Software
The Transcription Factor Encyclopedia
1 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, Canada
2 Evaluation and Research Services, Fraser Health Authority, 300 - 10334 152A Street, Surrey, British Columbia V3R 7P8, Canada
3 Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609-1809, USA
4 Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
5 Department 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, Canada
6 Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario N6A5B7, Canada
7 Genetics 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, Canada
8 Cell Biology and Neuroscience, Institute of Integrated Genome Biology, University of California at Riverside, 2115 Biological Sciences Building, Riverside, CA 92521, USA
9 SIMOPRO, Laboratory of Life Sciences (Laboratoire de Sciences du Vivant), CEA (Commissariat à l'Énergie Atomique), Gif-sur-Yvette, Saclay, Île-de-France 91191, France
10 Department Endocrinology, Metabolism and Cancer, INSERM (Unité 1016), Institut Cochin, 24 Rue du Faubourg Saint Jacques, Paris, Île-de-France 75014, France
11 Institut für Zellbiologie, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstrasse 55, Essen, Nordrhein-Westfalen 45122, Germany
12 Department of Surgery and Cancer, Division of Cancer, Imperial College London, Du Cane Road, London, London W12 0NN, UK
13 Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4BW, UK
14 Department 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, Spain
15 Division of Reproductive Health, Warwick Medical School, University of Warwick, Clifford Bridge Road, Coventry, West Midlands CV2 2DX, UK
16 Neurobiologia 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, Spain
17 Department of Molecular and Cellular Pathology, Institut Jacques Monod, Université Paris Diderot (Paris 7), 15 rue Hélène Brion, Paris, Île-de-France 75013, France
18 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense, Region Syddanmark 5230, Denmark
19 Terry Fox Laboratory, BC Cancer Agency, Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
20 Molecular and Cellular Pathology Program, Institut Jacques Monod, Université Paris Diderot (Paris 7), 15 rue Hélène Brion, Paris, Île-de-France 75013, France
21 Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, University of Nebraska, 985950 Nebraska Medical Center, Omaha, NE 68198-5950, USA
22 Department of Molecular Experimental Medicine, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
23 Departments of Molecular and Experimental Medicine and Immunology and Microbial Sciences (MEM 131), Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
24 Nuffield 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, UK
25 Department of Pediatrics, College of Medicine, University of Illinois at Chicago, 840 South Wood Street (M/C 856), Chicago, IL 60612, USA
26 Department of Medicine/Hematology, Stanford University School of Medicine, Stanford University, 875 Blake Wilbur Drive, Stanford, CA 94305, USA
27 Department of Medicine, University of Bern, Hochschulstrasse 4, Bern, Bern-Mittelland CH-3012, Switzerland
28 Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, 1650 Orleans Street Room 530, Baltimore, MD 21237, USA
29 Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, University of Nebraska, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
30 Institute of Experimental Endocrinology and Oncology (IEOS), CNR - National Research Council, via Pansini 5, Naples, Naples 80131, Italy
31 Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90089, USA
32 Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, Utrecht, Utrecht 3584 CG, The Netherlands
33 Nuffield Department of Clinical Laboratory Sciences, Medical Sciences Division, University of Oxford, Level 4 Academic Block, John Radcliffe Hospital, Headington, Oxford, Oxfordshire OX3 9DU, UK
34 Molecular Targeting in Breast Cancer research unit, Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
35 Institut 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, France
36 Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, 635 Barnhill Drive, Indianapolis, IN 46202, USA
37 Department of Physiological Chemistry, University Medical Centre Utrecht, Utrecht University, Universiteitsweg 100, Utrecht, Utrecht 3584 CG, The Netherlands
38 Department of Biochemistry, School of Medicine, Universidad Autonoma de Madrid, Arzobispo Morcillo, 4, Madrid, Madrid 28029, Spain
39 Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 190, Zurich, Zurich CH-8057, Switzerland
40 Department of Oncological Genetics, Medical Center of Postgraduate Education, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, Warsaw, Mazovia 02-781, Poland
41 Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Québec H3C 3J7, Canada
42 Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
43 Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, LD222, 402 North Blackford Street, Indianapolis, IN 46202, USA
44 Department of Medicine, Cancer Center, Massachusetts General Hospital, Harvard Medical School, 13th Street, Building 149, Room 7.103, Charlestown, MA 02129, USA
45 Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
46 Department 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, USA
47 Departments 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, USA
48 Department of Pathology and Molecular Medicine, Queen's Cancer Research Institute, Queen's University, 18 Stuart Street, Botterell Hall, Kingston, Ontario K7L 3N6, Canada
