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

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The wiki-based Transcription Factor Encyclopedia and a model for robust community participation Wyeth W. Wasserman 30 November 2010  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  TFe Goal: create an online encyclopedic collection of reviews about well-studied TFs, combining a mixture of expert-curated and automatic content. 9  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  +1 Australia  ~15% of contacted experts agreed to participate ~60% of participants completed an entry 14  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  Thanks! THE LAB  • 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  COLLABORATORS  • Phil Bradley and Amy Ticoll (FHCRC) • Frances Sladek (UC – Riverside) •~100 TFe Authors  THE APPRECIATED FUNDERS!  • National Institutes of Health • Genome Canada / Genome BC • Canadian Institutes for Health Research • Canada Foundation for Innovation  •And many alumni  20  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 proteinprotein 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 PortalesCasamar)  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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