Disease. ⢠GWAS Calalog. ⢠GWASdb. ⢠CADD. ⢠Cell-tissue type comparison. ⢠Enhancer, target genes,TFs. ⢠Enhancer network. ⢠Genome segmentation states.
HEDD: Human Enhancer Disease Database Zhen Wang, Quanwei Zhang, Zhengdong Zhang
Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
Introduction
Database use and access
HEDD | Search
HEDD | Details
http://10.53.50.11/1/hedd/detail.action.php?idno=80
HEDD: Human Enhancer Disease Database
• Database search and browsing (Fig 2) Home
Search
Download Data
Documentation
HEDD: Human Enhancer Disease Database
HEDD | Search results
Contact Us
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ASearch
Detail results of enhancer
Search results Enhancer ID: 80
Summary of the detail information records
Data table (there are 3 records matched the query, results download) download)
Chromosome is selected; Chromsome region is specified
928382
930824
931016 VWA1, RP4-758J18.10, HES4 TNFRSF4, RP11-465B22.5, TTLL10
Hepg2
931473
931734
Hepg2
chr1
Cell/tissue type
0 records download
C Detailed results
END
40269454
TargetGene
PPT1
CellType
H1hesc
Conservation
0.01/0.003
Source
ENCODE
• Gene list • Network
Input parameters
Analyze
TargetGene
PPT1
Score
2.064E-5
…
…
Apache/MySQL/PHP-based backend
Fig 1. Database content and construction.
Acknowledgements: This work is supported by the NIH.
• • • • • • • • • • • •
Disease GWAS Calalog GWASdb CADD Cell-tissue type comparison Enhancer, target genes,TFs Enhancer network Genome segmentation states DHS TFBS Histone modification Repeats
•
arteriosclerosis immunodeficiency 16 autoimmune diseases
nager asthma acrofacial dysostosis
Genomic functional regions
tropical spastic paraparesis
asthma atherosclerosis
13524314 Histone modification ID 2523822
1 Chr
280512 13534859
11
536588 13673082
11
626750 14328067
2633716
1
H1-hESC HepG2 HepG2
1095066 931175 931239
None931475 931529
2650446 931158 931316
None 931598 931726
CHD7_(A301-223A-1) TEAD4 GATA2
K562 HepG2 SH-SY5Y
738757
931158 2659436
None931598
TEAD4 HDAC6_(A301-341A)
HepG2 K562
724125
931239 2647713
None931529
LSD1FOXA2
HepG2 K562
760097 Start
1095077 End 931362
None931766 Treatment
NCoR Marker ZBTB7A
K562 Cell line HepG2,K562
SP1
H3K4me2 PCAF
A549 K562
11
931374 722278
931627 3897664
EtOH_0.02pct None
H3K4me2 SETDB1
A549 K562 HepG2 K562
931726
None None
EZH2_(39875) SUZ12_(05-1317)
End
Treatment
Marker
Cell line
17724023 7173427
11
1
741459 930781
930455
1366090 931718
933464
sex=M None
DEX_100nM
treatment=None H3K4me3
NHEK HepG2
17724024 7992298
11
788723 931440
1402294 931635
sex=M None
treatment=None H3K4me2
NHEK HMEC
1
931214
931758
DEX_100nM
1
931374
931627
EtOH_0.02pct
6561076 20678930 571297 7173427 401228
11
Chr 931090
1358464 7992298
11
931584 931440
1469874 9963077
1
© ZDZ Lab, a member of the Department of Genetics, Albert Einstein College of Medicine. All rights reserved.
1656731
1
12914384 2044263
20678930
1
1
1
925859 930654 930495
939629
930705
931543
929978
942722
930608
931786
None None None
None
H3K4me2
CA D D
EZH2_(39875) H3K27me3
932247
H3K4me3 H3K4me1 H3K79me2 H3K4me2
14 0
12 0
10 0
12 0
10 0
80
0.800062
0.35242
0.668691
DisGeNET
Search: 2
3
4
5
Next
Last
Genomic functional elements
1 400k
1 600k
1 800k
2 000k
2 200k
2 400k
2 600k
2 800k
3 000k
3 200k
3 400k
3 600k
3 800k
Ehancer
GWAS
SNV
DHS
TFBS
Histone
4 2…
Repets Highcharts.com
Cell types
Repets
3 600k
3 800k
4 000k
4 2…
M0_macrophage_CB
Histone
3 400k
Highcharts.com
9/28/17, 10:12 PM Lung
TFBS
3 200k
Left_Ventricle
DHS
3 000k
K562
SNV
2 800k
IMR90
2 600k
HepG2
2 400k
Coordinate ( bp)
HeLa_S3
2 200k
HUVEC_prol_CB
GWAS
2 000k
HUVEC
Ehancer
1 800k
HSMMtube
1 600k
HSMM
1 400k
HMEC
1 200k
REF
ALT
Source
Lung
K562
IMR90
HepG2
Raw score
Left_Ventricle
PMID
HeLa_S3
P-value
HUVEC
Disease/trait
HSMMtube
Risk allele
HSMM
ALT
HMEC
REF
HUVEC_prol_CB
Cell types
H9
Position
4 000k
Coordinate ( bp)
H9
1 000k
1
H1_trophoblast
800k
1 200k
9/28/17, 10:12 PM
Previous
PHRED
Chr
Position
REF
Regulatory network of enhancer andand its its binding TFs and itsits target genes Regulatory network of enhancer binding TFs and target genes
6
ALT
Raw score
Network ofofenhancer Network enhancerand andits itsneighboring neighboringenhancers enhancers
9/28/17, 10:12 PM
2 of 5
Start
End
State
Cell line
931245
931650
R
gm12878
942881
None
H3K27me3
923943
934190
1016146
EtOH_0.02pct
H3K4me1
1
H3K4me2
Chr Genome segmentation state (totally 6 records)
1 1
931650 931245
931845 931650
RT
gm12878 gm12878
A549
1 1
931694 931650
932523 931845
TR
h1hesc gm12878
A549
1
Dnd41 Dnd41
930257
Chr
3262066
1
1358464 3767063
1
931584 930188
941387 938374
EtOH_0.02pct None
EZH2_(39875)
H1-hESC
1469874 4272497
11
925859 923254
959430 942575
None None
H2A.Z H3K27me3
CD20+ H1-hESC
4675024 1656731
11
929898 930495
939469 939629
None None
H4K20me1 H4K20me1
H1-hESC CD20+_RO01794
4708632 2044263
11
924044 929978
1032880 942722
None None
HDAC2_(A300-705A) EZH2_(39875)
H1-hESC Dnd41
6743981
1
H3K4me1
HepG2
H3K79me2
ROADMAP
ROADMAP
9/28/17, 10:12 PM
Genome segmentation state (totally 6 records)
K562
GM12878
930306
9/28/17, 10:12 PM
A549 HMEC
H3K27me3
1
PHRED
HepG2 GM12878 Simple_repeat_2 HepG2 A549
CD20+_RO01794
1
ROADMAP
http://10.53.50.11/1/hedd/detail.action.php?idno=80
Class
H4K20me1
EZH2_(39875)
ROADMAP
P-value PMID Source http://10.53.50.11/1/hedd/detail.action.php?idno=80
A549
CD20+ HSMMtube
H4K20me1
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
Disease/trait
ROADMAP
ROADMAP
Risk allele
ROADMAP
ALT
ROADMAP
REF
ROADMAP
Position
ROADMAP
Chr
K562
H2A.Z H3K27me3
401228
None
60
0.440491
Fig 2. Interactive searching and browsing activity of HEDD.
