View source for Find regulatory regions with mutations (analysis)

;Analysis title
:[[File:Genome-enhancer-Find-regulatory-regions-with-mutations-icon.png]] Find regulatory regions with mutations
;Provider
:[[Biosoft]]
;Class
:{{Class|biouml.plugins.genomeenhancer.analysis.FindRegulatoryRegionsWithMutations}}
;Plugin
:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]

==== Description ====
This method creates a track of regulatory regions for input genes using information about genomic variations from mutation track. These regulatory regions can be used in "[[Site search on track (analysis)|Site search on track]]". Analysis scans genes extended with flanking regions by window of input size (promoter from and promoter to, 1100bp by default). It finds position with highest sum of mutation weights that got into the "window". If no mutations 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
* '''Mutation track''' – Track with weighted muations
* '''Weight''' (expert) – Track property for weight
* '''Gene''' (expert) – Track property for gene id
* '''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

[[Category:Analyses]]
[[Category:Genome enhancer (analyses group)]]
[[Category:Biosoft analyses]]
[[Category:Autogenerated pages]]