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The wiki-based transcription factor encyclopedia and a model for robust community participation Wasserman, Wyeth W. 2011-10-27

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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 2 3 4 Transcription Factors at the Centre of the Universe 5 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 6 Wiki-in-the-classroom 7 8 9TFe 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 Reader Interface 10 11 Authoring Interface 12 Author Recruitment  Stage 1 (alpha)  Friends  Friends of Friends  ~10  Stage 2 (beta)  PubMed mining to identify experts (> 10 published articles about a TF) with email solicitation  ~100 13 TFe Authors 14 +1 Australia ~15% of contacted experts agreed to participate ~60% of participants completed an entry Author Motivation  Sponsoring Journal  Scientists more willing to commit time and effort to projects that give authorships  Progress Scores  Many people are competitive and like to see their work achieve the best possible grade  Peer Review  Respect of peers and fixing weaknesses 15 TFe Article Scoring Procedure 16 17 PDFs 18 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 19 20 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 COLLABORATORS 21 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 22 Resources for the Study of TFs 23 Reader Interface -2 24 Authoring Interface - 2 25 Authoring Interface - 3 26 Authoring Interface - 4 27 TFBS Data Submission 28 Data within TFe 29 URL-based Data Extraction 30 System Map 31 Data Sources  PDB  Pfam  PAZAR  Gene Ontology  PubChem  BioGRID  MeSH  Entrez Gene  GeneRIF  MeSHOP  UCSC Genome Browser  Allen Brain Atlas  PubMed 32 PDF Generator - 2 33 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) 34 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) 35

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