None
40
-
A549
H3K4me2
End
None
20
TNFRSF4
H1_trophoblast
B_cells_PB_Roadmap
Aorta
A549
End
Start
Chr
CD8_Memory CD8_Memory
CD56 CD56
DisGeNET
H1_neuronal_progenitor
Aorta
End
Start
Chr
A549
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP CD4_Naive CD4_Naive
0.276175
HSMMtube
H4K20me1
2643707
• Online analysis tools
0.101852
A549
H3K27me3
None
EtOH_0.02pct None
959430 931945
H3K4me1
None
941387 931635
0.231223
2 of 5
SH-SY5Y
931727 1328449
None EtOH_0.02pct
0.440491
Comparation between cell/tissue types
A549 K562
GATA2
Start
931634
5
HepG2
DEX_100nM None
1
ROADMAP ROADMAP
K562 HepG2 HepG2,K562
931718 934190
-
CADD (totally 0 records)
HepG2
931758 1385336
11
snpID
HEDD | Details
HeLa-S3 HepG2 HepG2
RXRA
931558
None None
TNFRSF4
CD4+_CD25-_CD45RA+_Naive
H4K20me1 RXRA FOXA2
931475
CBX3_(SC-101004) SP1 ZBTB7A
Start 931727 931786
1
CD8_Memory
SUZ12_(05-1317) FOXA1 FOXA1
930608 1 930781 930306
0.95
CD56
None931496 931496
931090 736933
Repeat ID
0.9
DISEASES
CD4_Naive
1390886
931543
0.602049
CD4_Memory
931216 931216
930705
0.85
ROADMAP CD4+_CD25int_CD127+_Tmem ROADMAP ROADMAP ROADMAP CD4_Memory ROADMAP ROADMAP ROADMAP CD4_Naive ROADMAP ROADMAP ROADMAP CD56 ROADMAP ROADMAP ROADMAP CD8_Memory ROADMAP
H1-hESC HepG2 HepG2
931214 767680
1
DisGeNET
0.8
ROADMAP
SIRT6EP300 EP300
11
626750 Repeats (totally 1 records) 12914384
0.272999
0.75
CD4+_CD25int_CD127+_Tmem
None931497 931497
931945
0.7
CD4+_CD25-_Th
2641921 931173 931173
930654
0.729358
0.65
ROADMAP CD4+_CD25-_IL17-_PMA-Ionomycin_MACS_Th ROADMAP ROADMAP ROADMAP ROADMAP CD4+_CD25-_Th ROADMAP ROADMAP
H1-hESC HepG2
H3K4me1 NSD2_(ab75359)
1
0.61976
0.6
HepG2 http://10.53.50.11/1/hedd/detail.action.php?idno=80
Chr
536588
0.55
CD4+_CD25-_IL17-_PMA-Ionomycin_MACS_Th ROADMAP
SIRT6 HDAC2 HDAC2
HEDD | Details
Cell line
6561076 14389082
9963077
CD4_Memory CD4_Memory
CD4+_CD25-_Th CD4+_CD25-_Th
None931543 931543
TF
Histone modification ID
280512
0.424798
0.5
ROADMAP CD4+_CD25-_CD45RO+_Memory ROADMAP ROADMAP CD4+_CD25-_IL17+_PMA-Ionomcyin_Th17 ROADMAP ROADMAP CD4+_CD25-_IL17+_PMA-Ionomcyin_Th17 ROADMAP ROADMAP
P300_KAT3B
H1-hESC Cell line
931316
0.440491
0.45
ROADMAP
H3K27me3
None 931558 931766
930455 739510
0.4
CD4+_CD25-_CD45RO+_Memory
None 931650 931650 None
DEX_100nM None
Histone modification (totally 74 records)
CD4+_CD25int_CD127+_Tmem ROADMAP CD4+_CD25int_CD127+_Tmem ROADMAP
ROADMAP ROADMAP
CD4+_CD25-_IL17-_PMA-Ionomycin_MACS_Th ROADMAP CD4+_CD25-_IL17-_PMA-Ionomycin_MACS_Th ROADMAP
CD4+_CD25-_IL17+_PMA-Ionomcyin_Th17 ROADMAP CD4+_CD25-_IL17+_PMA-Ionomcyin_Th17 ROADMAP
CD4+_CD25-_CD45RO+_Memory ROADMAP CD4+_CD25-_CD45RO+_Memory ROADMAP
ROADMAP ROADMAP CD4+_CD25+_CD127-_Treg CD4+_CD25+_CD127-_Treg
CD4+_CD25-_CD45RA+_NaiveROADMAP ROADMAP CD4+_CD25-_CD45RA+_Naive
ROADMAP ROADMAP
CD3_Cord_BI CD3_Cord_BI
CD34_Cultured_Cells CD34_Cultured_Cells
CD34 CD34
CD19_Peripheral_UW CD19_Peripheral_UW
CD19_Cord_BI CD19_Cord_BI
CD3_Peripheral_UW CD3_Peripheral_UW
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
H3K27me3
931615
NHLF Hpde6e6e7,Hsmm NHLF Fibrobl Cd34mobilized,Jurkat Osteobl Cd34mobilized,Jurkat Osteobl
933464 2611574
1
0.964374
0.35
CD4+_CD25+_CD127-_Treg
1 1
-
0.3
CD3_Peripheral_UW
2429100
931515
3880048 931222 931362
742289
0.440491 0.25
CD3_Cord_BI
1 1
Huh75,Huh7
EZH2_(39875)
CHD7_(A301-223A-1) TF
931222
0.2
CD34_Cultured_Cells
2329749 13364249
11
746346
TNFRSF4
0.15
CD34
1
1
0.1
CD19_Peripheral_UW
11961161 2329749 2633716
11
DisGeNET
0.841203
CD19_Cord_BI
1
0.683926
0.440491
CD15
11661967 2079131 2523822
931495
Dnd41
931175
0.370542
-
ROADMAP
803429
1
DISEASES
CD14
1 1 1
0.232871
ROADMAP
6301191 2046975 2429100
0.0832744
Breast_vHMEC
758398
0.189049
Genomic functional elements
ROADMAP
1 1 1
0.440491
Breast_Myoepithelial
5454337 778240 778240
-
ROADMAP
747835
TNFRSF4
Brain_Substantia_Nigra
1 1 1
DisGeNET
ROADMAP
5431142 462849 462849
0.566032
Brain_Mid_Frontal_Lobe
1625657 931203 931203
0.230999
ROADMAP
746853
0.524412
Brain_Inferior_Temporal_Lobe
1 11
0.440491
ROADMAP
5431141 373912 373912
-
Brain_Hippocampus_Middle
None End End
TNFRSF4
Monocytes-CD14+_RO01746 Stellate,Hepg2
H4K20me1
Start
DisGeNET
9/28/17, 10:12 PM (totally 0 records) Comparation between cell/tissue types 9/28/17, 10:12GWAS PM http://10.53.50.11/1/hedd/detail.action.php?idno=80 H3K27me3 NHDF-Ad H3K27me3
931475
ROADMAP
2636181 Start
0.620034
K562
ENCODE
751389
0.294459
1
Cell Line
Adipose_Mesenchymal
1 Chr Chr
0.668479
Position
ENCODE
3608093 TFBS ID
0.440491
First
931139 931574 Chr
K562
TFBS ID
CADD (totally 0 records)
1
Huvec
None
Chr
ENCODE
3897460
snpID
Hepg2
700562
None
GWAS (totally 0 records)
ENCODE
1
None
4
Helas3
None
811042
945373 931345 952199 931365 950048 931465 931500 949536 931500 1019756
K562
-
0.95
Score
