Table 1. Keywords used to define segments the epigenetics database ...

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Table 1. Keywords used to define segments the epigenetics database. Keywords for Hotspot Map Table Rows. CPG ISLAND. HYP
Table 1.   Keywords used to define segments the epigenetics database.  Keywords for Hotspot Map Table Rows.  CPG ISLAND  BROMODOMAIN  HISTONE H2  HISTONE & DEACETYLATION  NUCLEAR PORE  UBIQUITYLAT  METHYLAT* CYTOSINE  HISTONE ACETYLTRANSFERASE  METHYLTRANSFERASE  PARAMUTATION  ANTIBODY  MASS SPEC  CLINICAL TRIAL  ANACARDIC ACID  CISPLATIN  GARCINOL 

HYPERMETHYLAT  CHROMODOMAIN  HISTONE H3  HISTONE & DEMETHYLATION  NUCLEAR PORE COMPLEX  DNA METHYLAT  ACETYLTRANSFERASE  HISTONE DEACETYLASE  BOOKMARK  PROMOTER  BISULFITE  MICROARRAY  CLINICAL TRIAL PHASE 1  AZACITIDINE  CURCUMIN EPIG DRUG  HDAC INHIBITOR 

METHYLATION PATTERN  TUDOR DOMAIN  HISTONE H4  HISTONE & METHYLATION  METHYLAT  DNA PHOSPHORYLAT  DEACETYLASE  HISTONE DEMETHYLASE  CHROMOSOME INACTIVATION  REPROGRAM  FRET  PCR  CLINICAL TRIAL PHASE 2  BIX‐01294  DECITABINE  HYDRALAZINE 

PIWI  HISTONE  HISTONE MODIFICATION  IMPORTIN  PHOSPHORYLAT  DNA SUMOYLAT  DEMETHYLASE  HISTONE METHYLTRANSFERASE  GENE SILENC  SIGNALLING  HPLC  PYROSEQUENC  ALLANTODAPSONE  CAMBINOL  DZNEP  ISTODAX 

MGCD?0103  PROCAINAMIDE  SAHA  VALPROIC ACID  ZOLINZA  14‐3‐3  CEA  IGF‐GENERAL  PSA  AKAP12  APOB  CADM1  CO3  CTCFL  DCR3  ELAFIN  GDF15  HMGB1  IFI27  IL10  LAMB2 

MS?275  PROCAINE  SIRTINOL  VIDAZA  BIOMARKER  ALPHA‐FETOPROTEIN  FASCIN  LEPTIN  THYROGLOBULIN  AMACR  B2M  CBLC  CPA4  CTGF  DJ‐1  EMILIN2  GRN  HPP1  IGF2  IL2RA  LTBP2 

NAB  RG108  SPLITOMICIN  VORINOSTAT  TETRASPANIN  B‐TYPE NATRIURETIC PEPTIDE  HER2_NEU  OSTEOPONTIN  AAT  APCS  CA125  CD59  CRIP1  CYTOGLOBIN  DKK3  EOTAXIN  GSTP1  HTRA1  IGFBP1  IL6  MESOTHELIN 

MMP2 

MMP3 

MMP7 

PANOBINOSTAT  ROMIDEPSIN  TRANYLCYPROMINE  VPA  THROMBOSPONDIN  CA 125  IGF1  P‐CADHERIN  AFP  APO‐1  CA15‐3  CHI3L1  CSPG2  DAPK  DSC2  EPCAM  HEPC  ICAM1  IGFBP3  IL8  MICROSATELLITE INSTABILITY  ASSAY  MMP9 

PRION  HISTONE H1  HISTONE & ACETYLATION  KARYOPHERIN  SUMOYLAT  DNA UBIQUITYLAT  DNMT1_3A_3B  METHYLASE  IMPRINTING  TRANSVECTION  IMMUNOPRECIPITATION  SANGER SEQUENC  AMI?5  CHAETOCIN EPIG DRUG  EGCG  METHYLTRANSFERASE  INHIBITOR  PHENELZINE  S110  TSA  ZEBULARINE  TROPONIN  CA 19‐9  IGF2  PROLACTIN  AFP‐L3  APOA1  CA19‐9  CKM  CST6  DCP  EFEMP1  FOLR1  HK2  IDH1  IGFBP4  KRT19  MIF  MPO 

