The Transcription Factor Encyclopedia

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.

• Publication year

  2012

• Venue

  Genome Biology

• Publication date

  2012-03-29

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/gb-2012-13-3-r24PMID 22458515PMCID 3439975
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Transcription Factor Encyclopedia

  2012cited by this paper
• The BioGRID Interaction Database

  2011cited by this paper
• The Pfam protein families database

  2011cited by this paper
• The UCSC Genome Browser database: update 2011

  2010cited by this paper
• The UCSC Genome Browser database: update 2010

  2009cited by this paper
• JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

  2009cited by this paper
• The Universal Protein Resource (UniProt) in 2010

  2009cited by this paper
• A census of human transcription factors: function, expression and evolution

  2009influential reference
• TFCat: the curated catalog of mouse and human transcription factors

  2009influential reference
• The Mouse Genome Database: enhancements and updates

  2009cited by this paper
• The Gene Wiki: community intelligence applied to human gene annotation

  2009cited by this paper
• The Allen Brain Atlas: 5 years and beyond

  2009cited by this paper
• Aniridia: current pathology and management

  2008cited by this paper
• Calling on a million minds for community annotation in WikiProteins

  2008cited by this paper
• The UCSC Genome Browser Database: update 2009

  2008cited by this paper
• Ensembl 2009

  2008cited by this paper
• A wiki for the life sciences where authorship matters

  2008influential reference
• A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

  2008cited by this paper
• GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

  2008cited by this paper
• The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

  2008influential reference
• PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

  2007cited by this paper
• Faculty Opinions recommendation of Induction of pluripotent stem cells from adult human fibroblasts by defined factors.

  2007cited by this paper
• The Pfam protein families database

  2007cited by this paper
• Mendelian Inheritance in Man and Its Online Version, OMIM

  2007cited by this paper
• The BioGRID Interaction Database: 2008 update

  2007influential reference
• Functional characterization of naturally occurring NR3C2 gene mutations in Italian patients suffering from pseudohypoaldosteronism type 1.

  2007cited by this paper
• Comparative Protein Structure Modeling Using MODELLER

  2007cited by this paper
• iHOP web services

  2007cited by this paper
• Induction of pluripotent stem cells from adult human fibroblasts by defined factors.

  2007cited by this paper
• Connecting protein structure with predictions of regulatory sites

  2007cited by this paper
• Entrez Gene: gene-centered information at NCBI

  2006influential reference
• GeneTests: an online genetic information resource for health care providers.

  2006cited by this paper
• Gene-function wiki would let biologists pool worldwide resources

  2006cited by this paper
• Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.

  2006cited by this paper
• Comparative Protein Structure Modeling Using Modeller

  2006cited by this paper
• LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts

  2005cited by this paper
• TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes

  2005cited by this paper
• Genetic and epigenetic control of skeletal muscle development.

  2005cited by this paper
• The Universal Protein Resource (UniProt)

  2004cited by this paper
• Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

  2004cited by this paper
• The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

  2003cited by this paper
• Announcing the worldwide Protein Data Bank

  2003cited by this paper
• GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium

  2002cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000influential reference
• Molecular Evolution of the GATA Family of Transcription Factors: Conservation Within the DNA-Binding Domain

  2000cited by this paper
• Medical Subject Headings (MeSH).

  2000influential reference
• A unified nomenclature system for the nuclear receptor superfamily.

  1999cited by this paper
• A unified nomenclature system for the nuclear receptor superfamily

  1999cited by this paper
• The role of ras and myc oncogenes in human solid tumours and their relevance in diagnosis and prognosis (review).

  1990cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• Causality-aware graph neural networks for functional stratification and phenotype prediction at scale

  2025cites this paper
• Cell-type specific epigenetic and transcriptional mechanisms in substance use disorder

  2025cites this paper
• An integrative analysis combining bioinformatics, network pharmacology and experimental methods identified key genes of EGCG targets in Nasopharyngeal Carcinoma

  2025cites this paper
• Accurate Transcription Factor Activity Inference to Decipher Cell Identity from Single‐Cell Transcriptomic Data with MetaTF

  2025cites this paper
• Identification of Trihelix Transcription Factors in Grapevine and Expression Dynamics in Response to Biotic Stress and Hormone Treatment

  2025cites this paper
• Immunohistochemistry Expression Gata3 Based on Subtypes of Ovarian Carcinoma at Haji Adam Malik General Hospital Medan 2019-2021

  2025cites this paper
• Transcriptome sequencing reveals regulatory genes associated with neurogenic hearing loss

