How Can I Get Coordinates Of Regulatory Elements Form Encode Published Dataset

Question

[Xiaofeng]

As the UCSC website showed us, the ENCODE project used chip-seq to find regulatory elements of human genome. Different type of antibody can combine to special element on DNA chain. I downloaded TFBS file containing the narrowPeak file and got coordinate of some elements. However, I could not get some more important elements directly, such as promoter, insulator, enhancer, silencer and LCR. There are some wig format files on UCSC, but those files just give tracks of those elements like the list below: http://genome.ucsc.edu/ENCODE/downloads.html

Regulation Super-track
DNase Clusters    Digital DNaseI Hypersensitivity Clusters from ENCODE
Layered H3K27Ac    H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from NCODE
Layered H3K4Me1    H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
Layered H3K4Me3    H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
Transcription    Transcription Levels Assayed by RNA-seq on 7 Cell Lines from ENCODE
Txn Factor ChIP    Transcription Factor ChIP-seq from ENCODE

How can I get coordinate of above regulatory elements? Thanks for your response!

Answer 1

[Gjain]

hi Xiaofeng,

you can do that in two ways:

1. download directly:

   • go to this link
   • then in the regulation section, for each group for example(ENCODE Transcription):
     • you can go to for example ,H3K4Me1 Mark and the link for that is http://hgwdev.cse.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2851161&g=wgEncodeRegMarkH3k4me1&hgTracksConfigPage=configure
     • from there you can hit the download button at the middle of page and it will take you to this http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k4me1/
   • I would suggest you to use wget for easier download.
   • Once you get the file you can use the tools from the "utilities" section in genome browser to convert bigwig file to bed file which will have coordinates.

2. Alternatively , which is a simple method is to go the table browser:

   • http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?command=start
   • You can select the clade = mammal, genome = human, assembly = HG19 or whatever you are working on.
   • In the group chose "Regulation" and then in the "track" you can choose different regulatory elements.
   • From the table you chose replicates, peaks or raw signals or hot spots.
   • In region you need to use "Define regions" and paste all the encode regions for Hg19, if you are working on HG18, then you will have an option for ENCODE REGIONS.
   • then if you scroll down to "output format" depending on what you want which in this case coordinates... choose "BED - browser extensible data" format.
   • you can either give the name of the output file which is highly recommended or leave it blank and
   • Hit the "get output" button.

One important thing is that if you are using the second method then you have to make sure that files which are bigger than say 100,000 lines... then you have change that limit.

I hope this helps.

[Xiaofeng]

Hi Gjain Thanks for your response about this problem. I followed the first advice to get data. And after searching on the UCSC website, I find that there is a bigWigToBedGraph tool. Is it the one I can use to get the coordinates of bigwig files? But I did not know how to use the tool on my own pc. Wait for your response again. My email is [e-mail].

[Gjain]

Hi Xiaofeng, If you are using a windows computer then you should install cygwin (http://www.cygwin.com/) and then run the program bigWigToBedGraph using these instruction:

[Gjain]

bedGraphToBigWig in.bedGraph chrom.sizes out.bw where in.bedGraph is a four column file in the format: [?] [?] [?] [?] and chrom.sizes is two column: [?] [?] and out.bw is the output indexed big wig file. The input bedGraph file must be sorted, use the unix sort command: sort -k1,1 -k2,2 unsorted.bedGraph > sorted.bedGraph options: -blockSize=N - Number of items to bundle in r-tree. Default 256 -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024 -unc - If set, do not use compression.

[Gjain]

bedGraphToBigWig v 4 - Convert a bedGraph program to bigWig.

The bigwig file will give you the coordinates.

Let me know if you have any other question.

[Xiaofeng]

Hi Gjain, as you known, bigWigToBedGraph tool from the "utilities" section is a binary file. I don't know how to use that tool on Linux environment.

[Gjain]

Hi Xizfeng,

Here is what you can do.

1. you can download and install cygwin cygwin.com).
2. once you open it you will linux environment.
3. now download the binary bigWigToBedGraph and put it in the folder where your bigwig files are.
4. Now open cygwin and you will see some ending with a $ type cd path_to_the_folder_containing_files_and_binary
5. now type and enter ./bigWigToBedGraph your_bigwig_file.bigWig output_bedGraph.bedgraph

This should convert it for you. Once you have the bedgraph file, you can the coordinates from that file.

Please let me know if you have any troubles.