Table 1.   Keywords used to define segments the epigenetics database.  NELL1  PCSK9  PRDX6  REG1  SLPI  TAC1  TNFRSF21  VIMENTIN, METHYLATED  ALK  BRAF V600E  FOSB  LYN  PI3K  ATM & GENE  FHIT  MLH1  S100A4  TSC1  NONCODING RNA  HIC1  MEG3  REPA  TSIX  miRNA‐NUMBER  miRNA‐0015  miRNA‐0021  miRNA‐0028  miRNA‐0034  miRNA‐0101  miRNA‐0124  miRNA‐0129  miRNA‐0135  miRNA‐0140  miRNA‐0145  miRNA‐0152  miRNA‐0183  miRNA‐0204  miRNA‐0214  miRNA‐0221  miRNA‐0239  miRNA‐0320 

NMU  PGP9.5  PRMT1  REG3  SMRP  TAGLN2  TRANSFERRIN  VWF  APC  EGFR  FYN  MAX & GENE  RAF1 RAF‐1  CDH1  FOXD3  NF1  SERPINB5  VHL  AIR & RNA  HOTAIR  MEN AND NONCODING  SAF & RNA  TUG1  miRNA‐0001  miRNA‐0016  miRNA‐0022  miRNA‐0029  miRNA‐0071  miRNA‐0103  miRNA‐0125  miRNA‐0130  miRNA‐0136  miRNA‐0141  miRNA‐0146  miRNA‐0153  miRNA‐0184  miRNA‐0205  miRNA‐0215  miRNA‐0222  miRNA‐0246  miRNA‐0322 

NPC2  PLTP  PROS1  SCCA  SOD3  TCF21  TRANSTHYRETIN  WNT10A  BCL2  EML4‐ALK  HRAS  MYC  SRC  CDH13  IGF2R  NF2  SMAD4  WT1  BC1  IGS RNAS  NKX2.2  SATIII  XIST  miRNA‐0007  miRNA‐0017  miRNA‐0024  miRNA‐0030  miRNA‐0092  miRNA‐0106  miRNA‐0126  miRNA‐0132  miRNA‐0137  miRNA‐0142  miRNA‐0148  miRNA‐0155  miRNA‐0185  miRNA‐0206  miRNA‐0217  miRNA‐0223  miRNA‐0290  miRNA‐0324 

P14  PNP  PTPRS  SCNN1A  SPINT2  TIMP1  TSH  ONCOGENE  BCR‐ABL  ERBB2  KRAS  NOTCH  TGFB  CDKN2B  MEN1  RASSF1  STK11  WWOX  EGO  KCNQ1OT1  P15AS  SCA8  ZEB2  miRNA‐0009  miRNA‐0018  miRNA‐0026  miRNA‐0031  miRNA‐0093  miRNA‐0107  miRNA‐0127  miRNA‐0133  miRNA‐0138  miRNA‐0143  miRNA‐0149  miRNA‐0181  miRNA‐0186  miRNA‐0210  miRNA‐0218  miRNA‐0224  miRNA‐0296  miRNA‐0330 

P16  POSTN  RASSF1A  SELENBP1  SST  TNF  TSP  AKT1  BRAF  FOS  LCK  NRAS  WNT  E2F1  MGMT  RUNX3  TP73  XRCC1  H19  KHPS1A  PINC  TERRA_TELRNA  MICRORNA GENERAL TERM  miRNA‐0010  miRNA‐0020  miRNA‐0027  miRNA‐0033  miRNA‐0096  miRNA‐0122  miRNA‐0128  miRNA‐0134  miRNA‐0139  miRNA‐0144  miRNA‐0151  miRNA‐0182  miRNA‐0188  miRNA‐0212  miRNA‐0219  miRNA‐023  miRNA‐0302  miRNA‐0335 

