In this example we seek to overlap ENCODE short RNA reads onto known small RNA loci in order to extract their expression level across a selected subset of cell lines and sub cellular fractionnation http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=nMzOtlm8JZ6n5x9u9B5t1B;loc=hg19::chr19:54134256..54310581
- 1 Retrieving K562 cells sub-cellular and sub-nuclear short RNA fractions from ENCODE
- 2 Adding a track with known sno & microRNA from UCSC
- 3 Displaying only reads co-localized with known microRNA
- 4 Displaying sno and miRNA transcript short RNA expression level
- 5 Retrieving a tab delimited table of sno and miRNA transcript short RNA expression level
Retrieving K562 cells sub-cellular and sub-nuclear short RNA fractions from ENCODE
DEX based datasource selection
The Data Explorer tab enable to retrieve all the K562 cells sub-cellular and sub-nuclear short RNA fractions from ENCODE.
We first select the "Expression experiments" sub-tab and search for wgEncodeCshlShortRnaSeqK562.
This retrieves 19 datasets containing the raw mappings of short RNA and not os short fractions from CSHL extracted from various sub-cellular and sub-nuclear fractions (cytosol, nucleus, nucleolus, ...).
We then create a single track from the union of all those sources (we will see further in this case study, how can can very easily breakdown this track into) by selecting them all and clicking on the "build tracks" button located on the upper right corner of the DEX page.
Doing so, opens a configure new track from data sources dialogue box allowing us to specify how we want the data to be displayed.
We will display the data as histogram representing the summed level of expression rather than displaying each tags and select area as the region rather than the default "5'end".
We also rename this track as Encode Cshl ShortRna K562
After clicking on "accept config" we are back to the DEX page and the upper right panel now show "1 tracks" ready to be displayed.
Clicking on "visualize", sends us to the ZENBU genome browser page with one visible track displaying the piling up of K562 cells sub-cellular and sub-nuclear short RNA fractions mapped reads
Adding a track with known sno & microRNA from UCSC
In order to compare the localization of the short RNA mapped tags to known microRNA, we decide to add the relevant track directly from the Glyph interface.
Going to the mir rich region hg19::chr19:54134265-54310581, we can see clearly see overlapping high intensity short RNA signal over known loci
Displaying only reads co-localized with known microRNA
We may want to only see reads that overlap with already known transcripts.
To do so, we first duplicate the "Encode Cshl ShortRna K562" track by clicking on the yellow square icon located along with the other track action icons on the upper left corner of the track.
We will then edit this track to specifically filter of overlapping reads with small RNA loci
We select on the "modify config" grey gear icon on the upper right corner of the replicated track.
This opens up the "track editing dialog box". In order to display only reads overlapping sno and mirRNA, in the "Stream Processing script" subpanel we select the processing script entitled hg19 sno-mirRNA based filtering
Displaying sno and miRNA transcript short RNA expression level
Not only would we want to see reads overlapping miRNA, we may want to get an overview of the entire transcript expression level (as the sum of all reads overlapping its exons)
To do so, we again duplicate the "Encode Cshl ShortRna K562" track and the "modify config" grey gear icon on the upper right corner of the track we just duplicated. This opens up the "track editing dialog box".
In the "Stream Processing script" subpanel we select the processing script entitled "hg19 sno-mirRNA based filtering".
Since we are interested in loci centric expression levels and msno mirRNA annotation do not have any intron/exon structure we modify the "Visualization" subpanel values and select "thick_arrow" as well as "color by score" and a color gradient of our choosing.
Retrieving a tab delimited table of sno and miRNA transcript short RNA expression level
Zenbu allows for scanning the entire genome using the very same processing as is displayed in the genome browser. Processing in done in parallel and is completed as fast as CPU, memory and disk access is allowed by concurrent process on the zenbu server
To download the entire , simply click on the download icon of the track (small blue downward arrow)
This opens up a panel allowinf the download as OSCtbale (aka a simple tab delimited file), BED or GTF format of either the visible area, a entire chromosome, or the complete genome
Choosing the later, we can see that ZENBU already computed 25% of the entire track.
Once completed it will be available for full download either from this very interface
Or from the User / Downloads interface, which also allows the monitoring of ther track cahche building
When completed "Downloading" into a file or the browser page can be made in any format ...
Here we chose tab delimilited (OSCtable) format with minimal metadadata content