and a model for robust community participation Wyeth W. Wasserman - - PowerPoint PPT Presentation

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and a model for robust community participation Wyeth W. Wasserman - - PowerPoint PPT Presentation

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The wiki-based Transcription Factor Encyclopedia and a model for robust community participation Wyeth W. Wasserman 30 November 2010 http://www.cisreg.ca/tfe Transcription Factors 101 Diverse set of proteins sharing common functional role

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The wiki-based Transcription Factor Encyclopedia and a model for robust community participation

Wyeth W. Wasserman

30 November 2010 http://www.cisreg.ca/tfe

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Transcription Factors 101

  • Diverse set of proteins sharing common

functional role in the regulation and production of RNA transcripts

  • Present in all species
  • For the purpose of today’s talk, TF will refer

to the subset of the proteins that bind to DNA in a sequence-specific manner

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Transcription Factors 102

  • Act cooperatively with other TFs to confer

specific patterns of gene activity in response to developmental, physiological and environmental conditions

  • Much of their function is defined by protein-

protein interactions

  • Understanding TFs is key to understanding

developmental and tissue differentiation

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Resources for the Study of TFs

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Wiki-in-the-classroom

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TFe

Goal: create an online encyclopedic collection of reviews about well-studied TFs, combining a mixture of expert-curated and automatic content. http://www.cisreg.ca/tfe

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Reader Interface

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Reader Interface -2

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Authoring Interface

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Authoring Interface - 2

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Authoring Interface - 3

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Authoring Interface - 4

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TFBS Data Submission

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Data within TFe

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URL-based Data Extraction

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System Map

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Author Recruitment

  • Stage 1 (alpha)

 Friends ¡  Friends ¡of ¡Friends ¡  ~10 ¡

  • Stage 2 (beta)

 PubMed ¡mining ¡to ¡iden5fy ¡experts ¡(> ¡10 ¡ published ¡ar5cles ¡about ¡a ¡TF) ¡with ¡email ¡ solicita5on ¡  ~100 ¡ ¡

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TFe Authors

20 +1 Australia

~15% of contacted experts agreed to participate ~60% of participants completed an entry

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Author Motivation

  • Sponsoring Journal

 Scien5sts ¡more ¡willing ¡to ¡commit ¡5me ¡and ¡ effort ¡to ¡projects ¡that ¡give ¡authorships ¡

  • Progress Scores

 Many ¡people ¡are ¡compe55ve ¡and ¡like ¡to ¡see ¡ their ¡work ¡achieve ¡the ¡best ¡possible ¡grade ¡

  • Peer Review

 Respect ¡of ¡peers ¡and ¡fixing ¡weaknesses ¡

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TFe Article Scoring Procedure

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PDFs

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PDF Generator - 2

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Other Features

  • Predicted Binding Domain Structures (Phil

Bradley, FHCRC)

  • MeSH Over-representation Profiles –

Attribute Clouds (Warren Cheung)

  • TF Binding Site Profiles (Elodie Portales-

Casamar)

  • Parent-Child Relationships (inherit ortholog

content if no species-specific version)

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Sustainability

  • Unclear if it can be sustained – not proven
  • Continuing journal sponsorships to motivate

authors to update articles (or for new authors to take on abandoned articles)

  • Focused TF Family-based papers (e.g.

Nuclear Receptors)

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Lessons Learned

  • Motivation for authors – Sponsor Journals
  • Simple interfaces with extremely short

learning periods to keep authors’ attention

  • Dedicated manager to engage authors,

suggest changes and resolve issues

  • Focus allows the system to be tailored to the

needs of the field

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Thanks!

  • National Institutes of Health
  • Genome Canada / Genome BC
  • Canadian Institutes for Health Research
  • Canada Foundation for Innovation
  • Dimas Yusuf
  • Elodie Portales-Casamar
  • Warren Cheung
  • Stefanie Butland
  • Magdalena Swanson
  • Virginie Bernard
  • Rebecca Hunt-Newbury
  • Andrew Kwon
  • Miroslav Hatas
  • David Arenillas
  • Jonathan Lim
  • Dora Pak
  • And many alumni

THE LAB THE APPRECIATED FUNDERS!

  • Phil Bradley and Amy Ticoll (FHCRC)
  • Frances Sladek (UC – Riverside)
  • ~100 TFe Authors – The people most

responsible for the success of the TFe

COLLABORATORS