Table 1.   Keywords used to define segments the epigenetics database.  miRNA‐0338  miRNA‐0363  miRNA‐0371  miRNA‐0382  miRNA‐0429  miRNA‐0466  miRNA‐0493  miRNA‐0512  miRNA‐0539  miRNA‐0592  miRNA‐0663  miRNA‐0873  miRNA‐1275 

miRNA‐0339  miRNA‐0365  miRNA‐0372  miRNA‐0383  miRNA‐0430  miRNA‐0468  miRNA‐0494  miRNA‐0517  miRNA‐0544  miRNA‐0596  miRNA‐0668  miRNA‐0923  miRNA‐1297 

miRNA‐0340  miRNA‐0367  miRNA‐0373  miRNA‐0409  miRNA‐0449  miRNA‐0483  miRNA‐0497  miRNA‐0519  miRNA‐0546  miRNA‐0615  miRNA‐0672  miRNA‐1224  miRNA‐BART‐5 

miRNA‐0342  miRNA‐0369  miRNA‐0375  miRNA‐0422  miRNA‐0451  miRNA‐0485  miRNA‐0498  miRNA‐0520  miRNA‐0574  miRNA‐0629  miRNA‐0709  miRNA‐1245  miRNA‐K12‐4‐5P 

miRNA‐0346  miRNA‐0370  miRNA‐0376  miRNA‐0424  miRNA‐0452  miRNA‐0486  miRNA‐0499  miRNA‐0532  miRNA‐0579  miRNA‐0632  miRNA‐0760  miRNA‐1256  miRNA‐MRN 

Keywords for Hotspot Map Table Columns.  CANCER  BLADDER CANCER 

CARCINOMA  BREAST CANCER 

ADENOCARCINOMA  BURKITT LYMPHOMA 

ANGIOGENESIS  CERVICAL CANCER 

COLON CANCER  EPITHELIAL*MESENCHYMAL 

COLORECTAL CANCER  ESOPHAGEAL CANCER,  ESOPHAGEAL CANCER  HEPATOCELLULAR CARCINOMA  MYELODYSPLASTIC  OVARIAN CANCER  TUMOR SUPPRESSOR  PREVENTION & CANCER  AUTISIM  BONE MARROW  MYOCARDIAL INFARCTION  COMPANION DIAGNOSTIC  HEPATITIS  PREDICTIVE BIOMARKER 

EMT  GASTRIC CANCER 

ENDOMETRIAL CANCER  GASTROINTESTINAL CANCER 

B‐CELL LYMPHOMA  CHRONIC LYMPHOCYTIC  LEUKEMIA  EPITHELIAL CANCER  GLIOBLASTOMA 

LEUKEMIA  MYELOID LEUKEMIA  PANCREATIC CANCER  DEVELOPMENT & CANCER  PROGRESSION & CANCER  NEURODEGENERATIVE  CARDIOVASCULAR  AGING, AGE RELATED  DIABETES  INFLAMMATION  PROGNOSTIC BIOMARKER 

LUNG CANCER  NECK CANCER  PROSTATE CANCER  EPIGENETIC CANCER  RISK & CANCER  NEUROLOGICAL DISEASE  HEMATOPOIESIS  ALLERGY  DISEASE  MICROVESICLE  SCHIZOPHRENIA 

MELANOMA  NON SMALL CELL LUNG CANCER  SQUAMOUS CELL CARCINOMA  GENE & CANCER  TUMOR & CANCER  NEURONAL  HEMATOPOIETIC  APOPTOSIS  EXOSOME  OBESITY  STEM CELL 

 

 

 

 

HEPATIC CANCER  METASTASIS  ORAL CANCER  THYROID CANCER  HYPERMETHYLATION & CANCER  ALZHEIMER  PARKINSON  HYPERTENSI  AUTOIMMUN  HEART DISEASE  PHARMACODYNAMIC  BIOMARKER  MATERNAL 

       

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10

7

36

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54

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CHROMODOMAIN

0

0

0

TUDOR DOMAIN

1

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0

0

0

0

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1898

299

61

77

16

22

211

5

20

15

64

91

18

HISTONE HISTONE H1

1

0

375

20

754

498

18

2

118

162

0

0

0

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1

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320

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115

74

98

7

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36

149

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435

224

105

708

57

415

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1295

169

19

88

51

271

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295

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937

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53

2

1

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1

2

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7

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6

22

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0

267

44

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178

4

1

0

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12

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1

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5

5

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1

0

1

1

0

0

2

12

2

0

6

1

3

0

1

0

1

0

1

3

0

11

11

0

39

13

2

10

5

38

HISTONE MODIFICATION

592

80

20

15

2

5

59

1

3

3

20

37

4

1

4

11

1

14

3

0

0

16

63

20

11

35

14

19

1

3

1

18

4

47

9

3

129

208

5

527

114

34

131

56

288

82

19

18

6

10

21

21

7

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1

8

12

0

0

1

53

2

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1

33

2

6

0

127

24

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1

20

0

1

2

11

6

0

3

0

2

0

8

0

0

0

2

22

6

6

6

5

7

HISTONE & METHYLATION

1117

168

30

28

3

11

127

2

14

8

46

66

6

7

5

17

3

42

9

0

0

34

156

47

27

66

46

47

IMPORTIN

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

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0

0

0

0

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KARYOPHERIN

0

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0

0

0

0

0

0

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0

0

0

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0

0

0

0

0

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NUCLEAR PORE

0

0

0

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0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

