Find regulatory regions (analysis)

Analysis title

Find regulatory regions

Provider

Biosoft

Class

FindRegulatoryRegions

Plugin

biouml.plugins.genomeenhancer (Genome Enhancer)

Description

This method creates a track of regulatory regions for input genes. These regulatory regions can be used in "Site search on track". If ChIP-seq peaks were selected, regulatory regions will tend to cover peaks intervals. The analysis will first select the peaks inside the input genes extended with flanks. Then intervals around the peak centers will be created, overlapped, and cut to input size (promoter from and promoter to, 1100bp by default). Finally, the closest to TSS interval will be selected as the result. The TSS is taken from Fantom/TSS database (CAGE TSS database parameter). If no peaks are found around the gene, Fantom promoter will be used if tissue type was selected and Ensembl promoter will be used if no tissue type was selected.

Parameters:

• Input genes – Input genes
• ChIP-seq peaks – ChIP-seq peaks
• Ensembl database – Ensembl database
• CAGE TSS database – Select type of database to extract TSSs
• Cell/Tissue condition – Cell/Tissue condition
• TSS selection – Selection of TSS if multiple TSSs are known
• Promoter from – Promoter from
• Promoter to – Promoter to
• Shift of left gene bound position (expert) – Shift of left gene bound position
• Shift of right gene bound position (expert) – Shift of right gene bound position
• Regulatory region from (expert) – Regulatory region from
• Regulatory region to (expert) – Regulatory region to
• Output path – Path for the output track