

FGD1

FYVE, RhoGEF and PH domain-containing protein 1

protein binding; small GTPase regulator activity; guanyl-nucleotide exchange factor activity

mesoderm development; skeletal system development

57

2.44

VCAM1

Vascular cell adhesion protein 1

hydrolase activity, acting on ester bonds; phosphatase activity; receptor activity

immune system process; muscle contraction; induction of apoptosis; cell cycle; cell surface receptor linked signal transduction; cell-cell signaling; cell-cell adhesion; protein metabolic process; cell motion; cell cycle; signal transduction; ectoderm development; mesoderm development; angiogenesis; nervous system development; muscle organ development

58

2.42

ANKRA2

Ankyrin repeat family A protein 2

DNA binding; transcription factor activity

antigen processing and presentation of peptide or polysaccharide antigen via MHC class II; cellular defense response

59

2.42

KCNK17

Potassium channel subfamily K member 17

cation transmembrane transporter activity; voltage-gated potassium channel activity; cation channel activity

neurological system process; cation transport

60

2.42

TXNDC15

Thioredoxin domain-containing protein 15

61

2.41

TBPL2

TATA box-binding protein-like protein 2

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

62

2.40

ALDH3A2

Fatty aldehyde dehydrogenase

oxidoreductase activity

carbohydrate metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; cellular amino acid and derivative metabolic process

63

2.40

LAMP3

Lysosome-associated membrane glycoprotein 3

lysosomal transport; intracellular protein transport; protein metabolic process

64

2.40

PNLIP

Pancreatic triacylglycerol lipase

hydrolase activity, acting on ester bonds

lipid metabolic process

65

2.37

C17orf28

UPF0663 transmembrane protein C17orf28

66

2.36

GPR137

Integral membrane protein GPR137

67

2.35

WARS

Tryptophanyl-tRNA synthetase, cytoplasmic

aminoacyl-tRNA ligase activity

protein metabolic process

68

2.34

C11orf35

Uncharacterized protein C11orf35

69

2.34

SCML2

Sex comb on midleg-like protein 2

DNA binding; chromatin binding; transcription factor activity

cell cycle; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; cell cycle; organelle organization; establishment or maintenance of chromatin architecture; ectoderm development; mesoderm development; nervous system development

70

2.33

GNL1

Guanine nucleotide-binding protein-like 1

GTPase activity; nucleic acid binding; receptor binding

intracellular protein transport; cell surface receptor linked signal transduction; intracellular signaling cascade; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; signal transduction

71

2.33

MORN1

MORN repeat-containing protein 1

kinase activity

cell surface receptor linked signal transduction; signal transduction

72

2.33

TMEM149

Transmembrane protein 149

73

2.32

AK4

Adenylate kinase isoenzyme 4, mitochondrial

kinase activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

74

2.32

TOMM34

Mitochondrial import receptor subunit TOM34

immune system process; protein metabolic process; response to stress

75

2.32

ZNHIT6

Zinc finger HIT domain-containing protein 6

76

2.31

BTG1

Protein BTG1

cell cycle; intracellular signaling cascade; signal transduction

77

2.30

GRAMD1A

GRAM domain-containing protein 1A

78

2.30

GRIK5

Glutamate receptor, ionotropic kainate 5

glutamate receptor activity; ligand-gated ion channel activity

neurological system process; cation transport; cell surface receptor linked signal transduction; synaptic transmission; signal transduction; cell-cell signaling

79

2.30

TDRKH

Tudor and KH domain-containing protein

hydrolase activity, acting on ester bonds;nucleic acid binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

80

2.30

TGIF1

Homeobox protein TGIF1

DNA-directed RNA polymerase activity; DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; ectoderm development; nervous system development

81

2.29

FAM81B

Protein FAM81B

82

2.29

MRPL9

39S ribosomal protein L9, mitochondrial

structural constituent of ribosome; nucleic acid binding

protein metabolic process

83

2.28

ANKRD46

Ankyrin repeat domain-containing protein 46

84

2.27

INSM1

Insulinoma-associated protein 1

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

85

2.27

PBX1

Pre-B-cell leukemia transcription factor 1

DNA-directed RNA polymerase activity; DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; ectoderm development; mesoderm development; nervous system development; hemopoiesis