600k
9/28/17, 10:12 PM
ENCODE
913564
911759
CD15 CD15
Breast_vHMEC Breast_vHMEC
1 1 1 1 1 1 11 1 1
907560
CD14 CD14
ROADMAP ROADMAP
ROADMAP ROADMAP Breast_Myoepithelial Breast_Myoepithelial
ROADMAP ROADMAP
ROADMAP ROADMAP Brain_Substantia_Nigra Brain_Substantia_Nigra
Brain_Mid_Frontal_Lobe Brain_Mid_Frontal_Lobe
Brain_Germinal_Matrix Brain_Germinal_Matrix
Brain_Inferior_Temporal_Lobe ROADMAP Brain_Inferior_Temporal_Lobe ROADMAP
Brain_Hippocampus_Middle ROADMAP ROADMAP Brain_Hippocampus_Middle
ROADMAP ROADMAP
ROADMAP ROADMAP Brain_Cingulate_Gyrus Brain_Cingulate_Gyrus
17177624 216141 18876456 216142 19238259 216143 216144 20515064 216144 20649712
13480701 Histone modification (totally 74 records)
14
ROADMAP ROADMAP
None
2079131
13
ROADMAP ROADMAP
943265 931325
894057
PLU1
RBBP5_(A300-109A) End
917091
2046975
3 of 5
None
Start
1 1
2892179 TFBSs (totally 9 records)
12
1027568
15349581 216140
TFBSs (totally 9 records)
HEDD | Details
830114
Chr
None
DisGeNET
TFBFs activity among the different cell types (totally 1 records) 1 931139 931574 Genome location
H1hesc
11
1034026
0.566032
Histone-5431141 400k 600k 800k 1 000k Histone-13524314 Histone-6301191 Histone-3764608 Histone-18876456 Histone-17177624 Histone-14367179 Histone-7846258 Histone-16223054 Histone-18723888 TFBFsHistone-4675024 activity among the different cell types (totally 1 records) Histone-13768390 Histone-2643707 Genome location Histone-16608189 Histone-12914384 Histone-626750 Histone-1358464
ENCODE
2 of 5 2 of 5 | Details HEDD
1
814883
0.230999
3
400k
0.85DisGeNET 0.9
0.8
0.524412
TNFRSF4 0.05
Source ♦
0.679441 0.75
0.7
ENCODE ENCODE Gm12878 ENCODE ENCODE ENCODE H1hesc ENCODE ENCODE ENCODE Helas3 ENCODE ENCODE ENCODE Hepg2 ENCODE ENCODE ENCODE Huvec ENCODE ENCODE ENCODE K562 ENCODE ROADMAP ROADMAP Adipose_Mesenchymal ROADMAP ROADMAP ROADMAP Adipose_Nuclei ROADMAP ROADMAP ROADMAP Adult_Liver ROADMAP ROADMAP ROADMAP Aorta ROADMAP ROADMAP ROADMAP Bone_Marrow_Mesenchymal ROADMAP ROADMAP ROADMAP Brain_Angular_Gyrus ROADMAP ROADMAP ROADMAP Brain_Anterior_Caudate ROADMAP ROADMAP ROADMAP Brain_Cingulate_Gyrus ROADMAP ROADMAP ROADMAP Brain_Germinal_Matrix ROADMAP ROADMAP ROADMAP Brain_Hippocampus_Middle ROADMAP ROADMAP ROADMAP Brain_Inferior_Temporal_Lobe ROADMAP ROADMAP ROADMAP Brain_Mid_Frontal_Lobe ROADMAP ROADMAP ROADMAP Brain_Substantia_Nigra ROADMAP ROADMAP ROADMAP Breast_Myoepithelial ROADMAP ROADMAP ROADMAP Breast_vHMECROADMAP ROADMAP ROADMAP CD14 ROADMAP ROADMAP ROADMAP CD15 ROADMAP ROADMAP ROADMAP CD19_Cord_BIROADMAP ROADMAP ROADMAP CD19_Peripheral_UW ROADMAP ROADMAP ROADMAP CD34 ROADMAP ROADMAP ROADMAP CD34_Cultured_Cells ROADMAP ROADMAP ROADMAP CD3_Cord_BI ROADMAP ROADMAP ROADMAP CD3_Peripheral_UW ROADMAP ROADMAP ROADMAP CD4+_CD25+_CD127-_Treg ROADMAP ROADMAP ROADMAP CD4+_CD25-_CD45RA+_Naive ROADMAP
13909090
DHS ID
1
gm12878 H1-hESC h1hesc H1-hESC helas3 H1-hESC hepg2 HUVEC huvec K562
TNFRSF4
0.365133 0.6 0.65
0.55
entries
Quantile ♦
0.440491
TNFRSF4
myocardial infarction Enhancer-80 DHS-216143 melanoma autoimmune diseases TFBS-2046975 0 TFBS-2429100 cancer Histone-14328067 Histone-13534859 Histone-5431141 colitis Histone-13524314 Histone-6301191 Histone-3764608 colorectal neoplasms Histone-18876456 Histone-17177624 Genomic functional regions Histone-14367179 Histone-7846258 Histone-16223054 Histone-18723888 Histone-4675024 Histone-13768390 Enhancer-80 Histone-2643707 DHS-216143 Histone-16608189 TFBS-2046975 Disease with high score relating to enhancer Histone-12914384 TFBS-2429100 Histone-626750 Histone-14328067 Histone-1358464 Histone-13534859
1 of 5 http://10.53.50.11/1/hedd/detail.action.php?idno=80 Cell line gm12878
-
0.828923 0.45 0.5
0.4
Top 10 high socres of Disease Score
H1_mesenchymal
PHRED
TNFRSF4
0.440491 0.3 0.35
0.25
acute coronary syndrome lupusatherosclerosis erythematosus, systemic
10
Probability ♦
H1_neuronal_progenitor
Raw score
1032259
20
D is ea se
G W AS
treacher collins syndrome
0.2
0.15
Gene-disease score ♦
H1_mesenchymal
ALT
TNFRSF4 0.05 0.1
0
Enh-gene score ♦
H1ESC
2
Tissue ♦
H1ESC
REF
944735
http://10.53.50.11/1/hedd/detail.action.php?idno=80
Last
Show
Gene name ♦
Gastric
Source
PHRED
1034691
Next
GM12878
PMID
Raw score
1019967
5
Gastric
P-value
ALT
1025495
4
Fetal_Thymus
Disease/trait
T EZH2_(39875) R H3K27me3 T P300_KAT3B E H3K27me3 T HDAC1_(SC-6298)
3
GM12878
Risk allele
931845 None 932523 None 932606 None 931734 None 933047 None
2
Fetal_Stomach
Source
R
1
Fetal_Thymus
PMID
931650
Previous
Fetal_Muscle_Trunk
P-value
DISEASES
Search:
Fetal_Stomach
Disease/trait
State
DisGeNET
Fetal_Muscle_Leg
PM
Last
Risk allele
End
0.668691
First
acute coronary syndrome
Gm12878
DHS (totally 5 records)
931650 814989 931694 795001 931000 832173 931473 913013 928000 814851
