NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

ENCODE Analysis Working Group (AWG)

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The Analysis Working Group is responsible for integrative analyses of Encode data. Analysis priorities are set by the Analysis Working Group Coordinating Committee, and carried out by the members of the AWG calling on the appropriate expertise and resources as is necessary. Some groups are part of the Data Analysis Center (DAC) funded to provide integrative analysis support and tools to the consortium. However membership of AWG is open to anyone who is able and willing to perform an analysis and is willing to work to the AWG schedules and demands.

Modus Operandi

Analyses are defined by the Analysis Working Group CC and prioritised by them

Members of the AWG volunteer for are assigned analyses, and register them through the wiki by curating a page. Initial steps are to write a short outline. Further steps are to update the page with analysis details and results as they are achieved.

The project manager (Ian Dunham) monitors progress on the analysis and will call for updates through the technical analysis phone calls, and otherwise.

Analysis group submits integrative analysis to DCC as consensus method is achieved.

Locations of standardized data for joint worm/fly/mouse/human analysis

If you would like editing permission please send an email to Anshul Kundaje (

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Mouse / Human RNA data files

Integration Paper Resources

ENCODE publication tracking for Nature

Nature will be listing ENCODE publications on their website, which will provide publicity for the project. In addition to the 30 papers in the official package, they would like to include other ENCODE papers that appear between September 5th and December 1st. They will update their site approximately every other week. In order for Nature to do this, we must report the papers to them. Please add information about ENCODE publications that are not part of the official package to the publication tracking spreadsheet below as soon as you can to have your publications included.

It is especially important for us to provide Nature with a list of ENCODE publications outside of the package that will be published in the first week (JBC, Cell, Science papers come to mind), and make sure Nature is aware of them.


Conference Calls

Date Time Group
Monday 1st Mar 8pm (GMT), 3pm (EST), noon (PST) Variation
Monday 1st Mar 6pm (GMT), 1pm (EST), 10am (PST) Large Scale Integration
Tuesday 2nd Mar 6pm (GMT), 1pm (EST), 10am (PST) Small Element Integration
Wednesday 3rd Mar 3pm (CST), 2pm (GMT), 9am (EST), 6am (PST) RNA
Thursday 4th Mar 6pm (GMT), 1pm (EST), 10am (PST) Comparative

Data Freezes

The next data freeze is 15th January 2011

Previous data freezes have been:

  • 21st June 2010
  • 15th January 2010
  • 30th September 2009
  • July 1st 2009.
  • February 2009.
  • November 2008. (Friday 21st November (end of week before Thanksgiving) was agreed as the data freeze date in the AWG_CC call of 4th September 2008).



Current Analyses by Task Group

A division of the submitted datasets into Broad, Peak or mixed classes in excel format is available (25-02-2009).

Email tags

At the December 2008 workshop meeting it was suggested that we continue to use the AWG mail list for all subgroup activity. To enable this please use the following subject tags with which to prefix the subject lines of emails, to facilitate mail processing, either by software, or by eye  ;-) . Please use the prefix for mails that are of interest primarily to that task group. Mails for the whole group should not have the prefix as before.

For ease of visual recognition use the prefix in upper case with the colon and a whitespace character before the subject.

  • ELEMENTS: Elements task group
  • RNA: RNA task group
  • LARGE-SCALE: Large-scale Behaviour task group
  • COMPARATIVE: Comparative Sequence Analysis task group
  • INTEGRATION: Data integration task group
  • VARIATION: Genome variation task group
  • STATISTICS: Statistics task group
  • ANNOTATION: Annotation task group
  • CELL: Gene expression for cellular phenotyping task group
  • STRATEGY: Strategy task group (although this might also be the ENCODE_AWG_CC list)

This is really just to facilitate communication while allowing everyone to follow the threads. Lets see how it works for now, and we can modify if we need to.

Future analyses

For future analyses that need to be done and not yet assigned, or things we think ought to be done.

Sandbox (Ideas)

General playground for ideas of things that might be useful to do.

DAC Groups

Birney Group (EBI).

Bickel Group (UC Berkeley)

Hardison/Miller Group (Penn State Hardison Miller).

Haussler/Kent Group (UCSC HausslerKent)

Gerstein Group (Yale)

Noble Group (U. Washington)

Weng Group (Boston U.)

