IDEAS Gene/cCRE Pairs Filtering
This is a tool for selecting candidate Cis-Regulatory Elements (cCRE) predicted for genes in hematopoetic cell types.
Download full files
here
Required selections:
Please enter your species of interest:
Mouse (mm10)
Human (hg38)
Chromosome
:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
X
*** MUST ALSO SELECT CHROMOSOME ***
Straight-forward Filters:
Please enter your
gene
of interest:
and/or
Please enter your
cCRE
of interest:
Filters on which we recommend a lower limit: (can be refined post-filter)
Correlation score greater than or equal to
(suggested 0.2)
:
Number of times selected during IDEAS leave-one-out regression
(suggested 1)
:
0
1
2
3
4
5
6
7
8
9
10
11
12
Filters for specific cells/epigenetic states/interaction frequency of gene/cCRE pairs: (can be refined post-filter)
Cell-type with non-0 (non-quiescent) IDEAS states:
LSK_BM
HPC7
CMP
MEP
G1E
ER4
CFU_E_ad
ERY_ad
ERY_fl
CFUMK
MK_imm_ad
MK_mat_fl
GMP
MONO_BM
NEU
CLP
NK_SPL
B_SPL
T_CD4_SPL
T_CD8_SPL
Epigenetic state predicted by IDEAS:
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
eRP score by cell type:
LSK_BM
HPC7
CMP
MEP
G1E
ER4
CFU_E_ad
ERY_ad
ERY_fl
CFUMK
MK_imm_ad
MK_mat_fl
GMP
MONO_BM
NEU
CLP
NK_SPL
B_SPL
T_CD4_SPL
T_CD8_SPL
cCRE location relative to gene:
Distal
Proximal
Only pairs within OnTAD level:
1
2
3
4
5
(
An et al. 2019, bioRxiv
)
Filters for compartments: (based on G1E-ER4 cell Hi-C, calculated with
Cscoretool
)
Compartment for cCRE:
A
B
Compartment for gene:
A
B
cCRE and gene are in the same predicted contiguous compartment with no change in compartment between them (enriched for proximal cCREs):
Yes
No
Filters to examine broad locations or gene expression types: (can be refined post-filter)
Gene group associated with pair:
1=Low mean, low sd
2=Low mean, high sd
3=High mean, high sd
4=High mean, low sd
Locate
gene TSS
between:
Locate
cCRE
between:
Contact
with problems or suggestions.
with problems or suggestions.