v7 major update - Long Range interaction view, SVG output

It's been quite a while since our last post in June. We've been busy preparing some big updates on our dear Epigenome Browser, and this morning we're very happy to deploy them on our public server so all of our dear users could benefit.

Long range genome interaction data visualization

The "long range genome interaction" data sets, as those generated by 5C, Hi-C, and ChIA-PET, capture 3-dimensional chromatin arrangement in cell nucleus. This type of data is very promising in improving our interpretation of high-throughput genomics assay results (e.g. TF ChIP-Seq, histone mark ChIP-Seq), and more importantly understanding how eukaryotic genomes function as nonlinear systems.

Now you can explore the long-range interaction data sets using our Browser! Just click the following link to see it in action:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&coordinate=chr7:26663835-28123541&gftk=IMR90_40kb_hindIII_combined,trihm,wgEncodeGisChiaPetK562CtcfInteractionsRep1,arc,refGene,full&hmtk=GSM521898,GSM521897,GSM521895,GSM521901,GSM469970,GSM521900,GSM521899,GSM788085_1,GSM733692_1,GSM608165_1,GSM945298_1,GSM945279_1,GSM945165_2,GSM945299_1,GSM945279_2,GSM945278_1,GSM945278_2,GSM945298_2,GSM945297_1,GSM945299_2,GSM733680_1,GSM945165_1,GSM945297_2,GSM733651_1,GSM521911,GSM521909,GSM733653_1,GSM521887,GSM469967,GSM469966,GSM521889,GSM469968,GSM733656_1,GSM945228_1,GSM608167_1,GSM945228_2,GSM733658_1,GSM521912,GSM469973,GSM521914,GSM521913,GSM469974,GSM733778_1,GSM607494_1,GSM733776_1&metadata=Histone%20Mark,11310,14018

This humongous URL yields a view with two long range interaction tracks and a set of histone mark tracks. With a few twists you can achieve a view like the following screen shot:

The triangular heatmap shows data from a Hi-C assay on IMR90 cells (Dixon JR, Bing Ren,Nature 485(7398):376-80).

The arcs shows data from a ChIA-PET assay on K562 cells (ENCODE Project data).

The bunch of histone mark tracks are active/repressive histone marks on IMR90 and K562 alike. Most of them are obtained from ENCODE project.

The region on chr7 contains the HOXA gene cluster.

We are busy preparing a manuscript for this exciting new update, and the above example constitutes part of a figure in the manuscript.

We invite our users to explore this function (tell me any bugs, xzhou82 AT gmail). Some helpful tips are available in a short chapter from the user manual: http://epigenomegateway.wustl.edu/browser/manual/#c-c

Presently, 44 long-range assay tracks for human, and 14 for mouse are available through our Browser, all of which are public data sets. New ones will be added whenever they are available.

SVG output

After so many earnest requests, the high-quality Browser Shot output is finally implemented. To do it, click "Apps" button in the small toolbox and select SVG option:

The generated SVG file can be viewed in your web browser. The file is usually large so please be patient while it's been transferred. Firefox and Chromium show no problem at displaying such files. With Chromimium you can print the SVG file to a PDF file.

The SVG file output function is totally different with UCSC's PDF/PS output function. Everything is done on client-side, no server-side rendering is involved.

This function is still a prototype. Let me know if it breaks. I'm still working to enable SVG outputs for the Bird's Eye View and the Companion panel from the long-range track view.

We sincerely recommend the Chromium web browser (http://www.chromium.org/Home), it is absolutely free, and available for all platforms. Epigenome Browser loves it!

v6 release - major bug fix

This code release comes with major bug fix. Please go to the source code archive on our server or Dropbox to download.

Bug fix

When the Browser was showing data at basepair level, the use of coordinate was wrong at multiple places:

1. requesting data for the genomic region exposed by panning
2. placing the blue square box indicator on the small chromosome ideogram on the top left of the page
3. on obtaining genomic sequence for the region under view

Now these problems that were visible to us have been fixed. If you notice any more, comment on our blog and let us know!

Minor improvements

Y axis scale can now be drawn in genome heatmap:

To show the scale, increase track height to 20 or more pixels and the scale will draw automatically on the left side of the canvas.

And here's a slight improvement on the control panel. At "Heatmap track" panel, contents for "Data sets" and "Configure track selection panel" have been re-styled as "tab-page". Click any of the two buttons at top of panel to see:

This tab-page style is also applied to Bird's eye view panel.

Finally, we start depositing our source code archives into a dropbox folder which is publicly accessible. I guess this serves a nice fallback in case tornado strikes our server room and demolishes the servers. The user manual however is not included in the archive anymore to shrink size as there's only a scant 3GB space with my account so it needs to be lean (besides Xin hasn't updated his user manual since stone age).

v5 release - gene indicating function

Version 5 of Wash U Browser is available now. Follow this link and obtain the source code: http://epigenomegateway.wustl.edu/source/

New features

Sometimes the genes can only have parts but not the whole displayed in genome browser. For example when viewing a short interval centering over transcription start sites of genes in Gene Set View:

Genes in the gene track are partially displayed in above view. As a result it would be difficult for user to view the gene's entire structure unless he/she quits Gene Set View and relocates to this gene.

Now this problem is solved with the gene indication function. You only need to click on this gene to invoke the tooltip balloon and it will show you:

On the top of balloon, a small graph is drawn to display the gene in its entirety. As usual, the thin lines indicate introns, thick blocks are exons, and the smaller blocks at each end are untranslated regions (UTRs). A yellow box marks the part of the gene that's currently visible in the gene track.

Size of this graph is constant, it won't change with the actual length of the gene or balloon size. And the graph won't show up for genes completely displayed in the track. Currently there's no clickable function attached to this graph, but I wonder if user will find it useful to be able to control the plotting color by clicking it? Anything else?

Like I promised, the gene tooltip balloon is turning into a fully loaded dashboard. More interesting and useful functions will be added here to let you know, recognize, study, and operate the gene under your focus. Hang on with us!

Bug fixes

1. Imprecise gene placement in the gene track during gene set view is fixed
2. Imprecise indicator (blue rectangle) placement over small chromosome ideogram on top left corner of the page is fixed.