Additional file 1:PDF of released article. The PDF version of the human FOXL2 article. Other PDF versions of released TFe articles can be accessed on the TFe website.
Additional file 2:Data of released articles. Additional data related to the released mini review articles to supplement the four-page PDF versions, arranged in alphabetical order by TF name.
Additional file 3:Classification of transcription factors in TFe. There are 803 human, mouse, and rat articles in TFe, most of which are organized into groups, families and subfamilies of TFs. The classification scheme utilized in TFe is derived from the work of Fulton et al. [5] in TFCat. There are 8 large groups, which are further subclassified into 34 families. Several TFs, namely nuclear receptors, are even further subclassified into subfamilies.
Additional file 4:The TFe article structure. Articles in TFe are organized into ten tabs labeled 'Summary', 'Structure', 'TFBS', 'Targets', 'Protein', 'Interactions', 'Genetics', 'Expression', 'Ontologies', and 'Papers'. Each tab, with the exception of the Ontologies and Papers tabs, typically begins with a brief overview written by the authors, followed by a mixture of tables and figures that features data from both the authors and second (that is, PAZAR) or third party (that is, BioGRID) sources.
Additional file 5:Binding models produced in the TFe project. Images of the binding models produced in TFe that are sufficiently characterized to be used in a study.
Additional file 6:PDB records depicting protein-DNA binding interface. A list of PDB records that depict a protein-DNA binding interface.
Additional file 7:Relationship Between Pfam domains and PDB records. A list of Pfam binding domains followed by PDB records in which the domains can be found.
Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, CanadaEvaluation and Research Services, Fraser Health Authority, 300 - 10334 152A Street, Surrey, British Columbia V3R 7P8, CanadaChildren's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609-1809, USAComputational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USADepartment of Bioinformatics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, CanadaDepartment of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A5B7, CanadaGenetics Program, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, CanadaCell Biology and Neuroscience, Institute of Integrated Genome Biology, University of California at Riverside, 2115 Biological Sciences Building, Riverside, CA 92521, USASIMOPRO, Laboratory of Life Sciences (Laboratoire de Sciences du Vivant), CEA (Commissariat à l'Énergie Atomique), Gif-sur-Yvette, Saclay, Île-de-France 91191, FranceDepartment Endocrinology, Metabolism and Cancer, INSERM (Unité 1016), Institut Cochin, 24 Rue du Faubourg Saint Jacques, Paris, Île-de-France 75014, FranceInstitut für Zellbiologie, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstrasse 55, Essen, Nordrhein-Westfalen 45122, GermanyDepartment of Surgery and Cancer, Division of Cancer, Imperial College London, Du Cane Road, London, London W12 0NN, UKCentre for Oral Health Research, School of Dental Sciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4BW, UKDepartment of Development and Differentiation, Centro de Biologia Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC) and CIBER de Enfermedades Raras (CIBERER), Nicolas Cabrera 1, Cantoblanco, Madrid, Madrid 28049, SpainDivision of Reproductive Health, Warwick Medical School, University of Warwick, Clifford Bridge Road, Coventry, West Midlands CV2 2DX, UKNeurobiologia Molecular Celular y del desarrollo, Centro de Biologia Molecular Severo Ochoa (CBMSO), Centro de Biologia Molecular Severo Ochoa and CIBER de Enfermedades Raras (CIBERER), Nicolas Cabrera 1, Cantoblanco, Madrid, Madrid 28049, SpainDepartment of Molecular and Cellular Pathology, Institut Jacques Monod, Université Paris Diderot (Paris 7), 15 rue Hélène Brion, Paris, Île-de-France 75013, FranceDepartment of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense, Region Syddanmark 5230, DenmarkTerry Fox Laboratory, BC Cancer Agency, Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, CanadaMolecular and Cellular Pathology Program, Institut Jacques Monod, Université Paris Diderot (Paris 7), 15 rue Hélène Brion, Paris, Île-de-France 75013, FranceEppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, University of Nebraska, 985950 Nebraska Medical Center, Omaha, NE 68198-5950, USADepartment of Molecular Experimental Medicine, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USADepartments of Molecular and Experimental Medicine and Immunology and Microbial Sciences (MEM 131), Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USANuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, Oxford NIHR Biomedical Research Centre, University of Oxford, Level 4 Academic Block, John Radcliffe Hospital, Headington, Oxford, Oxfordshire OX3 9DU, UKDepartment of Pediatrics, College of Medicine, University of Illinois at Chicago, 840 South Wood Street (M/C 856), Chicago, IL 60612, USADepartment of Medicine/Hematology, Stanford University School of Medicine, Stanford University, 875 Blake Wilbur Drive, Stanford, CA 94305, USADepartment of Medicine, University of Bern, Hochschulstrasse 4, Bern, Bern-Mittelland CH-3012, SwitzerlandDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, 1650 Orleans Street Room 530, Baltimore, MD 21237, USAEppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, University of Nebraska, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USAInstitute of Experimental Endocrinology and Oncology (IEOS), CNR - National Research Council, via Pansini 5, Naples, Naples 80131, ItalyDepartment of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90089, USADepartment of Molecular Cancer Research, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht, Utrecht 3584 CG, The NetherlandsNuffield Department of Clinical Laboratory Sciences, Medical Sciences Division, University of Oxford, Level 4 Academic Block, John Radcliffe Hospital, Headington, Oxford, Oxfordshire OX3 9DU, UKMolecular Targeting in Breast Cancer research unit, Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique, Montréal, Québec H3T 1J4, CanadaInstitut de Biologie de Lille, Institut Pasteur de Lille, Centre National de la Recherche Scientifique (CNRS) UMR 8161, 1 Rue du Pr Calmette, Lille, Nord-Pas-de-Calais 59021, FranceDepartment of Cellular and Integrative Physiology, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, 635 Barnhill