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Different types of super-enhancer queries


For Example

Function introduction and parameter explanation

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.

1) Strategies/Algorithm:The closest active, ROSE overlap, ROSE proximal, ROSE closest, Lasso and PreSTIGE.

2) Gene symbol:Only gene symbol can be supported.

Please click here to start the selection
Option explanation:
1) Biosample type: Cell type classification of samples.
2) Tissue type: Samples tissue type.
3) Data sources: Sources of sample, including ENCODE, Roadmap, NCBI GEO/SRA and GGR.
4) Biosample name: Biosample name is made of cell/tissue/cell line name, treatment condition, processing time, etc.
5) Chromosome: Chromosome.
6) Start position: The super-enhancer is at the start of the chromosome.
7) End position: The super-enhancer is at the end of the chromosome.
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) Advanced search by sample-based: 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.