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Review
. 2014 Jun 15;68(1):38-47.
doi: 10.1016/j.ymeth.2014.03.007. Epub 2014 Mar 15.

Navigating and mining modENCODE data

Nathan Boley  1 , Kenneth H Wan  2 , Peter J Bickel  3 , Susan E Celniker  4
Affiliations
Review

Navigating and mining modENCODE data

Nathan Boley et al. Methods. .

Abstract

modENCODE was a 5year NHGRI funded project (2007-2012) to map the function of every base in the genomes of worms and flies characterizing positions of modified histones and other chromatin marks, origins of DNA replication, RNA transcripts and the transcription factor binding sites that control gene expression. Here we describe the Drosophila modENCODE datasets and how best to access and use them for genome wide and individual gene studies.

Keywords: Chromatin; Drosophila; Mining; Transcription; modENCODE.

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Figures

Figure 1
Figure 1
modMine Genome Browser view of the Abdominal-B (Adb-B) gene region. 1) Sections for browser customization. 2) Data displayed in tracks. 3) Individual track features.
Figure 2
Figure 2
FlyBase gene report for Abdominal-B (Abd-B). 1) Current FlyBase version and Gene name. 2) Navigation bar for different sections: “Tools” section is useful for custom queries, batch downloads, and identifier conversion; “Files” section is useful for downloads; “Documents” section contains the Release Notes and Reference Manual; “Archives” section contains prior versions. 3) “Jump to Gene” bar, enter exact gene name here. 4) Link to GBrowse, choose the “Expression/Regulation” View to see modENCODE RNA-Seq data. 5) Links to download sequence files. 6) Other gene information, including high-level view of modENCODE Expression Data”.
Figure 3
Figure 3
Continuation of FlyBase gene report page for Abdominal-B (Adb-B), showing expanded “Expression Data” and “High-throughput Expression Data” subsections.
Figure 4
Figure 4
UCSC Genome Browser, displaying a custom track hub for the Abdominal-B (Abd-B) gene. The “My Data” menu allows users add custom sessions, tracks, and track hubs, Custom tracks are the simplest way to add custom tracks, but are removed automatically after a few weeks if they have not been accessed. Track hubs can be hosted on the user’s local servers and thus the data will not be automatically removed.
Figure 5
Figure 5
Heat map visualization of modENCODE ChIP-Seq (left) and RNA-Seq (right) data.
See this image and copyright information in PMC

References

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