Drive, Indianapolis, IN 46202, USADepartment of Physiological Chemistry, University Medical Centre Utrecht, Utrecht University, Universiteitsweg 100, Utrecht, Utrecht 3584 CG, The NetherlandsDepartment of Biochemistry, School of Medicine, Universidad Autonoma de Madrid, Arzobispo Morcillo, 4, Madrid, Madrid 28029, SpainInstitute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 190, Zurich, Zurich CH-8057, SwitzerlandDepartment of Oncological Genetics, Medical Center of Postgraduate Education, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, Warsaw, Mazovia 02-781, PolandDepartment of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Québec H3C 3J7, CanadaDepartment of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique, Montréal, Québec H3T 1J4, CanadaDepartment of Biology, School of Science, Indiana University-Purdue University Indianapolis, LD222, 402 North Blackford Street, Indianapolis, IN 46202, USADepartment of Medicine, Cancer Center, Massachusetts General Hospital, Harvard Medical School, 13th Street, Building 149, Room 7.103, Charlestown, MA 02129, USADepartment of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia 5005, AustraliaDepartment of Pediatrics and Biochemistry and Molecular Biology, Research Institute for Children, Children's Hospital at New Orleans, Louisiana State University Health Sciences Center, 200 Henry Clay Avenue, New Orleans, LA 70118, USADepartments of Pediatrics and Genetics, Research Institute for Children, Children's Hospital at New Orleans, Louisiana State University Health Sciences Center, 200 Henry Clay Avenue, New Orleans, LA 70118, USADepartment of Pathology and Molecular Medicine, Queen's Cancer Research Institute, Queen's University, 18 Stuart Street, Botterell Hall, Kingston, Ontario K7L 3N6, CanadaSchool of Medicine, Institut fuer Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universitaet Erlangen-Nuernberg, Fahrstrasse 17, Erlangen, Bavaria 91096, GermanyDepartment of Molecular Biology and Biochemistry, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, 635 Barnhill Drive, Indianapolis, IN 46202, USADepartment of Immunity and Infection, School of Medical and Dental Sciences, University of Birmingham, Wolfson Drive, Edgbaston, Birmingham, West Midlands B15 2TT, UKImmunobiology and Cancer Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USARadiation Oncology, Department of Pharmacology and Experimental Therapeutics, Jefferson University Hospital, 1020 Locust Street, Philadelphia, PA 19107, USADepartment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, University of Oklahoma, 100 North Lindsay Avenue, Oklahoma City, OK 73104, USADepartment of Biology, McMaster University, LSB-331, 1280 Main Street West, Hamilton, Ontario L8S4K1, CanadaSchool of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USADepartment of Pharmacology and Experimental Therapeutics, Jefferson Medical College, Thomas Jefferson University, 132 South 10th Street, 1170 Main, Philadelphia, PA 19107, USADiscipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia 5005, AustraliaInstitute of Cellular Medicine, Faculty of Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UKDepartment of Immunity and Immunology, School of Medical and Dental Sciences, University of Birmingham, Wolfson Drive, Edgbaston, Birmingham, West Midlands B15 2TT, UKDepartment of Cell Biology and Histology, Center for Immunology Amsterdam, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, Noord Holland 1105 AZ, The NetherlandsDivision of Cancer Imaging Research, Department of Radiology, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USAGenome Center, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USAUniversity of California at San Diego, 9500 Gilman Drive, San Diego, CA 92093, USADepartment of Biochemistry and Developmental Genomics Group, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott Street B3-303, Buffalo, New York 14203, USADepartment of Pathology and Molecular Medicine, Queen's Cancer Research Institute, Queen's University, 18 Stuart Street, Botterell Hall, Kingston, Ontario K7K 4G4, CanadaDepartment of Molecular and Cellular Biology, Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Centre, University of Toronto, 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, CanadaDepartment of Molecular and Cellular Biology, Sunnybrook Health Sciences Centre, University of Toronto, 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, CanadaInstitute of Cellular Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4HH, UKFaculty of Medical Sciences, Institute of Cellular Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4AA, UKDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095-1732, USARadiology and Oncology, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USADepartment of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USADepartment of Pharmacology and Toxicology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Drive Southwest, Atlanta, GA 30310, USADepartment of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 10-124 Translational Research Center, 3400 Civic Center Boulevard Building 421, Philadelphia, PA 19104-5158, USADepartment of Neurological Surgery, Seattle Children's Research Institute, University of Washington, 1900 Ninth Avenue, Seattle, WA 98101, USAFaculty of Biology and Medicine, Center for Integrated Genomics, University of Lausanne, CH-1015 Lausanne, Lausanne, Vaud CH-1015, SwitzerlandDepartment of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Duck Pond Drive, Blacksburg, VA 24061, USADepartment of Molecular Genetics and Cell Biology, University of Illinois at Chicago, 920 East 58th Street, Chicago, IL 60637, USACenter for Integrative Brain Research, Seattle Children's Research Institute, University of Washington, 1900 Ninth Avenue, Seattle, WA 98101, USAClinical Endocrinology Branch, National Institute of Diabetes, Digestive, and Kidney Disorders, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1772, USADepartment of Biosciences and Nutrition, Novum, Karolinska Institutet, Hälsovägen 7-9, Huddinge, Stockholm SE-141 83, SwedenDepartment of Biochemistry, University of Buffalo School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 701 Ellicott Street, Buffalo, NY 14203, USAReceived 2012 Feb 2; Revised 2012 Mar 19; Accepted 2012 Mar 29.Copyright © 2012 Yusuf et al.; licensee BioMed Central Ltd.This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.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.
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