Toggle navigation
SEanalysis
Home
Analysis
Pathway downstream analysis
Upstream regulatory analysis
Genomic region annotation
Search
Browse
Visualization
Download
Contact
Help
Home
Analysis
×
Genomic region annotation
ALLSEGENE.bed
Paste your data:
Upload a file:
Example of Upload File
Region definitions are ordinary 3-field bed file format. For example:
chr11 65239110 65264640
chr19 13947194 13962421
chr19 39888494 39901409
chr1 30649567 30655759
chr1 11345200 11359618
Information about
UCSC BED format
Tissue Type :
{{s}}
SE-Gene Linking Strategies :
ALL
Overlap
Proximal
Closest
Closest active
Fimo:
1.0E-9
1.0E-8
1.0E-7
1.0E-6
Pathway Enriciment Threshold
:
FDR Adjust
Example
Analyze
Reset
Function introduction
Guidance
Users can upload a ‘bed’ format file or a region list to identify
SEs
③
overlapping the queried regions,
genes
④
associated with these SEs,
TFs
②
binding to these SEs and their upstream
pathways
①
.
1) Tissue Type:
Select one sample tissue type or all.
2) SE-Gene Linking Strategies:
select different annotation strategies to link SEs with target genes.
3) Fimo:
Set different statistical thresholds to control for false positivity.
4) Pathway Enriciment Threshold:
Set a statistical significance threshold of pathway enrichment, which is calculated using hypergeometric test.
Minimum percentage of overlap :
%
(If not, the default value is 50%.)
Applied on our catalog of peaks
Applied on your submitted regions
Apply the minimum percentage of overlap on both data
(our catalog of peaks and your submitted regions)