SEdb 2.0
Search

For example

Function introduction:
Based on the tissue query, users can query the super-enhancer for all samples of a particular type of tissue.

Parameter explanation:
1) Species: Select Human or Mouse.
2) Biosample type: Cell type classification of samples.
3) Tissue name: Select the tissue of interest.

For example

Function introduction:
Users submit a gene and analyze super-enhancers associated with it via relationships between the super-enhancer and associated genes identified under different strategies are obtained from indeterminate samples.

Parameter explanation:
1) Species: Select Human or Mouse.
2) Strategies/Algorithm: The closest active, ROSE overlap, ROSE proximal, ROSE closest, Lasso and PreSTIGE.
3) Gene symbol: Only gene symbol can be supported.

For example

Function introduction:
In the sample-based advanced query, users determine the scope of the super-enhancer query by determining the sample and genome location for the results of interest.

Parameter explanation:
1) Genomic region: Chromosome,at the start of the chromosome and at the end of the chromosome.
2) Species: Select Human or Mouse.
3) Biosample type: Cell type classification of samples.
4) Tissue type: Samples tissue type.
5) Biosample name: Biosample name is made of cell/tissue/cell line name, treatment condition, processing time, etc.

For example

Function introduction:
Users submit a TF name and SEdb 2.0 will identify the SE bound by the TF and their associated samples. TF related SE are identified by motif scan analysis or TF ChIP-seq data.

Parameter explanation:
1) TF symbol: Only TF symbol can be supported.
2) Species: Select Human or Mouse.
3) Strategies/Algorithm: TF ChIP-seq and Motif scan.

Features:

1) Search super-enhancers by tissue category-based: Based on the tissue query, users can query the super-enhancer for all samples of a particular type of tissue.

2) Search super-enhancers by gene-based: In the gene-based query, users can query a gene of interest and SEdb will return all super-enhancers that match the super-enhancer-gene relationship for all samples.

3) Search super-enhancer by genomic region: In the sample-based advanced query, users determine the scope of the super-enhancer query by determining the sample and genome location for the results of interest.

4) Search super-enhancers by TF-based: In the TF-based query, users can query a TF of interest and SEdb will return all super-enhancers that match the super-enhancer-TF relationship for all samples.