Persius/hicric huggingface dataset:
OCA2
P protein, also known as melanocyte-specific transporter protein or pink-eyed dilution protein homolog, is a protein that in humans is encoded by the oculocutaneous albinism II (OCA2) gene. The P protein is believed to be an integral membrane protein involved in small molecule transport, specifically tyrosine - a precursor of melanin. Certain mutations in OCA2 result in type 2 oculocutaneous albinism.  OCA2 encodes the human homologue of the mouse p (pink-eyed dilution) gene.
The human OCA2 gene is located on the long arm (q) of chromosome 15, specifically from base pair 28,000,020 to base pair 28,344,457 on chromosome 15.

# Function
OCA2 provides instructions for making the protein called P protein which is located in melanocytes which are specialized cells that produce melanin. Melanin is responsible for giving color to the skin, hair, and eyes. Moreover, melanin is found in the light-sensitive tissue of the retina of the eye which plays a role in normal vision.
The exact function of protein P is unknown, but it has been found that it is essential for the normal coloring of skin, eyes, and hair; and likely involved in melanin production. This gene seems to be the main determinant of eye color depending on the amount of melanin production in the iris stroma (large amounts giving rise to brown eyes; little to no melanin giving rise to blue eyes).

# Clinical significance
Mutations in the OCA2 gene cause a disruption in the normal production of melanin; therefore, causing vision problems and reductions in hair, skin, and eye color. Oculocutaneous albinism caused by mutations in the OCA2 gene is called oculocutaneous albinism type 2. The prevalence of OCA type 2 is estimated at 1/38,000-1/40,000 in most populations throughout the world, with a higher prevalence in the African population of 1/3,900-1/1,500. Other diseases associated with the deletion of the OCA2 gene are Angelman syndrome (light-colored hair and fair skin) and Prader-Willi syndrome (unusually light-colored hair and fair skin). With both these syndromes, the deletion often occurs in individuals with either syndrome.
A mutation in the HERC2 gene adjacent to OCA2, affecting OCA2's expression in the human iris, is found common to nearly all people with blue eyes. It has been hypothesized that all blue-eyed humans share a single common ancestor with whom the mutation originated.
The His615Arg allele of OCA2 is involved in the light skin tone and the derived allele is restricted to East Asia with high frequencies, with highest frequencies in Eastern East Asia (49-63%), midrange frequencies in Southeast Asia, and the lowest frequencies in Western China and some Eastern European populations.
OCRL
Inositol polyphosphate 5-phosphatase OCRL-1 (INPP5F), also known as Lowe oculocerebrorenal syndrome protein, is an enzyme encoded by the OCRL gene located on the X chromosome in humans.
This gene encodes a phosphatase enzyme involved in actin polymerization, and is found in the trans-Golgi network.
Mutation in this gene are associated with oculocerebrorenal syndrome and also with Dent's disease.
OGFr
Opioid growth factor receptor, also known as OGFr or the -opioid receptor, is a protein which in humans is encoded by the OGFR gene. The protein encoded by this gene is a receptor for opioid growth factor (OGF), also known as -enkephalin. The endogenous ligand is thus a known opioid peptide, and OGFr was originally discovered and named as a new opioid receptor zeta (). However it was subsequently found that it shares little sequence similarity with the other opioid receptors, and has quite different function.

# Function
The natural function of this receptor appears to be in regulation of tissue growth, and it has been shown to be important in embryonic development, wound repair, and certain forms of cancer.
OGF is a negative regulator of cell proliferation and tissue organization in a variety of processes. The encoded unbound receptor for OGF has been localized to the outer nuclear envelope, where it binds OGF and is translocated into the nucleus. The coding sequence of this gene contains a polymorphic region of 60 nt tandem imperfect repeat units. Several transcripts containing between zero and eight repeat units have been reported.

# Mechanism of activation
The opioid growth factor receptor consists of a chain of 677 amino acids, which includes a nuclear localization sequence region. When OGF binds to the receptor, an OGF-OGFr complex is formed, which leads to the increase in the synthesis of the selective cyclin-dependent kinase (CDK) inhibitor proteins, p12 and p16. Retinoblastoma protein becomes activated through the phosphorylation from CDKs, and leads to the progression of the cell cycle from the G1 phase to the S phase. Because the activation of the OGF receptor, blocks the phosphorylation of retinoblastmoa proteins, retardation of the G1 phase occurs, which prevents the cell from further dividing.