  2025cites this paper
• Zinc finger transcription factor ZFP1 is associated with growth, conidiation, osmoregulation, and virulence in the Polygonatum kingianum pathogen Fusarium oxysporum

  2024cites this paper
• Mechanistic analysis of the hardening process of the thorns on stems of Bougainvillea glabra “Elizabeth Angus”

  2024cites this paper
• Promoter Methylation Leads to Hepatocyte Nuclear Factor 4A Loss and Pancreatic Cancer Aggressiveness

  2024cites this paper
• FOXO3 polymorphisms influence the risk and prognosis of rhabdomyosarcoma in children

  2024cites this paper
• Identification, characterization, and prognosis investigation of pivotal genes shared in different stages of breast cancer

  2023cites this paper
• МОДЕЛЮВАННЯ СТРУКТУРИ “УКРАЇНСЬКОЇ ЕЛЕКТРОННОЇ ЕНЦИКЛОПЕДІЇ ОСВІТИ”

  2023cites this paper
• The APC/C E3 ligase subunit ANAPC11 mediates FOXO3 protein degradation to promote cell proliferation and lymph node metastasis in urothelial bladder cancer

  2023cites this paper
• Targeted splicing therapy: new strategies for colorectal cancer

  2023cites this paper
• Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis

  2023cites this paper
• Disease-Associated Non-Coding Variants Alter NKX2-5 DNA-Binding Affinity

  2022cites this paper
• Theoretical Principles of Enhancer-Promoter Communication in Transcriptional Bursting

  2022cites this paper
• A novel HIF1α-STIL-FOXM1 axis regulates tumor metastasis

  2022cites this paper
• Effects of tobacco compound 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) on the expression of epigenetically regulated genes in lung carcinogenesis

  2021cites this paper
• PAX8, an Emerging Player in Ovarian Cancer.

  2021cites this paper
• Transcription at a Distance in the Budding Yeast Saccharomyces cerevisiae

  2021cites this paper
• Identification of novel genes and pathways regulated by the orphan nuclear receptor COUP-TFII in mouse MA-10 Leydig cells

  2021cites this paper
• Nanoparticle-based fluorescence probe for detection of NF-κB transcription factor in single cell via steric hindrance

  2021cites this paper
• Transcriptomic dynamics changes related to anthocyanin accumulation in the fleshy roots of carmine radish (Raphanus sativus L.) characterized using RNA-Seq

  2021cites this paper
• Hepatocyte nuclear factor 4α and cancer-related cell signaling pathways: a promising insight into cancer treatment

  2021cites this paper
• CES2 sustains HNF4α expression to promote pancreatic adenocarcinoma progression through an epoxide hydrolase-dependent regulatory loop

  2021cites this paper
• Experiment level curation of transcriptional regulatory interactions in neurodevelopment

  2021cites this paper
• Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

  2020cites this paper
• PAX6 mutation alters circadian rhythm and β cell function in mice without affecting glucose tolerance

  2020cites this paper
• Correction: Nuclear receptor HNF4α performs a tumor suppressor function in prostate cancer via its induction of p21-driven cellular senescence

  2020cites this paper
• Dynamics of the transcriptional landscape during human fetal testis and ovary development.

  2020cites this paper
• FOXO transcription factor family in cancer and metastasis

  2020cites this paper
• PAX6 mutation alters circadian rhythm and β cell function in mice without affecting glucose tolerance

  2020cites this paper
• FOXO3 gene polymorphisms influence the risk of acute lymphoblastic leukemia in Chinese children

  2020cites this paper
• PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation

  2019cites this paper
• Competition/antagonism associations of biofilm formation among Staphylococcus epidermidis Agr groups I, II, and III

  2019cites this paper
• Deciphering the Molecular Mechanisms Sustaining the Estrogenic Activity of the Two Major Dietary Compounds Zearalenone and Apigenin in ER-Positive Breast Cancer Cell Lines

  2019cites this paper
• The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis

  2019influential citation
• Transcription Factors

  2019cites this paper
• Supplemental Data

  2019cites this paper
• Genome-wide analysis of transcription factors related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots

  2019cites this paper
• Nuclear receptor HNF4α performs a tumor suppressor function in prostate cancer via its induction of p21-driven cellular senescence

  2019cites this paper
• HNF4α-deficient Fatty Liver Provides a Permissive Environment for Sex-independent Hepatocellular Carcinoma.

  2019cites this paper
• Transcriptomic profile of two developmental stages of the cestode parasite Mesocestoides corti.