49 School of Medicine, Institut fuer Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universitaet Erlangen-Nuernberg, Fahrstrasse 17, Erlangen, Bavaria 91096, Germany
50 Department of Molecular Biology and Biochemistry, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, 635 Barnhill Drive, Indianapolis, IN 46202, USA
51 Department of Immunity and Infection, School of Medical and Dental Sciences, University of Birmingham, Wolfson Drive, Edgbaston, Birmingham, West Midlands B15 2TT, UK
52 Immunobiology and Cancer Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
53 Radiation Oncology, Department of Pharmacology and Experimental Therapeutics, Jefferson University Hospital, 1020 Locust Street, Philadelphia, PA 19107, USA
54 Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, University of Oklahoma, 100 North Lindsay Avenue, Oklahoma City, OK 73104, USA
55 Department of Biology, McMaster University, LSB-331, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
56 School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
57 Department of Pharmacology and Experimental Therapeutics, Jefferson Medical College, Thomas Jefferson University, 132 South 10th Street, 1170 Main, Philadelphia, PA 19107, USA
58 Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
59 Institute of Cellular Medicine, Faculty of Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
60 Department of Immunity and Immunology, School of Medical and Dental Sciences, University of Birmingham, Wolfson Drive, Edgbaston, Birmingham, West Midlands B15 2TT, UK
61 Department of Cell Biology and Histology, Center for Immunology Amsterdam, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, Noord Holland 1105 AZ, The Netherlands
62 Division of Cancer Imaging Research, Department of Radiology, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
63 Genome Center, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
64 University of California at San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
65 Department 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, USA
66 Department of Pathology and Molecular Medicine, Queen's Cancer Research Institute, Queen's University, 18 Stuart Street, Botterell Hall, Kingston, Ontario K7K 4G4, Canada
67 Department 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, Canada
68 Department of Molecular and Cellular Biology, Sunnybrook Health Sciences Centre, University of Toronto, 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, Canada
69 Institute of Cellular Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4HH, UK
70 Faculty of Medical Sciences, Institute of Cellular Medicine, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, Tyne and Wear NE2 4AA, UK
71 Department 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, USA
72 Radiology and Oncology, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
73 Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
74 Department of Pharmacology and Toxicology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Drive Southwest, Atlanta, GA 30310, USA
75 Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 10-124 Translational Research Center, 3400 Civic Center Boulevard Building 421, Philadelphia, PA 19104-5158, USA
76 Department of Neurological Surgery, Seattle Children's Research Institute, University of Washington, 1900 Ninth Avenue, Seattle, WA 98101, USA
77 Faculty of Biology and Medicine, Center for Integrated Genomics, University of Lausanne, CH-1015 Lausanne, Lausanne, Vaud CH-1015, Switzerland
78 Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Duck Pond Drive, Blacksburg, VA 24061, USA
79 Department of Molecular Genetics and Cell Biology, University of Illinois at Chicago, 920 East 58th Street, Chicago, IL 60637, USA
80 Center for Integrative Brain Research, Seattle Children's Research Institute, University of Washington, 1900 Ninth Avenue, Seattle, WA 98101, USA
81 Clinical Endocrinology Branch, National Institute of Diabetes, Digestive, and Kidney Disorders, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1772, USA
82 Department of Biosciences and Nutrition, Novum, Karolinska Institutet, Hälsovägen 7-9, Huddinge, Stockholm SE-141 83, Sweden
83 Department of Biochemistry, University of Buffalo School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 701 Ellicott Street, Buffalo, NY 14203, USA
Genome Biology 2012, 13:R24 doi:10.1186/gb-2012-13-3-r24
Published: 29 March 2012Additional files
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.
Format: PDF Size: 1.9MB Download file
This file can be viewed with: Adobe Acrobat Reader
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.
Format: ZIP Size: 8.8MB Download file
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.
Format: XLS Size: 123KB Download file
This file can be viewed with: Microsoft Excel Viewer
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.
Format: PDF Size: 46KB Download file
This file can be viewed with: Adobe Acrobat Reader
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.
Format: PDF Size: 1008KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 6:
PDB records depicting protein-DNA binding interface. A list of PDB records that depict a protein-DNA binding interface.
Format: TXT Size: 7KB Download file
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.
Format: TXT Size: 32KB Download file
