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The Transcription Factor Encyclopedia
Dimas Yusuf, Stefanie Butland, Magdalena I. Swanson, Eugene Bolotin, Amy Ticoll, Warren Cheung, Xiao Yu Cindy Zhang, Christopher Td Dickman, Debra L. Fulton, Jonathan Lim, Jake Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N. de Leeuw, Elizabeth M. Simpson, Gerhart U. Ryffel, Eric W.‐F. Lam, Ralf Kist, Miranda Wilson, Raquel Marco-Ferreres, Jan J. Brosens, Leonardo Beccari, Paola Bovolenta, Bérénice A. Benayoun, Lara J. Monteiro, Helma D.C. Schwenen, Lars Grøntved, Elizabeth D. Wederell, Susanne Mandrup, Reiner A. Veitia, Harini Chakravarthy, Pamela A. Hoodless, Maria Michela Mancarelli, Bruce E. Torbett, Alison H. Banham, Sekhar P. Reddy, Rebecca Cullum, Michaela Liedtke, Mario P. Tschan, Michelle Vaz, Angie Rizzino, Mariastella Zannini, Seth Frietze, Peggy Farnham, Astrid Eijkelenboom, Philip J. Brown, David Laperrière, Dominique Leprince, Tiziana de Cristofaro, Kelly L. Prince, Marrit Putker, Luis del Peso, Gieri Camenisch, Roland H. Wenger, Michał Mikuła, Marieke Rozendaal, Sylvie Mader, Jerzy Ostrowski, Simon J. Rhodes, Capucine Van Rechem, Gaylor Boulay, Sam W.Z. Olechnowicz, Mary B. Breslin, Michael S. Lan, Kyster K. Nanan, Michael Wegner, Juan Hou, Rachel D. Mullen, Stephanie C. Colvin, Peter J. Noy, Carol F. Webb, Matthew E. Witek, Scott Ferrell, Juliet M. Daniel, Jason Y. Park, Scott A. Waldman, Daniel J. Peet, Michael J. Taggart, Padma-Sheela Jayaraman, Julien J. Karrich, Bianca Blom, Farhad Vesuna, Henriette O’Geen, Yunfu Sun, Richard M. Gronostajski, Mark W. Woodcroft, Margaret R. Hough, Edwin Chen, G Nicholas Europe-Finner, Magdalena Karolczak‐Bayatti, Jarrod Bailey, Oliver Hankinson, Venu Raman, David P. LeBrun, Shyam Biswal, Christopher J. Harvey, Jason P. DeBruyne, John B. Hogenesch, Robert F. Hevner, Christophe Héligon, Xin Luo, Marissa C. Blank, Kathleen J. Millen, David S. Sharlin, Douglas Forrest, Karin Dahlman‐Wright, Chunyan Zhao, Yuriko Mishima, Satrajit Sinha, Rumela Chakrabarti, Élodie Portales-Casamar, Frances M. Sladek, Philip Bradley, Wyeth W. Wasserman
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.
fundA Canadian funder is recorded on the work.
Bibliographic record
VenueGenome biology · 2012
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Chromatin Dynamics
Canadian institutionsHealth Sciences CentreSunnybrook Health Science CentreMcMaster UniversityQueen's UniversityFraser HealthProvincial Health Services AuthorityInstitute for Research in Immunology and CancerChild and Family Research InstituteBC Cancer AgencyUniversity of TorontoWestern UniversityUniversité de MontréalUniversity of British Columbia
FundersNational Institute of Environmental Health SciencesNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institute of Allergy and Infectious DiseasesNational Institute of General Medical SciencesNational Eye InstituteNational Human Genome Research InstituteNational Institute of Mental HealthNational Health and Medical Research CouncilBritish Heart FoundationMinisterio de Economía y CompetitividadNatural Sciences and Engineering Research Council of CanadaLeukaemia and Lymphoma ResearchFakultet Medicinskih Nauka, Univerziteta U KragujevcuInstitut Universitaire de FranceUniversité de MontréalCentre National de la Recherche ScientifiqueFlight Attendant Medical Research InstituteSimon Fraser UniversityMinistero dell’Istruzione, dell’Università e della RicercaZonMwNational Cancer InstituteUniversity Hospitals Coventry and Warwickshire NHS TrustSchweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungAgence Nationale de la RechercheNew York State Stem Cell ScienceDeutsche ForschungsgemeinschaftUniversité Paris DiderotMinisterio de Ciencia e InnovaciónAlexander and Margaret Stewart TrustAction Medical ResearchEuropean CommissionEuropean Foundation for the Study of DiabetesHeart and Stroke Foundation of CanadaNewcastle UniversityFondation pour la Recherche MédicaleNational Institute of Neurological Disorders and StrokeLeukemia and Lymphoma SocietyGenome British ColumbiaNational Heart, Lung, and Blood InstituteBiotechnology and Biological Sciences Research CouncilCancer Research UKWellcome TrustInstitut National de la Santé et de la Recherche MédicaleChild and Family Research InstituteMedical Research CouncilDiana Helis Henry Medical Research FoundationEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentGlaxoSmithKlineCancer Research SocietyCanadian Institutes of Health ResearchBreast Cancer CampaignU.S. Public Health ServiceAssociazione Italiana per la Ricerca sul CancroGenome CanadaUniversity of British ColumbiaMichael Smith Health Research BCNational Institutes of HealthFaculty of Medical Sciences, Newcastle UniversityLeukemia and Lymphoma Society of CanadaNational Science Foundation
KeywordsBiologyEncyclopediaGenome BiologyHuman geneticsComputational biologyEvolutionary biologyTranscription factorGeneticsComputational genomicsGenomicsGenomeLibrary scienceGeneComputer science
Abstract
Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.980
Threshold uncertainty score0.297
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.009
GPT teacher head0.226
Teacher spread0.217 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itQuick stats
Citations160
Published2012
Admission routes2
Has abstractyes