ArticleNucleic acids research2013
TFClass: an expandable hierarchical classification of human transcription factors.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 1 of them a synthesis that pooled it.
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Who cites it
92 citing papers in PubMed, 1 synthesis or guideline pooled it, 180 citations in OpenAlex.
- Improved linking of motifs to their TFs using domain information.Bioinformatics (Oxford, England) · 2020Pooled it
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- Cell Type-Specific Hormonal Signaling Configures Hypothalamic Circuits for Parenting.bioRxiv : the preprint server for biology · 2025Article
- Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing.Nucleic acids research · 2025Article
- Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2025Article
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms.RNA (New York, N.Y.) · 2024Article
- Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data.Scientific reports · 2024Article
- Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms.bioRxiv : the preprint server for biology · 2024Article
- Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.Nucleic acids research · 2024Article
- Structural underpinnings of mutation rate variations in the human genome.Nucleic acids research · 2023Article
- Systematic integration of protein-affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile.Cell reports methods · 2023Article
- A Survey of Transcription Factors in Cell Fate Control.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes.Advanced genetics (Hoboken, N.J.) · 2022Article
- Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina.Human molecular genetics · 2022Article
- Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing.International journal of molecular sciences · 2022Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors based on their DNA-binding domains. Transcription factors constitute a large functional family of proteins directly regulating the activity of genes. Most of them are sequence-specific DNA-binding proteins, thus reading out the information encoded in cis-regulatory DNA elements of promoters, enhancers and other regulatory regions of a genome. TFClass is a database that classifies human transcription factors by a six-level classification schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. Altogether, nine superclasses have been identified, comprising 40 classes and 111 families. Counted by genes, 1558 human TFs have been classified so far or >2900 different TFs when including their isoforms generated by alternative splicing or protein processing events. With this classification, we hope to provide a basis for deciphering protein-DNA recognition codes; moreover, it can be used for constructing expanded transcriptional networks by inferring additional TF-target gene relations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.