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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Introduction

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

https://docs.google.com/spreadsheet/ccc?key=0Am6FxqAtrFDwdFRNT0xJU3NiTklTX2d3bHFOUkN0RkE

If you would like editing permission please send an email to Anshul Kundaje (anshul@kundaje.net)

<embedurl> https://docs.google.com/spreadsheet/ccc?key=0Am6FxqAtrFDwdFRNT0xJU3NiTklTX2d3bHFOUkN0RkE </embedurl>

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.

<embedurl> https://docs.google.com/spreadsheet/ccc?key=0AuXBTeCNKFnTdFZrdTI2VHotUFVWUWdrUjQtYTdvbmc</embedurl>

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).

Workshops

Resources

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 listserv@list.nih.gov with "review ENCODE_AWG noheader" as the body text.

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

  • ba1@sanger.ac.uk Bronwen Aken
  • raymond.auerbach@yale.edu Raymond Auerbach
  • bernstein.bradley@mgh.harvard.edu Brad Bernstein
  • bickel@stat.berkeley.edu Peter Bickel
  • birney@ebi.ac.uk Ewan Birney
  • npboley@gmail.com Nathan Paul Boley
  • alan.boyle@duke.edu Alan Boyle
  • ben@newton.berkeley.edu Ben Brown
  • carninci@postman.riken.jp Piero Carninci
  • greg.crawford@duke.edu Greg Crawford
  • chao.cheng@yale.edu Chao Cheng
  • davisc@cshl.edu Carrie Davis
  • job.dekker@umassmed.edu Job Dekker
  • thomas.derrien@crg.es Thomas Derrien
  • dillonl@mail.nih.gov Laura Dillon
  • sarah.djebali@crg.es Sarah Djebali
  • mdomanus@anl.gov Marc Domanus
  • mod@u.washington.edu Michael Dorschner
  • tdreszer@soe.ucsc.edu Tim Dreszer
  • dunham@ebi.ac.uk Ian Dunham
  • elnitski@mail.nih.gov Laura Elnitski
  • epstein@broad.mit.edu Chuck Epstein
  • jernst@mit.edu Jason Ernst
  • ghia.euskirchen@yale.edu Ghia Euskirchen
  • feingole@mail.nih.gov Elise Feingold
  • flicek@ebi.ac.uk Paul Flicek
  • terry.furey@duke.edu Terry Furey
  • ajishg@gmail.com Ajish George
  • mark.gerstein@yale.edu Mark Gerstein
  • encode@gersteinlab.org Mark Gerstein
  • gingeras@cshl.edu Tom Gingeras
  • paulg@email.unc.edu Paul Giresi
  • goodp@mail.nih.gov Peter Good
  • graveley@neuron.uchc.edu Brenton Graveley
  • jgreally@aecom.yu.edu John Greally
  • egreen@nhgri.nih.gov Eric Green
  • phg@u.washington.edu Phil Green
  • cguda@albany.edu Chittibabu Guda
  • roderic.guigo@crg.es Roderic Guigo
  • lukas.habegger@yale.edu Lukas Habegger
  • hannon@cshl.edu Greg Hannon
  • rch8@psu.edu Ross Hardison
  • rsharris@bx.psu.edu Bob Harris
  • jla1@sanger.ac.uk Jennifer Harrow
  • hartera@soe.ucsc.edu Rachel Harte
  • haussler@soe.ucsc.edu David Haussler
  • jherrero@ebi.ac.uk Javier Herrero
  • mmh1@washington.edu Michael Hoffman
  • hoskins@fruitfly.org Roger Hoskins
  • cedric.howald@unil.ch Cedric Howald
  • hhuang@stat.berkeley.edu Haiyan Huang
  • th@sanger.ac.uk Tim Hubbard
  • vishy@mail.utexas.edu Vishy Iyer