# Therapeutic applications
Upregulation of OGFr and consequent stimulation of the OGF-OGFr system are important for the anti-proliferative effects of  imidazoquinoline drugs like imiquimod and resiquimod, which are immune response modifiers with potent antiviral and antitumour effects, used as topical creams for the treatment of skin cancers and warts.

# Structure
OGF contains a conserved N-terminal domain followed by a series of imperfect repeats.
OLR1
Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) also known as lectin-type oxidized LDL receptor 1 (LOX-1) is a protein that in humans is encoded by the OLR1 gene.
LOX-1 is the main receptor for oxidized LDL on endothelial cells, macrophages, smooth muscle cells, and other cell types. But minimally oxidized LDL is more readily recognized by the TLR4 receptor, and highly oxidized LDL is more readily recognized by the CD36 receptor.

# Function
LOX-1 is a receptor protein which belongs to the C-type lectin superfamily. Its gene is regulated through the cyclic AMP signaling pathway. The protein binds, internalizes and degrades oxidized low-density lipoprotein.
Normally, LOX-1 expression on endothelial cells is low, but tumor necrosis factor alpha, oxidized LDL, blood vessel sheer stress, and other atherosclerotic stimuli substantially increase LOX-1 expression.
LOX-1 may be involved in the regulation of Fas-induced apoptosis.  Oxidized LDL induces endothelial cell apoptosis through LOX-1 binding. Other ligands for LOX-1 include oxidized high-density lipoprotein, advanced glycation end-products, platelets, and apoptotic cells.
The binding of platelets to LOX-1 causes a release of vasoconstrictive endothelin, which induces endothelial dysfunction.
This protein may play a role as a scavenger receptor.

# Clinical significance
Binding of oxidized LDL to LOX-1 activates NF-B, leading to monocyte adhesion to enthothelial cells (a pre-requisite for the macrophage foam cell formation of atherosclerosis). Macrophage affinity for unmodified LDL particles is low, but is greatly increased when the LDL particles are oxidized. LDL oxidation occurs in the sub-endothelial space, rather than in the circulation. But oxidized cholesterol from foods cooked at high temperature can also be a source of oxysterols.
Mutations of the OLR1 gene have been associated with atherosclerosis, risk of myocardial infarction, and may modify the risk of Alzheimer's disease. When applied to human macrophage-derived foam cells in vitro, the dietary supplement berberine inhibits the expression of the ORL1 gene in response to oxidized low-density lipoprotein cholesterol, but this has not yet been demonstrated in a living animal or human.
OMA1
Metalloendopeptidase OMA1, mitochondrial is an enzyme that in humans is encoded by the OMA1 gene. As a metalloprotease, this protein is a substantial component of the quality control system in the inner membrane of mitochondria. Being activated by enzyme Bax and Bak, mitochondrial protease OMA1 promotes cytochrome c release which subsequently induces apoptosis.

# Structure

## Gene
The gene OMA1 encodes a metalloprotease, a founding member of a conserved family of membrane-embedded metallopeptidases in mitochondria. The human gene has 9 exons and locates at chromosome band 1p32.2-p32.1

## Protein
The human protein metalloendopetidase OMA1, mitochondrial is 60.1 kDa in size and composed of 524 amino acids with mitochondrial transition peptide (position 1-13). The mature protein has a theoretical pI of 8.44.

# Function
The inner membrane of mitochondrial houses two AAA proteases and these membrane-embedded peptidases were termed m- and i-AAA proteases to indicate their different topology in the inner membrane. The m-AAA protease is facing the matrix and the i-AAA protease is facing the intermembrane space. OMA1 was shown to share an overlapping proteolytic activity with m-AAA protease. However, OMA1 doesn't completely regulate the turnover of a model substrate, Oxa1, as what the m-AAA protease does. On the contrary, Oma1 only generates N- and C-terminal proteolytic fragments. It has been showed that the mammalian mitochondrial inner membrane fusion protein OPA1 can be degraded by OMA1 when mitochondria lose membrane potential or adenosine triphosphate. Such inducible proteolysis acts as a regulatory mechanism to proteolytically inactivate OPA1, thus preventing the fusion of the mitochondrial network.

# Clinical significance
OMA1 seems to play role in neurodegeneration Several mutations in OMA1 were identified in Amyotrophic Lateral Sclerosis patients.
OMIM

# Overview
The Mendelian Inheritance in Man project is a database that catalogues all the known diseases with a genetic component, and - when possible - links them to the relevant genes in the human genome and provides references for further research and tools for genomic analysis of a catalogued gene.

