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The transcription factor encyclopedia.

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.

SUBMITTER: Yusuf D

PROVIDER: S-EPMC3439975 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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The transcription factor encyclopedia.

Yusuf Dimas D Butland Stefanie L SL Swanson Magdalena I MI Bolotin Eugene E Ticoll Amy A Cheung Warren A WA Zhang Xiao Yu Cindy XY Dickman Christopher T D CT Fulton Debra L DL Lim Jonathan S JS Schnabl Jake M JM Ramos Oscar H P OH Vasseur-Cognet Mireille M de Leeuw Charles N CN Simpson Elizabeth M EM Ryffel Gerhart U GU Lam Eric W-F EW Kist Ralf R Wilson Miranda S C MS Marco-Ferreres Raquel R Brosens Jan J JJ Beccari Leonardo L LL Bovolenta Paola P Benayoun Bérénice A BA Monteiro Lara J LJ Schwenen Helma D C HD Grontved Lars L Wederell Elizabeth E Mandrup Susanne S Veitia Reiner A RA Chakravarthy Harini H Hoodless Pamela A PA Mancarelli M Michela MM Torbett Bruce E BE Banham Alison H AH Reddy Sekhar P SP Cullum Rebecca L RL Liedtke Michaela M Tschan Mario P MP Vaz Michelle M Rizzino Angie A Zannini Mariastella M Frietze Seth S Farnham Peggy J PJ Eijkelenboom Astrid A Brown Philip J PJ Laperrière David D Leprince Dominique D de Cristofaro Tiziana T Prince Kelly L KL Putker Marrit M del Peso Luis L Camenisch Gieri G Wenger Roland H RH Mikula Michal M Rozendaal Marieke M Mader Sylvie S Ostrowski Jerzy J Rhodes Simon J SJ Van Rechem Capucine C Boulay Gaylor G Olechnowicz Sam W Z SW Breslin Mary B MB Lan Michael S MS Nanan Kyster K KK Wegner Michael M Hou Juan J Mullen Rachel D RD Colvin Stephanie C SC Noy Peter John PJ Webb Carol F CF Witek Matthew E ME Ferrell Scott S Daniel Juliet M JM Park Jason J Waldman Scott A SA Peet Daniel J DJ Taggart Michael M Jayaraman Padma-Sheela PS Karrich Julien J JJ Blom Bianca B Vesuna Farhad F O'Geen Henriette H Sun Yunfu Y Gronostajski Richard M RM Woodcroft Mark W MW Hough Margaret R MR Chen Edwin E Europe-Finner G Nicholas GN Karolczak-Bayatti Magdalena M Bailey Jarrod J Hankinson Oliver O Raman Venu V LeBrun David P DP Biswal Shyam S Harvey Christopher J CJ DeBruyne Jason P JP Hogenesch John B JB Hevner Robert F RF Héligon Christophe C Luo Xin M XM Blank Marissa Cathleen MC Millen Kathleen Joyce KJ Sharlin David S DS Forrest Douglas D Dahlman-Wright Karin K Zhao Chunyan C Mishima Yuriko Y Sinha Satrajit S Chakrabarti Rumela R Portales-Casamar Elodie E Sladek Frances M FM Bradley Philip H PH Wasserman Wyeth W WW

Genome biology 20120101 3

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 scient ...[more]

PMID: 22458515

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Project description:Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, ?-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included ?-1,2 branched ?-1,6-mannans (87%) associated with unbranched ?-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. Importance: This report is the first to decipher the complex and unique macromolecular composition of the Candida biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed for protection from antifungal drugs. The availability of these biochemical analyses provides a unique resource for further functional investigation of the biofilm matrix, a defining trait of this lifestyle.

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The transcription factor encyclopedia.

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The transcription factor encyclopedia.

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