Brain_Anterior_Caudate Brain_Anterior_Caudate
13768388
1
931245
Brain_Angular_Gyrus Brain_Angular_Gyrus
12976027
1
Start
Aorta Aorta
11172466
1 Adult_Liver Adult_Liver
5149220
1
Bone_Marrow_Mesenchymal ROADMAP ROADMAP Bone_Marrow_Mesenchymal
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ROADMAP ROADMAP
ENCODEENCODE
1
4272486
Hepg2
Helas3
1
Helas3
H1hesc H1hesc
1
3764608
Adipose_Nuclei Adipose_Nuclei
1
Adipose_Mesenchymal Adipose_Mesenchymal
1 of 5
K562 K562
1
ENCODE ENCODE
1
Huvec
10
Chr
Huvec
HEDD | Details
0.35242
acute coronary syndrome
Comparation between cell/tissue types Genome segmentation state (totally 6 records) Comparation between cell/tissue types
0.800062
Fetal_Muscle_Trunk
Lung
DisGeNET
REF
Position
0.440491
-
ROADMAP
Position
Chr
9
ALT
TNFRSF4
Brain_Germinal_Matrix
Chr CADD (totally 0 records)
REF
DisGeNET
ROADMAP
ALT
0.276175
Fetal_Intestine_Small
K562 K562
Lung
IMR90 IMR90
Left_Ventricle Left_Ventricle
HepG2
HSMM HSMM
0.668691
HepG2
HeLa_S3 HeLa_S3
HMEC
HMEC
0.276175
HUVEC
H9
HUVEC
DisGeNET 1 of 5
HSMMtubeHSMMtube
DISEASES
DisGeNET
0.101852
atherosclerosis
Disease name ♦ melanoma Disease with high score relating to enhancer
Cell types
0.602049
0.729358
0.272999
ROADMAP
Position
0
Figures
Cell types
DisGeNET
DisGeNET
0.61976
Fetal_Muscle_Leg
DisGeNET
0.683926
0.231223
Brain_Anterior_Caudate
REF
0.424798
Top 10 high socres of Disease
Fetal_Intestine_Large
0.566032
0.272999
H9
H1_trophoblast H1_trophoblast
H1_neuronal_progenitor H1_neuronal_progenitor
H1_mesenchymal H1_mesenchymal
H1ESC
Next
0.370542
0.440491
Fetal_Intestine_Small
5
1
0.440491
ROADMAP
4
0.0832744 0.232871 DISEASES http://10.53.50.11/1/hedd/detail.action.php?idno=80
TNFRSF4 1 records download
Brain_Angular_Gyrus
3
74
TNFRSF4 74 records download
Fetal_Adrenal_Gland
DisGeNET
0.729358
0.35242
9
Count 0.602049
ROADMAP
Position
0.964374
Bone_Marrow_Mesenchymal
Chr
0.440491
nager acrofacial dysostosis
931139 931574
snpID
TNFRSF4 9 records download
Fetal_Intestine_Large
0.620034
0.424798
0.101852
DisGeNET
autoimmune diseases TFBS
ROADMAP
Previous
0.800062 H1ESC
Fetal_Thymus Fetal_Thymus
Search:
Gastric
2
0.440491
0.231223
Gastric
Fetal_Stomach Fetal_Stomach
1
0.440491
GM12878 GM12878
Fetal_Muscle_Trunk Fetal_Muscle_Trunk
Fetal_Muscle_Leg Fetal_Muscle_Leg
Fetal_Adrenal_Gland Fetal_Adrenal_Gland
EPC_VB EPC_VB
DND_41 DND_41
-
Fetal_Intestine_Small Fetal_Intestine_Small
CM_CD4_ab_T_cell_VB CM_CD4_ab_T_cell_VB
CD8_ab_T_cell_CB CD8_ab_T_cell_CB
CD4_ab_T_cell_VB CD4_ab_T_cell_VB
CD14CD16__monocyte_VB CD14CD16__monocyte_VB
Aorta
A549
CD14CD16__monocyte_CB CD14CD16__monocyte_CB
B_cells_PB_Roadmap B_cells_PB_Roadmap
Aorta
A549
End
End
Start
-
0.61976
0.566032
0.841203
adult t-cell lymphoma/leukemia
4 000k 4 2…9:41 9/28/17, Highcharts.com
DisGeNET
0.440491
0.230999
1
tropical spastic paraparesis
4 2…
DisGeNET
0.683926
-
0.524412
0.440491
EPC_VB
3 800k
0.370542
TNFRSF4
DisGeNET
TNFRSF4 1 records download
Fetal_Adrenal_Gland
3 600k
0.841203 0.964374
DisGeNET
0.620034
atherosclerosis TFBS activity
DND_41
3 400k
0.566032
Network of enhancer and its neighboring enhancers 0.524412 0.230999
0.440491
0.566032
0.294459
0.189049
CM_CD4_ab_T_cell_VB
3 200k
0.440491
-
0.230999
0.440491
DND_41
DisGeNET
entries
0.668479
TNFRSF4 5 records download
CD8_ab_T_cell_CB
0.679441
-
TNFRSF4
0.524412
asthma DHS
CM_CD4_ab_T_cell_VB
4 000k
Source ♦
TNFRSF4
Start
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
3 800k
atherosclerosis
TNFRSF4
0.440491
14 0
12 0
10 0
80
3 600k
10
Show 6
DisGeNET
TNFRSF4 6 records download
9/28/17, 10:07 PM
123
0.679441
asthma Genome segmentation state
autoimmune diseases
0
5 0.365133
0.440491
entries 3 400k
52
0.828923
0.440491
cancer Histone modification
M0_macrophage_CB M0_macrophage_CB
0.440491
Records of detail information results
Source ♦
TNFRSF4 123 records download
myocardial infarction
Repets 0.294459
Histone
1
Quantile ♦
TNFRSF4 0 records download
CD4_ab_T_cell_VB
3 000k
0.230999
74
Probability ♦
Functional arteriosclerosis neighboring enhancers
CD14CD16__monocyte_VB
TFBS 0.668479
2 800k
9
lupus erythematosus, systemic
Quantile ♦
Last
Gene-disease score ♦
adult (CADD t-cell lymphoma/leukemia SNV with score ≥ 20)
HEDD | Details
10
Next
1
Diseases (totally 5 target genes and 52 disease records)
3 200k
1
Enh-gene score ♦
0.440491
CD4_ab_T_cell_VB
2 600k
records download Tissue ♦
TNFRSF4 0 records download
colorectalimmunodeficiency neoplasms 16
Show
Previous
Summary of the detail information records
acute coronary GWAS syndrome
Highcharts.com
-
Gene name52 ♦
colitis Repeats treacher collins syndrome
DISEASES
colorectal neoplasms
ENCODE
Count
0.232871
931139 931574
1
123
First
0
0.95
0.0832744
TNFRSF4
Source
HEDD | Details
74
40
ROADMAP
20
