The Transcription Factor Encyclopedia
Dimas Yusuf,Stefanie L. Butland,Magdalena I. Swanson,Eugene Bolotin,Amy Ticoll,Warren A. Cheung,Xiao Yu Cindy Zhang,Christopher Td Dickman,Debra L. Fulton,Jonathan Lim,Jake Schnabl,Oscar H. P. Ramos,Mireille Vasseur-Cognet,Charles N. de Leeuw,Elizabeth M. Simpson,Gerhart U. Ryffel,Eric Lam,Ralf Kist,Miranda Sc Wilson,Raquel Marco-Ferreres,Jan J. Brosens,Leonardo Beccari,Paola Bovolenta,Bérénice A. Benayoun,Lara J. Monteiro,Helma Dc Schwenen,Lars Grøntved,Elizabeth D. Wederell,Susanne Mandrup,Reiner A. Veitia,Harini Chakravarthy,Pamela A. Hoodless,M. Michela Mancarelli,Bruce E. Torbett,Alison H. Banham,Sekhar P. Reddy,Rebecca L. Cullum,Michaela Liedtke,Mario P. Tschan,Michelle Vaz,Angie Rizzino,Mariastella Zannini,Seth Frietze,Peggy J. 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,Michal Mikula,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,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 M. Luo,Marissa Cathleen Blank,Kathleen J. Millen,David S. Sharlin,Douglas Forrest,Karin Dahlman-Wright,Chunyan Zhao,Yuriko Mishima,Satrajit Sinha,Rumela Chakrabarti,Elodie Portales-Casamar,Frances M. Sladek,Philip Bradley,Wyeth W. Wasserman +113 more
Reads0
Chats0
TLDR
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, is presented.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.read more
Citations
More filters
Journal ArticleDOI
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions.
Heonjong Han,Jae Won Cho,Sang Young Lee,Ayoung Yun,Hyo-Jin Kim,Dasom Bae,Sunmo Yang,Chan Yeong Kim,Muyoung Lee,Eunbeen Kim,Sungho Lee,Byunghee Kang,Dabin Jeong,Yaeji Kim,Hyeon Nae Jeon,Haein Jung,Sunhwee Nam,Michael Chung,Jong-Hoon Kim,Insuk Lee +19 more
TL;DR: A significant expansion in the database size and inclusion of the new web tool for TF prioritization mean that TRRUST v2 will be a versatile database for the study of the transcriptional regulation involved in human diseases.
Journal ArticleDOI
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
Anthony Mathelier,Xiaobei Zhao,Allen W. Zhang,François Parcy,Rebecca Worsley-Hunt,David J. Arenillas,Sorana Buchman,Chih-Yu Chen,Alice Yi Chou,Hans Ienasescu,Jonathan S. Lim,Casper Shyr,Ge Tan,Michelle Zhou,Boris Lenhard,Albin Sandelin,Wyeth W. Wasserman +16 more
TL;DR: The fifth major release greatly expands the heart of JASPAR—the JAS PAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles, mainly derived from published chromatin immunoprecipitation-seq experimental datasets.
Journal ArticleDOI
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Ilya E. Vorontsov,Ivan S. Yevshin,Ruslan N. Sharipov,Ruslan N. Sharipov,Alla D. Fedorova,Eugene I. Rumynskiy,Eugene I. Rumynskiy,Yulia A. Medvedeva,Yulia A. Medvedeva,Arturo Magana-Mora,Arturo Magana-Mora,Vladimir B. Bajic,Dmitry Papatsenko,Fedor A. Kolpakov,Vsevolod J. Makeev,Vsevolod J. Makeev,Vsevolod J. Makeev +19 more
TL;DR: A nearly doubled volume of published in vivo experiments on transcription factor (TF) binding is profited from to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities.
Journal ArticleDOI
Forkhead box proteins: tuning forks for transcriptional harmony
TL;DR: The functional complexities of FOX proteins are coming to light and have established these transcription factors as possible therapeutic targets and putative biomarkers for specific cancers.
Journal ArticleDOI
Benchmark and integration of resources for the estimation of human transcription factor activities.
Luz Garcia-Alonso,Christian H. Holland,Mahmoud M. Ibrahim,Dénes Türei,Dénes Türei,Julio Saez-Rodriguez +5 more
TL;DR: A collection of TF-target interactions for 1541 human TFs was assembled and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode of interaction with the chromatin, affect the predictions of TF activity.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
TL;DR: Induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions is demonstrated and iPS cells, designated iPS, exhibit the morphology and growth properties of ES cells and express ES cell marker genes.
Journal ArticleDOI
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Kazutoshi Takahashi,Koji Tanabe,Mari Ohnuki,Megumi Narita,Tomoko Ichisaka,Kiichiro Tomoda,Shinya Yamanaka +6 more
TL;DR: It is demonstrated that iPS cells can be generated from adult human fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Related Papers (5)
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more