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DNA Binding Site
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 (e.g. a genome) 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 (see site-specific recombination) and methyltransferases. DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding sites have potential to undergo fast evolutionary chan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription Factors DNA Binding Sites
Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the first step in gene expression ** Bacterial transcription, the generation of RNA transcripts of the genetic material in prokaryotes ** Eukaryotic transcription, the process of copying the genetic information stored in DNA into RNA in eukaryotes ** ''Transcription'' (journal), an academic journal about genetics ** Transcription factor, a protein that controls the rate of transcription of genetic information from DNA to messenger RNA Music * Transcription (music), notating, converting musical sound into visual musical notes (for any purpose) ** Piano transcription, a common type of music transcription * Transcription disc, a sound recording made during broadcasting for internal use by the broadcasting organization Speech transcription The pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP-chip
ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray (''"chip"''). Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA ''in vivo''. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications. The goal of ChIP-on-chip is to locate protein binding sites that may help identify functional elements in the genome. For example, in the case of a transcription factor as a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TRANSFAC
TRANSFAC (TRANScription FACtor database) 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. Introduction The origin of the database was an early data collection published 1988. The first version that was released under the name TRANSFAC was developed at the former German National Research Centre for Biotechnology and designed for local installation (now: Helmholtz Centre for Infection Research). In one of the first publicly funded bioinformatics projects, launched in 1993, TRANSFAC developed into a resource that became available on the Internet. In 1997, TRANSFAC was transferred to a newly established company, BIOBASE, in order to secure long-term financing of the database. Since then, the most up-to-date version has to be licensed, whereas older versions are free for non-commercial users. Since July 2016, TRA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RegulonDB
RegulonDB is a database of the regulatory network of gene expression in ''Escherichia coli'' K-12.{{Cite journal, last=Gama-Castro, first=Socorro, last2=Salgado, first2=Heladia, last3=Santos-Zavaleta, first3=Alberto, last4=Ledezma-Tejeida, first4=Daniela, last5=Muñiz-Rascado, first5=Luis, last6=García-Sotelo, first6=Jair Santiago, last7=Alquicira-Hernández, first7=Kevin, last8=Martínez-Flores, first8=Irma, last9=Pannier, first9=Lucia, date=2016-01-04, title=RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond, journal=Nucleic Acids Research, volume=44, issue=D1, pages=D133–143, doi=10.1093/nar/gkv1156, issn=1362-4962, pmc=4702833, pmid=26527724 RegulonDB also models the organization of the genes in transcription units, operons and regulons. A total of 120 sRNAs with 231 total interactions which all together regulate 192 genes are also included. RegulonDB was founded in 1998 and also contributes data to the EcoCyc datab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RegTransBase
RegTransBase is database of regulatory interactions and transcription factor binding sites in prokaryotes See also *Transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) 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 f ...s References External links * http://regtransbase.lbl.gov. Biological databases Transcription factors DNA Biophysics {{biophysics-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CollecTF
CollecTF is a database of transcription factor binding sites in the Bacteria domain. CollecTF compiles ''only'' experimentally validated TF-binding sites. This is accomplished through the manual curation of peer-reviewed literature with a special focus on the experimental process used to identify TF-binding sites. CollecTF entries are periodically submitted to NCBI for integration into RefSeq complete genome records as link-out features, maximizing the visibility of the data and enriching the annotation of RefSeq files with regulatory information. Seeking to facilitate comparative genomics and machine-learning analyses of regulatory interactions, in its initial release CollecTF provides domain-wide coverage of two TF families (LexA and Fur), as well as extensive representation for a clinically important bacterial family, the Vibrionaceae The Vibrionaceae are a family of Pseudomonadota given their own order, Vibrionales. Inhabitants of fresh or salt water, several species are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JASPAR
JASPAR is an open access and widely used database of manually curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFM) and transcription factor flexible models (TFFM) for TFs from species in six taxonomic groups. From the supplied PFMs, users may generate position-specific weight matrices (PWM). The JASPAR database was introduced in 2004. There were seven major updates and new releases in 2006, 2008, 2010, 2014, 2016, 2018, 2020 and 2022, which is the latest release of JASPAR. Availability The JASPAR database is an open-source and freely available for scientific community ahttp://jaspar.genereg.net/ Similar databases * TRANSFAC – Transcription Factor Database HOCOMOCO- HOmo sapiens COmprehensive MOdel COllection PAZAR- Database with focus on experimentally validated transcription factor binding sites TFe– the transcription factor encyclopedia * AnimalTFDB – Animal transcription factor database PlantCARE– cis- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
False Positive
A false positive is an error in binary classification in which a test result incorrectly indicates the presence of a condition (such as a disease when the disease is not present), while a false negative is the opposite error, where the test result incorrectly indicates the absence of a condition when it is actually present. These are the two kinds of errors in a binary test, in contrast to the two kinds of correct result (a and a ). They are also known in medicine as a false positive (or false negative) diagnosis, and in statistical classification as a false positive (or false negative) error. In statistical hypothesis testing the analogous concepts are known as type I and type II errors, where a positive result corresponds to rejecting the null hypothesis, and a negative result corresponds to not rejecting the null hypothesis. The terms are often used interchangeably, but there are differences in detail and interpretation due to the differences between medical testing and statist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RefSeq
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences ( DNA, RNA) and their protein products. RefSeq was first introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule (i.e. DNA, RNA or protein) for major organisms ranging from viruses to bacteria to eukaryotes. For each model organism, ''RefSeq'' aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. ''RefSeq'' is limited to major organisms for which sufficient data are available (121,461 distinct "named" organisms as of July 2022), while GenBank includes sequences for any organism submitted (approximately 504,000 formally described species). RefSeq categories RefSeq collection comprises different data types, with different origins, so it i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