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
2 400k
0.524412 Coordinate ( bp)
DHS
Hepg2
Aorta
GWAS SNV 0.440491
2 200k
Cell/tissue type
http://10.53.50.11/1/hedd/detail.action.php?idno=80
0
2 000k
ENCODE
5
m od ifi Re ca pe tio at n s
0.9
9
m od ifi ca tio n
Ehancer -
1 800k
0.440491
0.001
H is to ne
0.85
Re pe at s
H is to ne
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ROADMAP
ENCODE
ENCODE
0.8
0.189049
snpID Chr CADD (totally 0 records)
GM12878
1
1
Start
1
End
931000
932606
931694
1
State
T
932523
931473
helas3
R
931734
931000
Cell line
h1hesc
E
932606
hepg2
T
helas3
On the 'Analyze' webpage, for a gene set of interest, users can score enhancers in a gene network for their 'relatedness' to the gene set. Users can also use these scores in a subsequent correlation analysis, which diseases with highest absolute correlation coefficients (top 20) will be shown in bar charts . 2643707
1
929513
934453
930257
Correlation analysis
DHS ID
Dnd41
DHS (totally 5 records) 216140
Start
End
Cell Line
1
931325
931475
Stellate,Hepg2
DHS ID
Chr
963615
None
H3K9ac
HepG2
1
930188
938374
None
EZH2_(39875)
H1-hESC
216140
1
216141 216143
EZH2_(39875)
HepG2
Chr
929279
7501702
1
923254
942575
None
H3K27me3
H1-hESC
4675024 7756908
11
929898 928566
939469 944104
None None
H4K20me1 H3K27me3
H1-hESC HMEC
4708632 7846258
11
924044 924897
1032880 978455
None None
HDAC2_(A300-705A) H3K4me1
H1-hESC HMEC
926235
959239
None
H2A.Z
216141
HMEC
11
930605 929513
951861 934453
None None
EZH2_(39875) H3K4me1
HSMMtube HepG2
11947434
7095389
1
1
930081 929990
944275 938525
None None
CHD4_Mi2
H3K4me2
K562 HepG2
13768390
1
930009
942908
None
PLU1
K562
14367179
1
15098015
1
925598
7501702
15207446
1
1
926235
None
H3K9me3
Monocytes-CD14+_RO01746
7756908
15349596
1
1
928566
944104
None
H3K27me3 H3K27me3
HMEC
Monocytes-CD14+_RO01746
7846258 15665589
11
924897 931479
978455 938149
None None
H3K4me1 EZH2_(39875)
HMEC NH-A
15793434 9241326
11
924244 930605
979292 951861
None None
H3K4me2 EZH2_(39875)
NH-A HSMMtube
16223054 11947434
11
926447 930081
978752 944275
None None
H3K4me1 CHD4_Mi2
NH-A K562
16608189
1
1
930009
942908
None
None
EZH2_(39875)
NHDF-Ad
17724047
1
931497
936163
sex=M
treatment=None
NHEK
18223151
1
930044
937283
None
H3K27me3
NHEK
18723888
1
928769
935365
None
H4K20me1
NHEK
18876459
1
929931
941994
None
EZH2_(39875)
NHLF
End 931495
931475
11
931345 931465
931495 931615
216142 216144
11
931365 931500
931515 931650
216143
1
931465
931615
931500
931650
TFBSs (totally 9 records) 216144
9241326 6743981
Start 931345
1
931325
216142
HMEC
1
1
931365
1
7395275
1 1
929279
963615
923916
1033252
927726 923276 929604
930513
944880
None None
H3K9ac SIRT6
Cell line
373912
1
931203
931543
HDAC2
HepG2
931173
931497
EP300
931216
931496
FOXA1
2046975
462849
959752
None
H3K9ac
Monocytes-CD14+_RO01746
959239
None
H2A.Z
HMEC
942304 942863
938384
None
PLU1
K562
3 of 5
3 of 5
Cd34mobilized,Jurkat TF
373912
K562
Fibrobl
End
778240
HMEC
Hpde6e6e7,Hsmm Cd34mobilized,Jurkat
Start
462849
EZH2_(39875)
Huh75,Huh7 Fibrobl
Chr
TFBS ID
None
Hpde6e6e7,Hsmm
TFBS ID
9/28/17, 10:12TFBSs PM(totally 9 records)
HepG2
Cell Line Huh75,Huh7
Stellate,Hepg2
931515
1
Chr
1
Start
End
Analysis of enhancer distribution and disease association in 9p21 locus. Identification of potential regulatory causal variants for human complex diseases Building disease gene regulatory networks 7255869
Summary •
huvec
1
13768390
4 of 6
T
7255869
Application • • •
933047
GM12878
4272497
5 of 5
928000
DHS (totally 5 records)
H3K4me2
None
huvec
hepg2
None
944880
T
E
1016146
927726
H3K4me2
1
933047
931734
923943
1
None
H3K27me3
928000
931473
1
7395275
938525
None
None
1
1
3767063
929990
942881
1
7095389
3262066
• 10007
0.75
1
Genomic functional elements
1 600k
-
First
4 of 5
EnhID
0.7
0.440491
colitis
Gm12878 Gm12878
Query
40269357
0.65
-
cancer
8
Functional elements
Start
0.6 5
TNFRSF4
autoimmune diseases
Other annotation
Target gene Enhancer source Cell Types/Tissues Functional elements TF name Histone marker name
1
0.55
asthma
Genome location
1
GWAS (totally 0 records)
Enhancers
• • • • • •
Chr
1 400k
TFBFs activity among the different cell types (totally 1 records)
1
0.95 2 of 2 123
GWAS (totally 0 records) with high score relating to enhancer Disease
Diseases
oaded from https://academic.oup.com/nar/article-abstract/46/D1/D113/4564801 • Genome location bert Einstein College of Medicine user • Disease June 2018
10007
1 200k
TNFRSF4
Genome location
1
Target genes
EnhID
1 000k
TNFRSF4
TFBFs activity among the different cell types (totally 1 records) Regulatory network of enhancer and its binding TFs and its target genes asthma TNFRSF4
∼8.6 billion 11 062 356 10 040 306 22 801 1611 411 1 533 636
Detailed information
Results
800k