  2019cites this paper
• Retinoids induce antagonism between FOXO3A and FOXM1 transcription factors in human oral squamous cell carcinoma (OSCC) cells

  2019cites this paper
• Peroxisome Proliferator-Activated Receptors - Alpha in Chronic Inflammation - Mini-Review

  2019cites this paper
• METTL3 Promotes the Proliferation and Mobility of Gastric Cancer Cells

  2019cites this paper
• Sodium Acetate Responses in Saccharomyces cerevisiae and the Ubiquitin Ligase Rsp5

  2018cites this paper
• Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver

  2018cites this paper
• Functional roles of heterogeneous nuclear ribonucleoprotein K in post-transcriptional gene regulation

  2018cites this paper
• NBDC RDF portal: a comprehensive repository for semantic data in life sciences

  2018cites this paper
• Benchmark and integration of resources for the estimation of human transcription factor activities

  2018cites this paper
• Characterization of OglDREB2A gene from African rice (Oryza glaberrima), comparative analysis and its transcriptional regulation under salinity stress

  2018cites this paper
• Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering

  2018cites this paper
• Roles of pH in control of cell proliferation

  2018cites this paper
• Biomolecular Assemblies: Moving from Observation to Predictive Design.

  2018cites this paper
• A hnRNP K–AR-Related Signature Reflects Progression toward Castration-Resistant Prostate Cancer

  2018cites this paper
• Aberrant expression of alternative isoforms of transcription factors in hepatocellular carcinoma

  2018cites this paper
• The multisystemic functions of FOXD1 in development and disease

  2018cites this paper
• RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia

  2018cites this paper
• Linking the Transcriptional Landscape of Bone Induction to Biomaterial Design Parameters

  2017cites this paper
• Genome-scale modeling of yeast: chronology, applications and critical perspectives

  2017cites this paper
• Cancer cell line specific co-factors modulate the FOXM1 cistrome

  2017cites this paper
• Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open‐angle glaucoma

  2017cites this paper
• Glyceollins trigger anti-proliferative effects through estradiol-dependent and independent pathways in breast cancer cells

  2017cites this paper
• ACSL3 promotes intratumoral steroidogenesis in prostate cancer cells

  2017cites this paper
• Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites

  2017cites this paper
• The FOXO3-FOXM1 axis: A key cancer drug target and a modulator of cancer drug resistance

  2017cites this paper
• Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation

  2017cites this paper
• WNT signalling events near the cell membrane and their pharmacological targeting for the treatment of cancer

  2017cites this paper
• Up-Frameshift Protein UPF1 Regulates Neurospora crassa Circadian and Diurnal Growth Rhythms

  2017cites this paper
• Transcription Factors Responding to Pb Stress in Maize

  2017cites this paper
• TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

  2017cites this paper
• Effects of hyperthermia and HSP70 protein overexpression on FOXO3a levels in Acute Lymphoblastic T-cells

  2017cites this paper
• MicroRNA Signatures and Transcriptional Regulatory Networks in Glioblastoma

  2017cites this paper
• Towards the complete picture: combining modelling and experimental data in a systems biology approach

  2017cites this paper
• HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

  2017cites this paper
• Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution

  2016cites this paper
• Systematic target function annotation of human transcription factors

  2016cites this paper
• Coordination of signalling networks and tumorigenic properties by ABL in glioblastoma cells

  2016cites this paper
• GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler

  2016influential citation
• Cleaving for growth: threonine aspartase 1—a protease relevant for development and disease

  2016cites this paper
• FOXM1 promotes invasion and migration of colorectal cancer cells partially dependent on HSPA5 transactivation

  2016cites this paper
• HNF1B variants associate with promoter methylation and regulate gene networks activated in prostate and ovarian cancer

  2016cites this paper
• A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

  2016cites this paper
• Hypoxia-Inducible Factor 2α Mutation-Related Paragangliomas Classify as Discrete Pseudohypoxic Subcluster

  2016cites this paper
• Opportunities in the design and application of RNA for gene expression control

  2016cites this paper
• A comparative analysis of the 'other roles' of transcriptional factors from pathogenic organisms.

  2016cites this paper
• Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

  2016cites this paper
• Gene signatures related to HAI response following influenza A/H1N1 vaccine in older individuals

  2016cites this paper
• Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

  2016cites this paper
• System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination

  2016cites this paper
• Investigating the association between germ line specification and sequence evolution in vertebrates

  2015cites this paper
• Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation

  2015cites this paper
• Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition.

  2015cites this paper
• Research resource: the dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis.

  2015cites this paper
• Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

  2015cites this paper
• Computer-assisted curation of a human regulatory core network from the biological literature

  2015cites this paper
• Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

  2015cites this paper