# Versions
It is available as a book named after the project, and it is currently in its 12th edition. The online version is called Online Mendelian Inheritance in ManTM (OMIMTM), which can be accessed with the Entrez database searcher of the National Library of Medicine and is part of the NCBI project Education.

# Collection process
The information in this database is collected and processed under the leadership of Dr. Victor A. McKusick at Johns Hopkins University, assisted by a team of science writers and editors. Relevant articles are identified, discussed and written up in the relevant entries in the MIM database

# The MIM code
Every disease and gene is assigned a six digit number of which the first number classifies the method of inheritance.
If the initial digit is 1, the trait is deemed autosomal dominant; if 2, autosomal recessive; if 3, X-linked. Wherever a trait defined in this dictionary has a MIM number, the number from the 12th edition of MIM, is given in square brackets with or without an asterisk (asterisks indicate that the mode of inheritance is known; a number symbol (#) before an entry number means that the phenotype can be caused by mutation in any of 2 or more genes) as appropriate e.g., Pelizaeus-Merzbacher disease  is a well-established, autosomal, dominant, mendelian disorder.
OPN5
Neuropsin is a protein that in humans is encoded by the OPN5 gene. It is a photoreceptor protein sensitive to ultraviolet (UV) light. The OPN5 gene was discovered in mouse and human genomes and its mRNA expression was also found in neural tissues. Neuropsin is bistable at 0 C and activates a UV-sensitive, heterotrimeric G protein Gi-mediated pathway in mammalian and avian tissues.

# Function
Opsins are members of the G protein-coupled receptor superfamily. Human neuropsin is expressed in the eye, brain, testes, and spinal cord. Neuropsin belongs to the seven-exon subfamily of mammalian opsin genes that includes peropsin (RRH) and retinal G protein coupled receptor (RGR). Neuropsin has different isoforms created by alternative splicing.

# Photochemistry
When reconstituted with 11-cis-retinal, mouse and human neuropsins absorb maximally at 380 nm. When illuminated these neuropsins are converted into blue-absorbing photoproducts (470 nm), which are stable in the dark. The photoproducts are converted back to the UV-absorbing form, when they are illuminated with orange light (> 520 nm).

# Phylogeny
The neuropsins constitute one of the four subclades of the Go/RGR group of opsins, also known as RGR/Go or Group 4. Go/RGR is one of the four major subclades of type-II opsins, also known as metazoan or animal opsins. Go/RGR comprises Go-coupled, RGR, peropsins, and neuropsins. Type-II opsins comprise four subclades: C-opsins (ciliary), R-opsins (rhabdomeric), Cnidops (cnidarian), and Go/RGR. Three of these subclades occur only in Bilateria (all but Cnidops). However, the bilaterian clades constitute a parphyletic taxon without Cnidops.

# Species Distribution
Neuropsin and its orthologs have been found experimentally in a small number of animals, among them human, house mouse (Mus musculus), chicken (Gallus gallus domesticus), the Japanese quail (Coturnix japonica), the European brittle star Amphiura filiformis (related to starfish), the tardigrade water bear (Hypsibius dujardini), and the tadpole of Xenopus laevis.
Searches of publicly available databases of genetic sequences have found putative neuropsin orthologs in both major branches of Bilateria: protostomes and deuterostomes. Among protostomes, putative neuropsins have been found in the molluscs owl limpet (Lottia gigantea) (a species of sea snail) and Pacific oyster (Crassostrea gigas), in the water flea (Daphnia pulex) (an arthropod), and in the annelid worm Capitella teleta.
ORC6
Origin recognition complex subunit 6 is a protein that in humans is encoded by the ORC6 (ORC6L) gene.

# Background
The origin recognition complex (ORC) is a highly conserved six subunit protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins.

# Function
The protein encoded by this gene is a subunit of the ORC complex. It has been shown that this protein and ORC1 are loosely associated with the core complex consisting of ORC2, -3, -4 and -5. Gene silencing studies with small interfering RNA demonstrated that this protein plays an essential role in coordinating chromosome replication and segregation with cytokinesis.

# Interactions
ORC6 has been shown to interact with MCM5, ORC2, Replication protein A1, ORC4, DBF4, ORC3, CDC45-related protein, MCM4 and Cell division cycle 7-related protein kinase.
Oklo
Oklo is a region near the town of Franceville, in the Haut-Ogooue province of the Central African state of Gabon.
The discovery in September 1972 of several natural nuclear fission reactors in the uranium mines situated there has fired the imagination and aroused the curiosity of scientists.