arteriosclerosis
with risk SNPs of glaucoma and CAD (Supplementary Figmentary the Figure S1D). We used a list of 242 schizophrenia Score enhancer-disease connection S2B). We found that and enhancers in high genes to benchmark the running time for networksand that The probability of connection between anall enhancer a geneure (pEG ) or between a gene a disease (pGD).linkage disequilibrium those riskpEG SNPs––rs523096 (46), rs4977756 of we available It usually takesan several minutes Themake probability of online. connection between enhancer andto a disease (pED) bywith multiplying and pGD, the two probabilities (49), rs1063192 (50), rs7865618 (51), score enhancers, connections depending onwith the an selected gene network, their respective intermediate gene: pED = (47,48), pEG x pGDrs1333037 . rs2157719 (52) and rs7866783 (53) for glaucoma; rs1537370 and correlation analysis takes about half an hour. (54), rs1333049 (55,56), rs10738607 (57), rs4977574 (58) Score enhancers based on a gene set and rs2891168 (59) for CAD––have the highest scores with Given a gene set of interest (e.g., differentially expressed genes or disease/trait-related genes), an online software tool in APPLICATION these two diseases in this block. In block C, all the enHEDD can score enhancers based on their connections to genes and the centrality of genes in a gene network using the hancers have the highest score with the small cell lung canAnalysis of enhancer distribution and algorithm disease association in highly successful Google PageRank that we implemented before (Christophe Lemetre et.al, 2013). cer (SCLC) among other diseases. Near one of these en9p21 locus hancers is a SNP––rs4246856––associated with D-dimer Gene set-disease analysis Chromosome 9p21 locus correlation is a 13.3-Mb gene-poor genomic level (Supplementary Figure S2C), which has been shown region, contains many set genetic variants to provide useful information forHEDD predicting the prognosis Given a which functionally coherent of genes (e.g.,associated from a differential gene expression analysis), can suggest their with multiple human diseases, including coronary of patients withbetween SCLC (60). BlockofDenhancer containsscores: enhancers in of related diseases as acomplex form of functional annotation based on the correlation two sets scores artery diseasebetween (CAD), glaucoma, and several can- of enhancers TEK, a gene that on also contains a in SNP associconnections enhancers diabetes, and a disease and scores based the gene set the(rs2273720) gene network. cers. Most of the risk variants in this region are non-coding, ated with endothelial growth factor levels that are correlated suggesting that they influence gene expression and may act with the formation of blood vessels. Interestingly, enhancers in cis (45). We analyzed the genomic distribution of enin this block have the highest scores with venous malforhancers in 9p21 and found eight regions with high densimations, •multiple DHS cutaneous and mucosal, diseases related • ENCDOE ties •of enhancers (Supplementary Figure S3A, Supplemento blood •vessels (Supplementary Histone modification Figure S2D). Block E and FANTOM5 tary• Table S1). The genomic distribution of enhancers with • genes TFBSwith multiple risk SNPs associated with F contains RoadMap disease association is mostly consistent with the overall dis• Repeats obesity (Supplementary Figure S2E) and amyotrophic lattribution of enhancers. Using enhancer-disease associations eral sclerosis (Supplementary Figure S2F), respectively. Enwith the top 10% highest scores, we screened for diseases ashancers of these genes show higher scores for those two dis• DISEASES sociated with each enhancer cluster and found the majority eases than other diseases. In block G, an enhancer strongly • MalaCards • Conservation score of these clusters are highly associated with cancer (Suppleassociated congenital disorder of glycosylation was • DisGeNET HEDD • with Network mentary Figure S3B, Supplementary Table S1). found near (61), a risk SNP related to igG gly• rs10971170 GWAS Catalog Enhancers overlapping or near these risk variants could cosylation Figure S2G), and could be the • (Supplementary GWASdb be the regulatory • element CADD underlying the genetic signal of the risk • genomic ENCDOE functional elements underlying their disease• association. SNP. • Genome segmentation state FANTOM5 Indeed, we identified several blocks of 9p21• region • TFBS activity GTExin which enhancers are scored high for corresponding variant-associated diseases (Supplementary Figure S2A). Block B contains two genomic regions enriched
•
600k
Fetal_Intestine_Large Fetal_Intestine_Large
349 566
Note: 1. The number of markers.
