In molecular biology, a transcription factor (TF) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division, cell growth, and cell death throughout life; cell migration and organization during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone. There are approximately 1600 TFs in the human genome. Transcription factors are members of the proteome as well as regulome.
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair.
A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence or have a general affinity to DNA. Some DNA-binding domains may also include nucleic acids in their folded structure.
The Open Regulatory Annotation Database is designed to promote community-based curation of regulatory information. Specifically, the database contains information about regulatory regions, transcription factor binding sites, regulatory variants, and haplotypes.
High-mobility group protein HMG-I/HMG-Y is a protein that in humans is encoded by the HMGA1 gene.
Krueppel-like factor 5 is a protein that in humans is encoded by the KLF5 gene.
Transcription factor SOX-6 is a protein that in humans is encoded by the SOX6 gene.
Anders Krogh is a bioinformatician at the University of Copenhagen, where he leads the university's bioinformatics center. He is known for his pioneering work on the use of hidden Markov models in bioinformatics, and is co-author of a widely used textbook in bioinformatics. In addition, he also co-authored one of the early textbooks on neural networks. His current research interests include promoter analysis, non-coding RNA, gene prediction and protein structure prediction.
BIOBASE is an international bioinformatics company headquartered in Wolfenbüttel, Germany. The company focuses on the generation, maintenance, and licensing of databases in the field of molecular biology, and their related software platforms.
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence and (2) they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known as transcription factors, and are thus linked to transcriptional regulation. The sum of DNA binding sites of a specific transcription factor is referred to as its cistrome. DNA binding sites also encompasses the targets of other proteins, like restriction enzymes, site-specific recombinases and methyltransferases.
Therapeutic Target Database (TTD) is a pharmaceutical and medical repository constructed by the Innovative Drug Research and Bioinformatics Group (IDRB) at Zhejiang University, China and the Bioinformatics and Drug Design Group at the National University of Singapore. It provides information about known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Detailed knowledge about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. TTD is freely accessible without any login requirement at https://idrblab.org/ttd/.
YEASTRACT is a curated repository of more than 48000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references. It also includes the description of about 300 specific DNA binding sites for more than a hundred characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains more than 7100 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks.
In molecular biology, the BEN domain is a protein domain which is found in diverse proteins including:
TRANSFAC is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites.
The WRKY domain is found in the WRKY transcription factor family, a class of transcription factors. The WRKY domain is found almost exclusively in plants although WRKY genes appear present in some diplomonads, social amoebae and other amoebozoa, and fungi incertae sedis. They appear absent in other non-plant species. WRKY transcription factors have been a significant area of plant research for the past 20 years. The WRKY DNA-binding domain recognizes the W-box (T)TGAC(C/T) cis-regulatory element.
Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in chromatin immunoprecipitation followed by sequencing (ChIP-seq) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
Ivan Erill is a Spanish computational biologist known for his research in comparative genomics and molecular microbiology. His work focuses primarily on bacterial comparative genomics, through the development of computational methods for analyzing regulatory networks and their evolution.
HOCOMOCO is an open-access database providing curated and benchmarked binding motifs of human and mouse transcription factors. It captures the following data types: Homo sapiens (human) and Mus musculus (mouse) transcription factors, their DNA binding site motifs, and motif subtypes.
