Transcription Factor Class
Names
More detailed information about this field from each metasource.
Transcription Factor Class
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
TFClass
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Transcription Factor Class
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
TFClass
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
Transcription Factor Class
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
TFClass
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. TFClass provides corresponding sequence collections in FASTA format; sequence logos and phylogenetic trees at different classification levels; predicted TF binding sites for human, mouse, dog and cow genomes; and links to several external databases.
Description
More detailed information about this field from each metasource.
TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. TFClass provides corresponding sequence collections in FASTA format; sequence logos and phylogenetic trees at different classification levels; predicted TF binding sites for human, mouse, dog and cow genomes; and links to several external databases.
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors (TFs), 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 updates earlier attempts to classify eukaryotic transcription factors (1, 2); it is a database that classifies (so far) 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. 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.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://tfclass.bioinf.med.uni-goettingen.de/index.jsfWebpage
More detailed information about this field from each metasource.
http://tfclass.bioinf.med.uni-goettingen.de/index.jsf
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
http://tfclass.bioinf.med.uni-goettingen.de/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
TFClass: expanding the classification of human transcription factors to their mammalian orthologs
PMID: 29087517
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
TFClass: expanding the classification of human transcription factors to their mammalian orthologs
PMID: 29087517
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
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TFClass: expanding the classification of human transcription factors to their mammalian orthologs
PubMed citations: 42.
42 articles citing: TFClass: expanding the classification of human transcription factors to their mammalian orthologs
Glucocorticoid Receptor Maintains Vasopressin Responses in Kidney Collecting Duct Cells. PMID:35685285
Nuclear Receptor Coregulators in Hormone-Dependent Cancers. PMID:35626007
Transcription Factors in the Regulation of Leydig Cell Gene Expression and Function. PMID:35464056
Genome-Wide Identification and Expression Analysis of the Basic Leucine Zipper (bZIP) Transcription Factor Gene Family in Fusarium graminearum. PMID:35456413
Prognostic significance of AP-2α/γ targets as cancer therapeutics. PMID:35361846
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. PMID:35240993
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. PMID:34986601
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
A Core Response to the CDX2 Homeoprotein During Development and in Pathologies. PMID:34759958
DNA methylation atlas of the mouse brain at single-cell resolution. PMID:34616061
Biologically relevant transfer learning improves transcription factor binding prediction. PMID:34579793
Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PMID:34559835
The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells. PMID:34544361
A clinically applicable integrative molecular classification of meningiomas. PMID:34433969
Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma. PMID:34370013
A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID-19. PMID:34099831
Impairments of Photoreceptor Outer Segments Renewal and Phototransduction Due to a Peripherin Rare Haplotype Variant: Insights from Molecular Modeling. PMID:33801777
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. PMID:33770473
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
GTRD: an integrated view of transcription regulation. PMID:33231677
nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. PMID:33209992
miR‑7/SP1/TP53BP1 axis may play a pivotal role in NSCLC radiosensitivity. PMID:33125142
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
Prediction of genome-wide effects of single nucleotide variants on transcription factor binding. PMID:33077858
Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data. PMID:32825662
Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs. PMID:32661179
Bcl-6 is the nexus transcription factor of T follicular helper cells via repressor-of-repressor circuits. PMID:32572238
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. PMID:32393327
Progesterone through Progesterone Receptor B Isoform Promotes Rodent Embryonic Oligodendrogenesis. PMID:32295179
Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules. PMID:32153638
The Role of mPRδ and mPRε in Human Glioblastoma Cells: Expression, Hormonal Regulation, and Possible Clinical Outcome. PMID:32077034
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
Substrate docking-mediated specific and efficient lysine methylation by the SET domain-containing histone methyltransferase SETD7. PMID:31324717
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules. PMID:31011409
Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. PMID:30679424
Anchor: trans-cell type prediction of transcription factor binding sites. PMID:30567711
Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. PMID:30469390
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. PMID:30364927
A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer. PMID:29977600
Tags:
Tags
More detailed information about this field from each metasource.
binding
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
transcription factor binding site prediction
metasource: Fairsharing.org
version: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
binding
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
transcription factor binding site prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: TFClass; Transcription Factor Class; DOI: https://doi.org/10.25504/FAIRsharing.XykycZ; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
binding binding site gene expression transcription transcription factor binding site prediction nucleic acid sequence transcription
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