# History
Gabon was a French colony when prospectors from the French nuclear energy commissariat (the industrial parts, which later became the COGEMA) discovered uranium in the remote region in 1956. France immediately opened mines operated by Comuf (Compagnie des Mines d'Uranium de Franceville) near Mounana village in order to exploit the vast mineral resources and the State of Gabon was given a minority share in the company.
For forty years, France mined for uranium in Gabon. Once extracted, the uranium was used for electricity production in France and much of Europe. Gabon's miners half-joked that it was thanks to them that France's high-speed TGV trains could operate. Today, however, the uranium deposits are exhausted, and the mine is no longer worked. Currently, reclamation work is ongoing in the region affected by the mine operations.
There is strong geochemical evidence that the Oklo uranium deposit behaved as a natural nuclear fission reactor in Precambrian times: Some of mined uranium was found to have a lower concentration of U235 than expected, as if it had already been in a reactor. Geologists found that it had been in a reactor before -- two billion years ago. At that time the natural uranium had a concentration of about 3% U235, and could have gone critical with natural water as neutron moderator.
Olea

# Overview
Olea (/oli/) is a genus of about 40 species in the family Oleaceae, native to warm temperate and tropical regions of southern Europe, Africa, southern Asia and Australasia. They are evergreen trees and shrubs, with small, opposite, entire leaves. The fruit is a drupe. Leaves of Olea contain Tricho sclereids.
For humans, the most important species is by far the Olive (Olea europaea), native to the Mediterranean region. O. paniculata is a larger tree, attaining a height of 1518 m in the forests of Queensland, and yielding a hard and tough timber. The yet harder wood of the Black Ironwood O. laurifolia, an inhabitant of Natal, is important in South Africa.
Olea species are used as food plants by the larvae of some Lepidoptera species including Double-striped Pug.

# Selected species
- Olea ambrensis H.Perrier
- Olea borneensis Boerl.
- Olea brachiata (Lour.) Merr.
- Olea capensis L.  Small Ironwood
- Olea caudatilimba L.C.Chia
- Olea chimanimani Kupicha
- Olea chrysophylla Lam.
- Olea cordatula H.L.Li
- Olea dioica Roxb.
- Olea europaea L.  Olive
- Olea exasperata Jacq.
- Olea gagnepainii Knobl.
- Olea gamblei C.B.Clarke
- Olea guangxiensis B.M.Miao
- Olea hainanensis H.L.Li
- Olea javanica (Blume) Knobl.
- Olea lancea Lam.
- Olea laurifolia Lam.  Black Ironwood
- Olea laxiflora H.L.Li
- Olea moluccensis Kiew
- Olea neriifolia H.L.Li
- Olea obovata (Merr.) Kiew
- Olea oleaster Hoffmanns. & Link  Wild-olive
- Olea palawanensis Kiew
- Olea paniculata R.Br.
- Olea parvilimba (Merr. & Chun) B.M.Miao
- Olea polygama Wight
- Olea rosea Craib
- Olea rubrovenia (Elmer) Kiew
- Olea salicifolia Wall. ex G.Don
- Olea schliebenii Knobl.
- Olea sylvestris Mill.
- Olea tetragonoclada L.C.Chia
- Olea tsoongii (Merr.) P.S.Green
- Olea undulata (Sol.) Jacq.
- Olea welwitschii (Knobl.) Gilg & G.Schellenb.
- Olea wightiana Wall. ex G.Don
- Olea woodiana Knobl.
- Olea yuennanensis Hand.-Mazz.

## Formerly placed here
- Chionanthus foveolatus (E.Mey.) Stearn (as O. foveolata E.Mey.)
- Ligustrum compactum var. compactum (as O. compacta Wall. ex G.Don)
- Nestegis cunninghamii (Hook.f.) L.A.S.Johnson (as O. cunninghamii Hook.f.)
- Noronhia emarginata (Lam.) Thouars (as O. emarginata Lam.)
- Osmanthus americanus (L.) Benth. & Hook.f. ex A.Gray (as O. americana L.)
- Osmanthus heterophyllus (G. Don) P.S.Green (as O. aquifolium Siebold & Zucc. or O. ilicifolia Siebold ex Hassk.)
Osha
Osha (Ligusticum porteri) is a perennial herb used for its medicinal properties. Osha grows in parts of the Rocky Mountains especially in the North American Southwest.
L. porteri (Osha) root or L. wallichii (Ligusticum) root can be steeped in ethanol (whisky, vodka, etc.) for at least a month. The resulting tincture is an effective, albeit pungent, liniment for sore muscles that can be stored (in a cool place) indefinitely.