Mail Addresses

If you are a subscriber to the mailing list, you can get a full list of all the subscribers by sending a message to with "review ENCODE_AWG noheader" as the body text.

Email Addresses for Analysis Working Group members (as of 4 December 2008) are:

  • Bronwen Aken
  • Raymond Auerbach
  • Brad Bernstein
  • Peter Bickel
  • Ewan Birney
  • Nathan Paul Boley
  • Alan Boyle
  • Ben Brown
  • Piero Carninci
  • Greg Crawford
  • Chao Cheng
  • Carrie Davis
  • Job Dekker
  • Thomas Derrien
  • Laura Dillon
  • Sarah Djebali
  • Marc Domanus
  • Michael Dorschner
  • Tim Dreszer
  • Ian Dunham
  • Laura Elnitski
  • Chuck Epstein
  • Jason Ernst
  • Ghia Euskirchen
  • Elise Feingold
  • Paul Flicek
  • Terry Furey
  • Ajish George
  • Mark Gerstein
  • Mark Gerstein
  • Tom Gingeras
  • Paul Giresi
  • Peter Good
  • Brenton Graveley
  • John Greally
  • Eric Green
  • Phil Green
  • Chittibabu Guda
  • Roderic Guigo
  • Lukas Habegger
  • Greg Hannon
  • Ross Hardison
  • Bob Harris
  • Jennifer Harrow
  • Rachel Harte
  • David Haussler
  • Javier Herrero
  • Michael Hoffman
  • Roger Hoskins
  • Cedric Howald
  • Haiyan Huang
  • Tim Hubbard
  • Vishy Iyer
  • Edwin Jacox
  • Laura Kavanaugh
  • Damian Keefe
  • Manolis Kellis
  • Jim Kent
  • Peter Kharchenko
  • Ekta Khurana
  • Felix Kokocinski
  • Anshul Kundaje
  • Julien LaGarde
  • Eric Lai
  • Bryan Lajoie
  • Gail Lamoureux
  • JMLandolin@LBL.GOV Jane Landolin
  • Timo Lassmann
  • Soohyun Lee
  • Jo Leonardo
  • Qunhua Li
  • Qunhua Li
  • Shirley Liu
  • Zhi John Lu
  • Dave MacAlpine
  • Elliott Margulies
  • Ken McCue
  • Gayle McEwen
  • Larry Meyer
  • Tarjei Mikkelsen
  • Webb Miller
  • Ali Mortazavi
  • Mike Muratet
  • Rick Myers
  • Bill Noble
  • Brian Oliver
  • Peter Park
  • Benedict Paten
  • Shirley Pepke
  • Hena Petrovich Shulha
  • Mike Pheasant
  • Barbara Pusey
  • Debasish Raha
  • Rami Rauch
  • Tim Reddy
  • Nicolas Robine
  • Kate Rosenbloom
  • Joel Rozowsky
  • Yijun Ruan
  • Richard Sandstrom
  • Parantu Shah
  • Gavin Sherlock
  • Noam Shoresh
  • Mike Snyder
  • George Stamatoyannopoulos
  • John Stamatoyannopoulos
  • James Taylor
  • Scott Tenenbaum
  • Bob Thurman
  • Michael Tolstorukov
  • Jeltje van Baren
  • Yue Wan
  • Jie (Jessie) Wang
  • Ting Wang
  • Chia Lin Wei
  • George Weinstock
  • Zhiping Weng
  • Steven Wilder
  • Barbara Wold
  • Adam Woolfe
  • Simon Xi
  • Jia Xu
  • Mary Yang
  • Zheng Zha
  • Deyou Zheng


  • When is the data freeze?
    The next data freeze is 15th January 2011
    Previous data freezes have been:
    • 21st June 2010
    • 15th January 2010
    • 30th September 2009
    • July 1st 2009.
    • February 2009.
    • November 2008. (Friday 21st November (end of week before Thanksgiving) was agreed as the data freeze date in the AWG_CC call of 4th September 2008).
  • How do I become a member of the AWG mailing list?
    Mail Caroline Kelly ( at NHGRI with your request. You probably want to join the consortium list as well
  • Where is the analysis paper outline, and vignettes?
  • Where to put files to use for, or generated by the analysis?
    see Files_for_ENCODE_Analysis.