86

2.27

TPRG1

Tumor protein p63-regulated gene 1 protein

87

2.26

SEPT4

Septin-4

GTPase activity;structural constituent of cytoskeleton; protein binding

mitosis; cytokinesis

88

2.25

FAM159B

UPF0514 membrane protein FAM159B

89

2.24

AKAP8

A-kinase anchor protein 8

mitosis; chromosome segregation

90

2.24

FAM83A

Protein FAM83A

91

2.24

MAG

Myelin-associated glycoprotein

receptor activity; structural constituent of myelin sheath; receptor binding

B cell mediated immunity; cell surface receptor linked signal transduction; cell-cell adhesion; signal transduction; ectoderm development; nervous system development; response to stimulus

92

2.24

SCN9A

Sodium channel protein type 9 subunit alpha

cation transmembrane transporter activity; voltage-gated sodium channel activity; cation channel activity

neuronal action potential propagation; cation transport

93

2.23

ASTN1

Astrotactin-1

94

2.23

RAB7L1

Ras-related protein Rab-7 L1

GTPase activity; protein binding

neurotransmitter secretion; intracellular protein transport; exocytosis; endocytosis; cell cycle; cell surface receptor linked signal transduction; intracellular signaling cascade; signal transduction

95

2.22

RASA3

Ras GTPase-activating protein 3

protein binding; small GTPase regulator activity

signal transduction

96

2.22

TMEM59L

Transmembrane protein 59-like

97

2.21

CACNB3

Voltage-dependent L-type calcium channel subunit beta-3

cation transmembrane transporter activity; voltage-gated calcium channel activity; cation channel activity

muscle contraction; neurotransmitter secretion; synaptic transmission; cell-cell signaling

98

2.21

PLCD3

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-3

hydrolase activity, acting on ester bonds; calcium ion binding

cell surface receptor linked signal transduction; lipid metabolic process; signal transduction

99

2.21

PLCH1

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase eta-1

hydrolase activity, acting on ester bonds; calcium ion binding; receptor binding; small GTPase regulator activity; guanyl-nucleotide exchange factor activity

cell surface receptor linked signal transduction; intracellular signaling cascade; lipid metabolic process; signal transduction

100

2.21

TULP1

Tubby-related protein 1

visual perception; sensory perception; ectoderm development; nervous system development

101

2.20

EFCAB6

EF-hand calcium-binding domain-containing protein 6;EFCAB6

calcium ion binding; receptor binding; calmodulin binding; enzyme regulator activity

cation transport; cell cycle;signal transduction; cell cycle; signal transduction

102

2.19

PTPN6

Tyrosine-protein phosphatase non-receptor type 6

hydrolase activity, acting on ester bonds; phosphatase activity; receptor activity

immune system process; intracellular protein transport; mitosis; cell surface receptor linked signal transduction; intracellular signaling cascade; cell-matrix adhesion; cell-cell adhesion; protein metabolic process; cytokinesis; cell motion; signal transduction; nervous system development; cellular glucose homeostasis

103

2.18

GPR155

Integral membrane protein GPR155

receptor activity

104

2.18

PSPN

Persephin

receptor binding

neurological system process; cell surface receptor linked signal transduction; cell-cell signaling; signal transduction; ectoderm development; nervous system development

105

2.18

STAM2

Signal transducing adapter molecule 2

transmembrane transporter activity; protein binding; kinase activator activity; kinase regulator activity

lysosomal transport; intracellular protein transport; endocytosis; intracellular signaling cascade; signal transduction

106

2.17

AGXT2L2

Alanine--glyoxylate aminotransferase 2-like 2

transaminase activity

visual perception; sensory perception; vitamin biosynthetic process; cellular amino acid and derivative metabolic process