Table 3.

All links mentioned in this publication are collected in this table

ENCODE: http://encodeproject.org

Genome Browser: http://genome.ucsc.edu

Five-level scoring metric filtering options: http://www.gencodegenes.org/gencode_biotypes.html

UCSC download server (human): http://encodeproject.org/ENCODE/downloads.html

UCSC download server (mouse): http://encodeproject.org/ENCODE/downloadsMouse.html

ENCODE Analysis Hub: http://genome.ucsc.edu/cgi-bin/hgHubConnect

ENCODE uniform processing pipeline: http://code.google.com/p/align2rawsignal

GEO ENCODE summary page: http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html

Integrative Analysis of ENCODE data: http://encodeproject.org/ENCODE/analysis.html

ENCODE portal: Quality Metrics: http://encodeproject.org/ENCODE/qualityMetrics.html

ENCODE portal: Software tools: http://encodeproject.org/ENCODE/softwareTools.html

ENCODE portal: Analysis tools: http://encodeproject.org/ENCODE/analysisTools.html

ENCODE portal: platform characterization: http://encodeproject.org/ENCODE/platform_characterization.html

ENCODE portal: publications: http://encodeproject.org/ENCODE/pubs.html

ENCODE file formats: http://genome.ucsc.edu/FAQ/FAQformat.html#ENCODE

Tutorial and training materials by OpenHelix: http://openhelix.com/ENCODE2

Introductory tutorial: http://openhelix.com/ENCODE

OpenHelix QRC: http://www.openhelix.com/cgi/qrcOrder.cgi

ENCODE announcement list: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/encode-announce