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NUCLEAR PORE COMPLEX

6

4

0

0

0

0

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

2

2

0

1

0

METHYLAT (CHEM MODIF)

4261

1245

269

77

38

85

530

10

74

39

211

482

24

38

24

56

32

236

33

2

1

208

454

325

112

284

PHOSPHORYLAT (CHEM MODI

180

51

10

7

0

0

21

0

1

1

8

8

4

0

0

9

2

5

1

0

0

9

19

9

5

SUMOYLAT (CHEM MODIF)

13

0

0

0

0

0

2

0

0

0

0

0

1

0

0

1

0

0

0

0

0

0

0

0

0

UBIQUITYLAT (CHEM MODIF) DNA METHYLAT (CHEM MODIF DNA PHOSPHORYLAT (CHEM M DNA SUMOYLAT (CHEM MODIF DNA UBIQUITYLAT (CHEM MOD

228

43

7

0

0

16

2

0

0

3

15

3

0

0

12 9

84

27

25

20

12

23

13

9

15

10

28

2

7

9

1

5

2

1

2

1

5

2

14

6

9

4

3

35

13

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82

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118

152

39

99

25

162

17

3

5

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2

1

1

0

0

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92

4

4

387

2

1

200

2

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36

36

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106

28

5

20

5

72

6

280

381

10

998

240

61

223

85

577

0

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5

71

258

240

33

1307

1229

25

3727

1425

167

834

505

2497

2

4

12

10

0

56

52

1

136

16

3

39

8

95

0

0

2

0

0

4

7

0

12

0

1

2

0

73

23 8

82

2

4

67

62

0

12

81

135

0

20

8

9

4

2

4

HISTONE & DEMETHYLATION

0

41

1665

430

20

HISTONE & DEACETYLATION

0

546

1715

69

1

1

951

7 4

55

10

0

1

280

15

2

0

10

149

24

0

319

6

0

49

134

11

0

HISTONE H4

2

0

64

25

15

0

HISTONE H3

476

0

22

79

5

0

HISTONE H2

HISTONE & ACETYLATION

4

47

13

6

0

PROGRESSION & CANCER

0

0

4

55

7

0

PREVENTION & CANCER

1

0

21

27

21

0

EPIGENETIC CANCER

0

0

8

66

12

0

DEVELOPMENT & CANCER

0

0

31

53

24

0

PROSTATE CANCER

0

0

0

19

141

10

0

LEUKEMIA

BREAST CANCER

0

0

0

79

39

27

0

HEPATOCELLULAR CARCINOMA

BLADDER CANCER

0

0

0

26

176

59

0

HEPATIC CANCER

B-CELL LYMPHOMA

0

0

0

63

151

17

GLIOBLASTOMA

ANGIOGENESIS

0

0

0

EMT

ADENOCARCINOMA

0

0

4

CARCINOMA

0

2

7

CANCER

0

10

112

113

1

TUMOR & CANCER

0

1

BROMODOMAIN

59

1

1

RISK & CANCER

0

PRION

1

0

1

HYPERMETHYLATION & CANCER

0

GENE & CANCER

0

0

TUMOR SUPPRESSOR

2

0

THYROID CANCER

15

11

0

0

SQUAMOUS CELL CARCINOMA

15

136

0

0

3

0

PANCREATIC CANCER

63

21

3

0

82

0

OVARIAN CANCER

6

29

1

0

251

12

0

ORAL CANCER

GASTROINTESTINAL CANCER

14

12

2

0

134

48

10

0

NON SMALL CELL LUNG CANCER

GASTRIC CANCER

9

25

1

0

16

26

5

1

NECK CANCER

EPITHELIAL*MESENCHYMAL

11

11

44

0

14

36

25

0

MYELOID LEUKEMIA

EPITHELIAL CANCER

6

222

19

0

20

160

114

4

MYELODYSPLASTIC

COLORECTAL CANCER 184

89

11

74

694

490

METASTASIS

COLON CANCER 79

10

6 0

339

1854

METHYLATION PATTERN

MELANOMA

CHRONIC LYMPHOCYTIC LEUKEMIA 14

41

1046

HYPERMETHYLAT

LUNG CANCER

CERVICAL CANCER 16

7

ENDOMETRIAL CANCER

BURKITT LYMPHOMA 3

CPG ISLAND

PIWI

ESOPHAGEAL CANCER, ESOPHAGEAL CANCER

Figure 2.  Excerpt of the Technology Publication Hotspot Map for Epigenetics Space. 

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51

23

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341

