ProteinCenter User Manual
Table of Contents

Appendix D. GOslim Categories

Table of Contents

D.1. GeneOntology
D.1.1. Cellular component
D.1.2. Molecular function
D.1.3. Biological process

This appendix provides an overview of the GOslim used in ProteinCenter™:

D.1. GeneOntology

Gene ontology terms linked to specific proteins are obtained using mappings from the gene ontology consortium website.

The following sources are used to obtain GO data:

  1. UniProt Knowledge base keywords

  2. EC numbers (Enzyme Commission)

  3. InterPro domains (obtained from IPI)

  4. Pfam domains (created by Thermo Fisher Scientific by searching PFAM with rpsBLAST)

  5. Ensembl key to GO id mappings

The GO identifiers obtained this way often describe the corresponding proteins at a high level of detail. While this level of detail can be advantageous in many cases, it is not necessarily well suited to give a quick overview of a large set of proteins or to perform statistics. For this purpose we have defined a GOslim that reduces the number of terms to approximately 20 large groups for each of the three term types.

A detailed description of GeneOntology and GO terms can be found at the Gene Ontology Consortium website: http://geneontology.org.

A general introduction: http://geneontology.org/GO.doc.shtml. And GOslims in particular: http://geneontology.org/GO.slims.shtml.

D.1.1. Cellular component

The GOslim categories for cellular component are described in Table D.1, “GOslim categories for Cellular Component”

Table D.1. GOslim categories for Cellular Component

GOslim Cellular Component Description & Notes
cell surfaceProteins that are attached to the external part of the cell wall and/or cell membrane.
chromosomeA structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
cytoplasmAll of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoskeletonAny of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
cytosolThat part of the cytoplasm that does not contain membranous or particulate subcellular components..
endosomeA membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
Endoplasmatic ReticulumThe irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slit-like cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
extracellularThe space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term only applies to proteins that are not attached to the cell surface. This term covers the host cell environment outside an intracellular parasite.
GolgiA compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations.
membraneDouble layer of lipid molecules that encloses all cells, and, in eukaryotic, many organelles; may be a single or double lipid bilayer; also includes associated proteins. Note: this term is not restricted to the plasma membrane, but applies to all types of membranes present in the cell, i.e. also nuclear membranes and mitochondrial membranes.
mitochondrionA semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
nucleusA membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
SpliceosomeA ribonucleoprotein complex, containing RNA and small nuclear ribonucleoproteins (snRNPs) that is assembled during the splicing of messenger RNA primary transcript to excise an intron.
protein complexAny protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
ribosomeAn intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA).
vacuoleA closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
Organelle lumenThe volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear membrane lumen.

Note, that the annotation is continuously updated and improved, hence these numbers represent a snapshot from February 2008.

Click the reset button to set the input field to all possible Cellular components in current dataset. Then remove the ones that are not of interest.

D.1.2. Molecular function

The GOslim categories for molecular function are described in Table D.2, “GOslim categories for Molecular Function” .

Table D.2. GOslim categories for Molecular Function

GOslim Molecular Function Description & Notes
antioxidant activityInhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
catalytic activityCatalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein.
DNA bindingInteracting selectively with DNA (deoxyribonucleic acid).
enzyme regulator activityModulates the activity of an enzyme.
metal ion bindingInteracting selectively with any metal ion.
motor activityCatalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate.
nucleotide bindingInteracting selectively with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose moiety.
protein bindingInteracting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
receptor activityCombining with an extracellular or intracellular messenger to initiate a change in cell activity.
RNA bindingInteracting selectively with an RNA molecule or a portion thereof.
signal transducer activityMediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell.
structural molecule activityThe action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell.
transcription regulator activityPlays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.
translation regulator activityAny substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
transporter activityEnables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

Click the reset button to set the input field to all possible Molecular function in current dataset. Then remove the ones that are not of interest.

D.1.3. Biological process

The GOslim categories for biological process are described in Table D.3, “GOslim categories for Biological Process” .

Table D.3. GOslim categories for Biological Process

GOslim Biological Process Description & Notes
cell communicationAny process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
cell deathThe specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
cell differentiationThe process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate.
cell divisionThe processes resulting in the physical partitioning and separation of a cell into daughter cells.
cell growthThe process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
cell homeostasisThe processes involved in the maintenance of an internal equilibrium at the level of the cell.
cell motilityAny process involved in the controlled movement of a cell.
cell organization and biogenesisA process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
cell proliferationThe multiplication or reproduction of cells, resulting in the rapid expansion of a cell population.
coagulationThe process by which a fluid solution, or part of it, changes into a solid or semisolid mass.
conjugationThe union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
defense responseReactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
developmentThe biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
metabolic processProcesses that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
regulation of biological processAny process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
reproductionThe production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
response to stimulusA change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
transportThe directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.