cell biology Cell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living an ...

, a biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in the cell. Such a pathway can trigger the assembly of new molecules, such as a

fat In nutrition science, nutrition, biology, and chemistry, fat usually means any ester of fatty acids, or a mixture of such chemical compound, compounds, most commonly those that occur in living beings or in food. The term often refers specif ...

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

. Pathways can also turn

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s on and off, or spur a cell to move. Some of the most common biological pathways are involved in

metabolism Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...

, the

regulation of gene expression Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...

and the transmission of signals. Pathways play a key role in advanced studies of

genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...

Types of biological pathways

Most common types of biological pathways: *

Metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and Metabolic intermediate, intermediates of an enzymatic reaction are known as metabolites, which are ...

* Genetic pathway *

Signal transduction pathway A signal is both the process and the result of transmission of data over some media accomplished by embedding some variation. Signals are important in multiple subject fields including signal processing, information theory and biology. In ...

Neuroanatomy

In neuroanatomy, a

neural pathway In neuroanatomy, a neural pathway is the connection formed by axons that project from neurons to make synapses onto neurons in another location, to enable neurotransmission (the sending of a signal from one region of the nervous system to ano ...

is the connection formed by

axons An axon (from Greek ἄξων ''áxōn'', axis) or nerve fiber (or nerve fibre: see spelling differences) is a long, slender projection of a nerve cell, or neuron, in vertebrates, that typically conducts electrical impulses known as action pot ...

that project from

neurons A neuron (American English), neurone (British English), or nerve cell, is an membrane potential#Cell excitability, excitable cell (biology), cell that fires electric signals called action potentials across a neural network (biology), neural net ...

to make

synapses In the nervous system, a synapse is a structure that allows a neuron (or nerve cell) to pass an electrical or chemical signal to another neuron or a target effector cell. Synapses can be classified as either chemical or electrical, depending o ...

onto neurons in another location, to enable

neurotransmission Neurotransmission (Latin: ''transmissio'' "passage, crossing" from ''transmittere'' "send, let through") is the process by which signaling molecules called neurotransmitters are released by the axon terminal of a neuron (the presynaptic neuron ...

(the sending of a signal from one region of the nervous system to another).{{Cite book, title = Clinically Oriented Anatomy, last1 = Moore, first1 = Keith, last2 = Dalley, first2 = Arthur, publisher = LWW, year = 2005, isbn = 0-7817-3639-0, edition = 5th, page
47
quote = A bundle of nerve fibers (axons) connecting neighboring or distant nuclei of the CNS is a tract., url-access = registration, url = https://archive.org/details/clinicallyorient00moor_1/page/47

Pathways databases

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...

Pathway database is a popular pathway search database highly used by biologists. * WikiPathways is a community curated pathway database using the "wiki" concept. All pathways have an open license and can be freely used. * Reactome is a free and manually curated online database of biological pathways. * NCI-Nature Pathway Interaction Database is a free biomedical database of human cellular signaling pathways (new official name: NCI Nature Pathway Interaction Database: Pathway, synonym: PID). *

PhosphoSitePlus Cell Signaling Technology, Inc. (CST) is a privately held company that develops and produces Antibody, antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study the cell signaling pathways that impact human health ...

is a database of observed post-translational modifications in human and mouse proteins; an online

systems biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological system ...

resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. * BioCyc database collection is an assortment of organism specific Pathway/Genome Databases. *

Human Protein Reference Database The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore, India. This data ...

is a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome (the last release was #9 in 2010). * PANTHER (Protein ANalysis THrough Evolutionary Relationships) is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. * TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles (provided by geneXplain GmbH). *

MiRTarBase miRTarBase is a curated database of MicroRNA-Target Interactions. As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining ...

is a curated database of MicroRNA-Target Interactions. *

DrugBank The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. A ...

is a comprehensive, high-quality, freely accessible, online database containing information on drugs and drug targets. * esyN is a network viewer and builder that allows to import pathways from the biomodels database or from biogrid, flybase pombase and see what drugs interact with the proteins in your network. *

Comparative Toxicogenomics Database The Comparative Toxicogenomics Database (CTD) is a public website and research tool launched in November 2004 that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, ...

(CTD) is a public website and research tool that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules; CTD illuminates how environmental chemicals affect human health. *

Pathway Commons Pathway Commons is a database of biological pathways and interactions. See also * Biological pathway * Reactome References External links pathwaycommons Biological databases Metabolism Systems biology {{Biodatabase-stub ...

is a project and database that uses BioPAX language to convert, integrate and query other biological pathway and interaction databases.

Sources

Molecular biology