Annotaion Based On The Genomic Range

Question

[ancient_learner]

Hello all I have some data like this related to mouse genome

chr1 3000000 3000090
chr2 4339993 4389898
chr5 3000330 3003339
chr7 3323233 3390393

I know that by using UCSC genome browser we can get the information related to the presence of genes, proteins at those regions. however i am more interested in identifying all functional elements (may be promoters, enhancers tfs etc) with in that region. is there any way to do that. With in UCSC is there any option like that?

Answer 1

[Alex Reynolds]

[Bioinformatist Newbie]

@Alex Can you please help me with this question How to assigning Active Enhancer to every genes within 10 kb region?. Thanks

Answer 2

[Sukhi Singh]

You have to define promoters and enhancers by yourself, there is no proper definition. Get a list of all genes, refer this Fetching Transcription Start And End For A Custom Gene List From Ucsc (Hg18/Ncbi36) for that, change the organism and build. If you know R or any other language, add and subtract the number of bases or a region of some KB (eg +/-1KB) from the TSS (labelled as txStart in the table) strand specifically. This number depends on how you define promters and then use the intersectBed tool from Bedtools. Check this How To Determine Overlaps From Coordinates or manual for usage.

For Enhancers, some people say they are 5-10KB far, but a way to do it would be overlay the ChIP-Seq data(peaks) of p300 (marker for enhancers) on the genome to get the list of enhancers and then intersect with you own file If you know Galaxy, then this might be helpful, From BED Coordinates to Genes

Cheers

[ancient_learner]

Thank you sukhdeep for your reply. i have obtained the chip-seq from GEO database. An enhancer might be of 500 bps (avg). but the chip-seq data shows only the areas where p300 binding is present. so i can regard +/- 200bps from the peak start region of chip-seq as enhancer?

Answer 3

[Irsan]

If you want information on annotating genomic intervals in general see some similar Biostars-posts:

• Annotating Genomic Intervals
• Databases Of Annotated Regulatory Sequences
• Software For Analyzing Gene Annotation On Genomes
• Is There A Better Promoter Annotation Than Just Taking The 5-Prime Ends Of Ucsc Known Genes"?
• Annotation Of Genomic Regions
• R Package For Annotations Of Genomic Regions

Answer 4

[Emily]

No idea about UCSC, but you can do that using the Ensembl Region Report tool.http://www.ensembl.org/tools.html

This allows you to inout genomic coordinates, then see everything that's within them. There's a tick box list where you can choose what to see. The options are:

Genes, Transcripts and Proteins

Genomic Sequence

Constrained Elements (Conserved Regions)

Variations (SNPs and InDels)

Structural Variations (CNVs etc)

Regulatory Features

[ancient_learner]

Thank you for the reply. i am more interested in Constrained Elements (Conserved Regions) feature. does this tool supports graphical view? I know ECR browser does but I cannot give each coordinate manually.

[Emily]

This will just give you a list.

Answer 5

[Ashutosh Pandey]

If you are comfortable with little programming and unix or you can use snpEff software and set up databases for different genomic elements like genes, transcription factor binding sites, enhancers etc then it is pretty simple thing to do. You can get most of the files you need from ENSEMBL

http://useast.ensembl.org/info/data/ftp/index.html

The cis-regulatory elements information could be derived from Regulations gff file and Regulation data files.