# Synonymy
Osha is also known by the following names:
- Osha root, Porter's Lovage, Porter's Licorice-root, Lovage, Wild Lovage, Porter's Wild Lovage, Loveroot, Porter's Ligusticum, Bear Medicine, Bear Root, Colorado Cough Root, Indian Root, Indian Parsley, Wild Parsley, Mountain Ginseng, Mountain Carrot, Nipo, Empress Of The Dark Forest, Chuchupate, Chuchupati, Chuchupaste, Chuchupatle, Guariaca, Hierba del cochino, Raiz del cochino, Washia (tarahumara), Yerba de cochino
In the Jicarilla language, osha is called haichidee. The White Mountain Apache (WMA)call it '"Ha 'il chii' gah".
Osha is still commonly used widely by the Apaches and other native tribes. According to WMA Elders, they would use it as a snake and insect repellant:It has a strong smell. Apaches use this herb to aid in the curing of common colds, sore throats, cough, sinusitis, and other side effects of the winter season.
It is said that when put in water over your woodstove, it will help in keeping you immune in winter times.
P4HB
Protein disulfide-isomerase, also known as the beta-subunit of prolyl 4-hydroxylase (P4HB), is an enzyme that in humans encoded by the P4HB gene. The human P4HB gene is localized in chromosome 17q25. Unlike other prolyl 4-hydroxylase family proteins, this protein is multifunctional and acts as an oxidoreductase for disulfide formation, breakage, and isomerization. The activity of P4HB is tightly regulated. Both dimer dissociation and substrate binding are likely to enhance its enzymatic activity during the catalysis process.

# Structure
P4HB has four thioredoxin domains (a, b, b, and a), with two CGHC active sites in the a and a domains. In both the reduced and oxidized state, these domains are arranged as a horseshoe shape. In reduced P4HB, domains a, b, and b' are in the same plane, while domain a' twists out at an 45 angle. When oxidized, the four domains stay in the same plane, and the distance between the active sites is larger than that in the reduced state. The oxidized form also exposes more hydrophobic areas and possesses a larger cleft to facilitate substrate binding. P4HB has been shown to dimerize in vivo via noncatalytic bb' domains. Formation of dimer blocks substrate-binding site and inhibits P4HBs activity.

# Function
This gene encodes the beta subunit of prolyl 4-hydroxylase, a highly abundant multifunctional enzyme that belongs to the protein disulfide isomerase family. When present as a tetramer consisting of two alpha and two beta subunits, this enzyme is involved in hydroxylation of prolyl residues in preprocollagen. This enzyme is also a disulfide isomerase containing two thioredoxin domains that catalyze the formation, breakage and rearrangement of disulfide bonds. Other known functions include its ability to act as a chaperone that inhibits aggregation of misfolded proteins in a concentration-dependent manner, its ability to bind thyroid hormone, its role in both the influx and efflux of S-nitrosothiol-bound nitric oxide, and its function as a subunit of the microsomal triglyceride transfer protein complex.

# Clinical significance
P4HB is a risk factor of amyotrophic lateral sclerosis (ALS). Studies have shown significant genotypic associations for two SNPs in P4HB with FALS (familial ALS), rs876016 (P=0.0198) and rs2070872 (P=0.0046). Together with other ER stress markers, P4HB is greatly elevated in ALS spinal cord. P4HB can also be nitrosylated, and elevation of nitrosylated P4HB has been shown in Parkinson's and Alzheimer's disease brain tissue, as well as in transgenic mutant superoxide dismutase 1 mouse and human sporadic amyotrophic lateral sclerosis spinal cord tissues. In addition to neurodegenerative diseases, P4HB level is upregulated in glioblastoma multiforme (GBM) (brain tumor). Inhibition of P4HB attenuates resistance to temozolomide, a standard GBM chemotherapeutic agent, via the PERK arm of endoplasmic reticulum stress response pathway. Furthermore, heterozygous missense mutation in P4HB can cause Cole-Carpenter syndrome, a severe bone fragility disorder.

# Interactions
P4HB has been shown to interact with UBQLN1, ERO1LB and ERO1L.
PAG1
Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 is a protein that in humans is encoded by the PAG1 gene.
The protein encoded by this gene is a type III transmembrane adaptor protein that binds to the tyrosine kinase csk protein. It is thought to be involved in the regulation of T cell activation.

# Interactions
PAG1 has been shown to interact with FYN, C-src tyrosine kinase, Sodium-hydrogen antiporter 3 regulator 1 and Abl gene.