  • jacoxe@mail.nih.gov Edwin Jacox
  • lak10@duke.edu Laura Kavanaugh
  • dkeefe@ebi.ac.uk Damian Keefe
  • manoli@mit.edu Manolis Kellis
  • kent@soe.ucsc.edu Jim Kent
  • pkharche@receptor.med.harvard.edu Peter Kharchenko
  • ekta.khurana@yale.edu Ekta Khurana
  • felix@kokocinski.net Felix Kokocinski
  • akundaje@stanford.edu Anshul Kundaje
  • julien.lagarde@crg.es Julien LaGarde
  • laie@mskcc.org Eric Lai
  • Bryan.Lajoie@umassmed.edu Bryan Lajoie
  • gail.lamoureux@yale.edu Gail Lamoureux
  • JMLandolin@LBL.GOV Jane Landolin
  • timolassmann@gmail.com Timo Lassmann
  • duplexa@bu.edu Soohyun Lee
  • leonardo@cshl.edu Jo Leonardo
  • qunhua.li@gmail.com Qunhua Li
  • qli@stat.berkeley.edu Qunhua Li
  • xsliu.dfci@gmail.com Shirley Liu
  • zhi.lu@yale.edu Zhi John Lu
  • david.macalpine@duke.edu Dave MacAlpine
  • elliott@nhgri.nih.gov Elliott Margulies
  • mccue@caltech.edu Ken McCue
  • mceweng@mail.nih.gov Gayle McEwen
  • larrym@soe.ucsc.edu Larry Meyer
  • tarjei@broad.mit.edu Tarjei Mikkelsen
  • webb@bx.psu.edu Webb Miller
  • alim@its.caltech.edu Ali Mortazavi
  • mmuratet@hudsonalpha.org Mike Muratet
  • rmyers@hudsonalpha.org Rick Myers
  • wnoble@u.washington.edu Bill Noble
  • briano@niddk.nih.gov Brian Oliver
  • peter_park@harvard.edu Peter Park
  • benedict@soe.ucsc.edu Benedict Paten
  • spepke@cacr.caltech.edu Shirley Pepke
  • hena@bu.edu Hena Petrovich Shulha
  • mikep@soe.ucsc.edu Mike Pheasant
  • bpusey@hudsonalpha.org Barbara Pusey
  • debasish.raha@yale.edu Debasish Raha
  • rrauch@stanford.edu Rami Rauch
  • treddy@stanford.edu Tim Reddy
  • robinen@mskcc.org Nicolas Robine
  • kate@soe.ucsc.edu Kate Rosenbloom
  • joel.rozowsky@yale.edu Joel Rozowsky
  • ruanyj@gis.a-star.edu.sg Yijun Ruan
  • sull@u.washington.edu Richard Sandstrom
  • parantu.shah@gmail.com Parantu Shah
  • sherlock@genome.stanford.edu Gavin Sherlock
  • nshoresh@broad.mit.edu Noam Shoresh
  • michael.snyder@yale.edu Mike Snyder
  • gstam@u.washington.edu George Stamatoyannopoulos
  • jstam@u.washington.edu John Stamatoyannopoulos
  • james.taylor@emory.edu James Taylor
  • stenenbaum@albany.edu Scott Tenenbaum
  • rthurman@u.washington.edu Bob Thurman
  • tolstorukov@gmail.com Michael Tolstorukov
  • jeltje@wustl.edu Jeltje van Baren
  • ywan@stanford.edu Yue Wan
  • jessie.wangjie@gmail.com Jie (Jessie) Wang
  • tingwang@soe.ucsc.edu Ting Wang
  • weicl@gis.a-star.edu.sg Chia Lin Wei
  • geowei@mac.com George Weinstock
  • zhiping.weng@umassmed.edu Zhiping Weng
  • swilder@ebi.ac.uk Steven Wilder
  • woldb@caltech.edu Barbara Wold
  • woolfea@mail.nih.gov Adam Woolfe
  • simonxi_home@yahoo.com Simon Xi
  • xujia@bu.edu Jia Xu
  • yangma@mail.nih.gov Mary Yang
  • zhengzha2000@gmail.com Zheng Zha
  • dzheng@aecom.yu.edu Deyou Zheng

FAQ

  • 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 (caroline.kelly@nih.gov) 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.