8

44

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125

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20

15

38

15

140

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126

295

173

69

167

88

97

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11

102

44

175

117

15

765

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20

2455

879

129

528

359

1540

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3

196

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15

103

0

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2

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20

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6

4

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29

6

26

28

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26

132

44

44

1

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3

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26

72

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10

182

235

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598

116

34

147

25

403

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0

0

2

METHYLAT* CYTOSINE

235

ACETYLTRANSFERASE

75

8

DEACETYLASE

756

125

4 1

0 0

0

1

2

0

1

0

1

0

4

3

0

1

0

37 6

7

1

9 1

3 0

17 0

30

48

7

12

84

1

14

14

2

39

28

51

DEMETHYLASE (ENZ)

116

17

3

3

1

1

12

0

1

0

3

5

0

5

0

4

0

2

15

2

2

3

0

1

0

5

0

24

1

94

14

2

19

6

54

DNMT1_3A_3B

248

64

15

5

3

4

31

0

8

3

17

26

1

4

2

2

0

12

1

0

0

18

40

17

6

9

15

18

2

4

0

2

5

11

8

0

105

62

6

206

74

9

31

28

147

HISTONE ACETYLTRANSFERAS

68

7

0

5

1

0

6

0

0

0

0

1

2

0

0

2

0

0

1

0

0

3

18

1

0

1

1

6

0

0

1

1

1

7

1

0

9

19

0

58

6

3

9

6

29

HISTONE DEACETYLASE (EPIG

784

131

30

48

8

12

97

1

15

7

27

33

10

8

4

15

2

22

5

0

0

25

139

41

29

54

46

47

1

9

3

21

27

77

15

7

190

229

8

616

119

34

152

24

419

HISTONE DEMETHYLASE (ENZ

64

HISTONE METHYLTRANSFERA

105

METHYLASE METHYLTRANSFERASE

 

7

0

0

0

2

0

2

0

0

0

0

3

1

1

7

1

0

3

2

1

12

0

1

1

6

1

0

0

2

0

3

0

0

0

11

0

1

1

0

0

2

0

0

1

0

0

0

1

0

0

0

0

0

0

0

0

0

0

0

1

2

0

0

1

0

0

0

0

0

0

2

1

0

0

4

1

0

6

0

0

1

0

2

24

8

7

92

3

8

4

34

63

5

7

3

8

2

37

4

2

1

41

140

44

22

39

52

47

2

8

2

15

19

41

17

2

244

222

22

658

221

26

113

65

440

36

2 8

2

1

2

12

0 5

0

0

0

0

0 0

0

2

1

10

1

0

15

40

30

4

10

2

2

3

2

2

153

 

1

1

6

2

0

0

775

8

0

0

35

21 32

0 1

48 89

5 12

0 0

12

3

26

13

29 60

 

FFigure 3.  Measurring the speed off publication for sselected segmentts relative to the entire epigeneticc database (see FFig. 1).  The measurement for  eeach segment ressults in a rating th hat runs from +1 to ‐1.   A “+1” rating means that ssegment is growiing much faster tthan might be expected from  tthe  database  as  a  whole.    A  “‐1””  rating  means  that  growth  is  much  below  the  database  d as  whoole.    A  “0”  ratingg  means  that  thee  segment  is  ggrowing at the saame speed as the e epigenetics dataabase.    Fig. 3a ggives measurements for some of tthe epigenetic “m machinery” components.  Fig.  3 3b gives acceleration measurements for selected ttarget disease staates.