•
ENCODE
ENCODE
ENCODE
400k
adult t-cell lymphoma/leukemia
0.9
Disease Disease name ♦
7
2 of 2
0.85
Diseases (totally 5 target genes and 52 disease records)
HUVEC_prol_CB HUVEC_prol_CB
523 109
ENCODE ENCODE
HINT HPRD HIPPIE PIPs CCSB IID UniHI
Tables
Hepg2
Nodes 11 984 9 460 16 567 5 445 4 230 18 080 17 685
2 793 316
ENCODE
399 124 65 359 2 328 833 44 581 49 492 429 036 35 329 314 237 ∼8.6 billion 11 062 356 10 040 306 22 801 1611 411 –– –– 13 812 66 943 26 393 329 Edges 53 405 36 985 276 051 37 343 13 427 915 091 364 777
1
•
0.5
HEDD | Details
ENCODE ENCODE
Network
6 –– 111 –– –– –– –– –– –– 6 120 68 91 19 –– –– ––
Total
ENCODE ENCODE
SNV Genome segmentation state DHS TFBS activity TFBS Histone modification Repeats Conservation Target gene connection
ENCODE FANTOM5 RoadMap DISEASES MalaCards DisGeNET GWAS Catalog GWASdb v2 CADD UCSC UCSC Ensembl UCSC UCSC UCSC UCSC ENCODE FANTOM5 GTEx
Number of records
0.8
6
TFBS-2046975 TFBS-2429100 DHS 5 records download Genomic functional elements Histone-14328067 Example: H3K27ac, H3K27me3 or H3K9ac 1 Histone-13534859 Enhancer-80 TFBS activity 1 records download Histone-5431141 DHS-216143 Histone-13524314 TFBS-2046975 Histone-6301191 TFBS-2429100 TFBS 9 records download Submit Histone-14328067 Histone-3764608 Histone-18876456 Histone-13534859 Histone modification 74 records download Histone-17177624 Histone-5431141 Histone-14367179 Histone-13524314 Histone-7846258 Histone-6301191 Repeats 1 records download Histone-16223054 Histone-3764608 Histone-18723888 Histone-18876456 Histone-4675024 Histone-17177624 Histone-13768390 Histone-14367179 Histone-2643707 Histone-7846258 Histone-16608189 Histone-16223054 Histone-18723888 Histone-12914384 Histone-4675024 Histone-626750 © ZDZ Lab, a member of the Department of Genetics, Albert Einstein College of Medicine. All rights reserved. Histone-13768390 Histone-1358464 Diseases (totally 5 target genes and 52 disease records) Histone-2643707 400k 600k 800k 1 000k 1 200k 1 400k 1 600k 1 800k 2 000k 2 200k 2 400k 2 600k 2 800k 3 000k Histone-16608189 Disease name ♦ Gene name ♦ Tissue ♦ Enh-gene score ♦ Gene-disease Probability ♦ Coordinate (score bp) ♦ Histone-12914384 Histone-626750 acuteHistone-1358464 coronary syndrome TNFRSF4 0.440491 Ehancer GWAS SNV DHS 0.828923 TFBS Histone 0.365133 Repets
Chr
GWAS
0.45
Genome segmentation state 6 records download DHS-216143 Histone antibody/target : Enter a histone antibody/target name
Cell-types/tissue
0.75
Score
Genomic functional regions Enhancer-80
Chr
Disease
0.4
Enter a transcription factor name SNV (CADD with score ≥ 20) 0 records download
ENCODE ENCODE
Enhancer
0.35
0.021
Count
CD14CD16__monocyte_CB
0.3
0
74 records download 931734 © ZDZ Lab, a member of the Department of Genetics, Albert Einstein College of Medicine. All rights reserved. 1 records download 0 TNFRSF4, VWA1, RP4-758J18.10, RP11-465B22.5, TTLL10
CD14CD16__monocyte_VB
0.25
0 records download
Example: YY1, SP1 or NFKB1 Functional neighboring enhancers 123 records download
Source
0.7
Score
Genomic functional regions Transcription factor :
Table 1. Summary of data sources (as of April 2017)
0.65
ROADMAP
0.2
0.6
ROADMAP
0.15
0.55
ROADMAP
0.1
0.5
60
0.05
0.45
ROADMAP
0
GWAS
0.4
ENCODE
80
9 records download 931473
Repeats Target gene
ROADMAP
• Data sources (Table 1) and database content and construction (Fig 1)
0.35
0.002
60
TFBS Start
0
Fu nc tio G na en lN om ei e gh se bo gm rin e nt TF g a en BS tio ha ac n nc tiv st TF D at er H ity BS e S s
Nucleic Acids Research, 2018, Vol. 46, Database issue D117
0.3
0.004
40
1 records download 1
Histone modification End
0
CA D D
tropical spastic paraparesis melanoma
Cell/tissue type Hepg2 atherosclerosis 0.05 0.1 0.15 0.2 0.25 DHS0 Genomic functional acute coronary syndrome lupus Source erythematosus, TFBS ENCODE elements : systemic myocardial infarction Histone modification Disease melanoma 52 records download Repeats
ENCODE
0
m od ifi ca tio n
TFBS activity Chr
CD8_ab_T_cell_CB
TNFRSF4, VWA1, RP4-758J18.10, RP11-465B22.5, TTLL10
1
9/28/17, 9:41 PM
52
D is ea se
931734
0.005
6
Fu nc tio G na en lN om ei e gh se bo gm rin en TF g t at en BS io ha ac n nc tiv st TF D at er H ity BS e S s
Top 10 high socres of Disease
G W AS
Materials and Methods
Records of detail information results
ROADMAP
931473
Source ♦
52
6 records download 5 records download
Adult_Liver
autoimmune diseases Start
nager acrofacial dysostosis
