Table 2. Reference
data of regulatory elements.
|
Transcriptional
regulation |
|
|
|
TF binding regions |
|
|
Transcription
Factor Binding Sites by ChIP-seq from ENCODE/HAIB |
|
|
Transcription
Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard |
|
|
Transcription
Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of
Chicago |
|
|
Open
Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) |
|
|
CTCF
Binding Sites by ChIP-seq from ENCODE/University of Washington |
|
|
Predicted TF
binding sites and TF binding motifs |
|
|
JASPAR(1) |
|
|
ENCODE-motif
(2) |
|
|
UCSC
conserved TFBS(3) |
|
|
TRANSFAC(4) |
|
|
Chromatin
interactive regions |
|
|
Chromatin
Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan |
|
|
Chromatin
Interactions by 5C from ENCODE/Dekker Univ. Mass. |
|
|
Chromatin
Interactions by 5C from ENCODE/University of Washington |
|
|
Topologically
associated domains (TADs) |
|
|
ENCODE
Hi-C proceed data |
|
Post-transcriptional
regulation |
|
|
|
Mature miRNAs |
|
|
miRBase(5) |
|
|
miRNA target
sites |
|
|
TargetScan
(6) |
|
|
miRNAda(7) |
|
|
lncRNAs |
|
|
LNCipedia(8) |
|
|
circRNAs |
|
|
CircNet(9) |
Table 3.
Reference data for E-G pair analysis
|
|
miRNA - gene
pairs |
|
|
miR2Disease(10) |
|
|
miRTarBase(11) |
|
|
TargetScan
(6) |
|
|
miRNAda(7) |
|
|
lncRNA-gene
pairs |
|
|
LncRNA2Target(12) |
Table 4.
Reference data for extended analysis
|
Type |
Reference
database |
|
Association
between variant and disease |
GWAS
catalog(13);HGMD(14) |
|
Association
between variant and mRNA abundance |
seeQTL(15);
SCAN(16); NCBI eQTL browser (17); http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/(18-23); RTeQTL database (25);
BrainEAC (26); skin eQTL database(27); GTEx Portal(28) |
|
Linkage
disequilibrium (LD) correlations between SNPs |
International
HapMap Consortium(29,30) ; MaCH(31) |