Transcription factorIn 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 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.
Transcription (biology)Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). mRNA comprises only 1–3% of total RNA samples. Less than 2% of the human genome can be transcribed into mRNA (Human genome#Coding vs. noncoding DNA), while at least 80% of mammalian genomic DNA can be actively transcribed (in one or more types of cells), with the majority of this 80% considered to be ncRNA.
Transcriptional regulationIn molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response.
FractionA fraction (from fractus, "broken") represents a part of a whole or, more generally, any number of equal parts. When spoken in everyday English, a fraction describes how many parts of a certain size there are, for example, one-half, eight-fifths, three-quarters. A common, vulgar, or simple fraction (examples: and ) consists of an integer numerator, displayed above a line (or before a slash like ), and a non-zero integer denominator, displayed below (or after) that line.
Gene predictionIn computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.
Irreducible fractionAn irreducible fraction (or fraction in lowest terms, simplest form or reduced fraction) is a fraction in which the numerator and denominator are integers that have no other common divisors than 1 (and −1, when negative numbers are considered). In other words, a fraction a/b is irreducible if and only if a and b are coprime, that is, if a and b have a greatest common divisor of 1. In higher mathematics, "irreducible fraction" may also refer to rational fractions such that the numerator and the denominator are coprime polynomials.
Egyptian fractionAn Egyptian fraction is a finite sum of distinct unit fractions, such as That is, each fraction in the expression has a numerator equal to 1 and a denominator that is a positive integer, and all the denominators differ from each other. The value of an expression of this type is a positive rational number ; for instance the Egyptian fraction above sums to . Every positive rational number can be represented by an Egyptian fraction.
Unit fractionA unit fraction is a positive fraction with one as its numerator, 1/n. It is the multiplicative inverse (reciprocal) of the denominator of the fraction, which must be a positive natural number. Examples are 1/1, 1/2, 1/3, 1/4, 1/5, etc. When an object is divided into equal parts, each part is a unit fraction of the whole. Multiplying two unit fractions produces another unit fraction, but other arithmetic operations do not preserve unit fractions.
Protein function predictionProtein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction.
ChIP sequencingChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations. ChIP-seq is primarily used to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms.
Binding siteIn biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins (resulting in a protein-protein interaction), enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function.
Zinc fingerA zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells.
Cis-regulatory elementCis-regulatory elements (CREs) or Cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology. CREs are found in the vicinity of the genes that they regulate. CREs typically regulate gene transcription by binding to transcription factors.
Enhancer (genetics)In genetics, an enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors. Enhancers are cis-acting. They can be located up to 1 Mbp (1,000,000 bp) away from the gene, upstream or downstream from the start site. There are hundreds of thousands of enhancers in the human genome. They are found in both prokaryotes and eukaryotes.
Nuclear receptorIn the field of molecular biology, nuclear receptors are a class of proteins responsible for sensing steroids, thyroid hormones, vitamins, and certain other molecules. These intracellular receptors work with other proteins to regulate the expression of specific genes thereby controlling the development, homeostasis, and metabolism of the organism. Nuclear receptors bind directly to DNA regulating the expression of adjacent genes; hence these receptors are classified as transcription factors.
Generalized continued fractionIn complex analysis, a branch of mathematics, a generalized continued fraction is a generalization of regular continued fractions in canonical form, in which the partial numerators and partial denominators can assume arbitrary complex values. A generalized continued fraction is an expression of the form where the an (n > 0) are the partial numerators, the bn are the partial denominators, and the leading term b0 is called the integer part of the continued fraction.
DNA sequencingDNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics.
Greedy algorithm for Egyptian fractionsIn mathematics, the greedy algorithm for Egyptian fractions is a greedy algorithm, first described by Fibonacci, for transforming rational numbers into Egyptian fractions. An Egyptian fraction is a representation of an irreducible fraction as a sum of distinct unit fractions, such as 5/6 = 1/2 + 1/3. As the name indicates, these representations have been used as long ago as ancient Egypt, but the first published systematic method for constructing such expansions was described in 1202 in the Liber Abaci of Leonardo of Pisa (Fibonacci).
Chromatin immunoprecipitationChromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly define cistromes. ChIP also aims to determine the specific location in the genome that various histone modifications are associated with, indicating the target of the histone modifiers.
Continued fractionIn mathematics, a continued fraction is an expression obtained through an iterative process of representing a number as the sum of its integer part and the reciprocal of another number, then writing this other number as the sum of its integer part and another reciprocal, and so on. In a finite continued fraction (or terminated continued fraction), the iteration/recursion is terminated after finitely many steps by using an integer in lieu of another continued fraction. In contrast, an infinite continued fraction is an infinite expression.