Gm12878 Cell types/tissues : tropical spastic paraparesis End treacher collins syndrome H1hesc atherosclerosis 16 acuteimmunodeficiency coronary syndrome Helas3 Target gene autoimmunesystemic diseases lupus erythematosus, Hepg2 nagermyocardial acrofacial infarction dysostosis Huvec
0 records download 123 records download
DHS
B_cells_PB_Roadmap
1
immunodeficiency 16
Conservation median ♦
http://10.53.50.11/1/hedd/detail.action.php?idno=80
Re pe at s
Top 10 high socres Summaryof of Disease the detail information records
Enhancer ID: 80
1 of 2
TNFRSF4;VWA1; RP4-758J18.10; RP11-465B22.5;TTLL10 ENCODE Hepg2
GWAS Search results
SNV (CADD with score ≥ 20)
treacher collins syndrome Chr Enhancer source : ENCODE
0.022
52 records download
Detail enhancer Functionalresults neighboringof enhancers http://zdzlab.einstein.yu.edu/1/hedd/search.php http://10.53.50.11/1/hedd/detail.action.php?idno=80 Genome segmentation state
Enhancer ID: 80
Gm12878
H is to ne
Home »
Optional input
NA
Fu nc tio G na en lN om ei e gh se bo gm ri en ng TF ta en BS tio ha ac n nc tiv s TF D ta er H ity BS te S s
http://10.53.50.11/1/hedd/detail.action.php?idno=80
HEDD | Search HEDD | Details
Conservation mean ♦
Disease
Search:
Example: B4GALT1
Cell type ♦
931734
Source
HEDD | Details Target gene : Enter a gene name Detail results of enhancer
Target gene ♦
HEDD: Human Enhancer Disease Database
Example: glaucoma
Search results
928200
chr1gene Target
80
Enter a disease name
Disease :
chr1 End
931473
M0_macrophage_CB
HEDD: Human Enhancer Disease Database
End ♦
14 0
79
The genome location will be ignored, if it is only partially specified or greater than 1 Mb.
Start ♦
Start
78
HEDD | Details
Example: chr1:1-1000000
Chr ♦
entries
Records of detail information results
D is ea se
EnhID ♦ http://10.53.50.11/1/hedd/detail.action.php?idno=80
- 931734
EPC_VB
: 928200
Brain_Cingulate_Gyrus
Chr 1
Genome location :
10
Show
1
G W AS
Chr
CA D D
Required input ( * at least one)
Home »
Search results Search results
BSearch results
Search parameters
HEDD | Details
http://10.53.50.11/1/hedd/search.action.php
Search
CD14CD16__monocyte_CB
Home »
Analyze
Adipose_Nuclei
• Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. • To facilitate studies of enhancers and their roles in the molecular mechanism of human complex diseases, we developed the Human Enhancer Disease Database (HEDD), the first integrated and interactive online knowledge base of enhancers and their disease associations. • HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php.
http://zdzlab.einstein.yu.edu/1/hedd/search.php
2079131
778240
2329749
1 1 1
2046975
1
2079131 2329749
1 1 1
931203
931175
931173
931222
931216
931158
931543
931475
931497
931558
931496
931598
TF
HDAC2
RXRA
EP300 SP1
FOXA1 TEAD4
HepG2
Cell line
HepG2 HepG2 HepG2
HepG2
HepG2
HepG2
HepG2
931175
931475
RXRA
HepG2
1
931222
931558
SP1
HepG2
1
931158
931598
TEAD4
HepG2
9/28/17, 10:12 PM
9/28/17, 10:12 PM
9/28/17, 10:15 PM
We have built an integrated database for human enhancers and their disease associations. Our goal is to provide a comprehensive data resource and a set of interactive analysis tools to facilitate genomic research of enhancers and their roles in human9/28/17, complex diseases. We will continue to update the 10:12 PM database with the latest data sets when they become available. In the future, we will add more genetic and epigenetic information about enhancers, such as the topologic associated domains and the retargeting of enhancers in different cell type/tissues or cancers. We believe that our enhancer database will be of particular interest to researchers working on the gene regulatory networks of human disease 20649723
1
926697
942330
None
P300_KAT3B
Osteobl
1388787
1
839812
1012575
EtOH_0.02pct
H4K20me1
A549
Reference
Result survey/analysis • • • • •
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, Vol. 489. Lizio M, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol, 2015, vol.16, 22 . Roadmap Epigenomics Consortium, Kundaje, Anshul, et.al. Integrative analysis of 111 reference human epigenomes. Nature, 2015, Vol. 518, 317–330. Aziz Khan, Xuegong Zhang. dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Research, 2016, Vol. 44, Database issue. Christophe Lemetre, Quanwei Zhang, Zhengdong D. Zhang. SubNet: a Java application for subnetwork extraction. Bioinformatics, 2013, Vol. 29 no. 19.
Wang Z, Zhang Q, Zhang W, Lin JR, Cai Y, Mitra J, Zhang ZD. HEDD: Human Enhancer Disease Database (2018). Nucleic Acids Res, 46, D113-D120.
