Persius/hicric huggingface dataset:
PNKD
PNKD is the abbreviation for a human neurological movement disorder  paroxysmal nonkinesiogenic dyskinesia. Like many other human genetics disorders, PNKD also refers to the disease, the disease gene and the encoded protein. (PNKD) is a protein that in humans is encoded by the PNKD gene. Alternative splicing results in the transcription of three isoforms.  The mouse ortholog is called brain protein 17 (Brp17).

# Structure
This gene is located on chromosome 2 at the band 2q35 and contains 12 exons. At least three isoforms of varying lengths (long, medium, and short) can be produced by alternative splicing of this gene. While the gene products of the long (PNKD-L) and medium (PNKD-M) isoforms contain the C-terminal -lactamase domain, the short (PNKD-S) isoform, commonly referred to as myofibrillogenesis regulator-1 (MR-1), contains only three exons and lacks homology to any known protein. These isoforms also differ in their tissue-specific expression and subcellular localization. Specifically, PNKD-L is only expressed in the central nervous system whereas PNKD-M and PNKD-S are ubiquitously expressed across tissues. Moreover, PNKD-L localizes to the cell membrane, PNKD-S to the cytoplasm and nucleus, and PNKD-M to the mitochondrion.

# Function
The function of PNKD proteins are unknown but the long and medium isoforms of PNKD contain a conserved -lactamase domain which suggest it may function as an enzyme. The closest mammalian homolog to PNKD is  HAGH, an enzyme involves in a two-step reaction to hydrolyze SLG and produce D-lactic acid and reduced GSH. However, the hydrolytic activity of PNKD is minimal.
The long form of PNKD is neuronal specific and encodes a synaptic protein that localizes dominantly to the pre-synaptic membrane. Post-synaptic area and vesicular structure also occasionally has PNKD long form. PNKD long form interacts with pre-synaptic protein RIM and inhibits synaptic exocytosis. PNKD with disease mutations is less effective in inhibition thus the synaptic release is increased. This would cause excessive neurotransmitter release in the brain and maybe the root cause for triggering epilepsy in PNKD patients.

# Clinical significance
Point mutations in PNKD exon 1 cause an inherited neurological movement disorder in human, paroxysmal non-kinesigenic dyskinesia. Overexpression of PNKD has also been associated with multiple cancers, including pancreatic ductal adenocarcinoma, gastric cancer, ovarian cancer, and breast cancer and may serve as a therapeutic target for treating these cancers or a biomarker for assessing patient outcome. The signaling pathways involved may vary depending on the cancer. For instance, in human breast cancer (MCF7) cells, PNKD may promote tumor cell proliferation by activating the MEK/ERK signaling pathway, while in human hepatoma (HepG2) cells, PNKD may operate through the MLC2/FAK/AKT pathway.

# Interactions
PNKD has been shown to interact with:
- Rab3-interacting molecule (RIM)1
- RIM2
PNPO
Pyridoxine-5'-phosphate oxidase is an enzyme that in humans is encoded by the PNPO gene.
Vitamin B6, or pyridoxal 5-prime-phosphate (PLP), is critical for normal cellular function, and some cancer cells have notable differences in vitamin B6 metabolism compared to their normal counterparts. The rate-limiting enzyme in vitamin B6 synthesis is pyridoxine-5-prime-phosphate (PNP) oxidase (PNPO; EC 1.4.3.5).

# Model organisms
Model organisms have been used in the study of PNPO function. A conditional knockout mouse line, called Pnpotm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty four tests were carried out on mutant mice and two significant abnormalities were observed.  No homozygous mutant embryos were identified during gestation, and therefore none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice; no additional significant abnormalities were observed in these animals.
POLG
DNA polymerase subunit gamma (POLG or POLG1) is an enzyme that in humans is encoded by the POLG gene. Mitochondrial DNA polymerase is heterotrimeric, consisting of a homodimer of accessory subunits plus a catalytic subunit. The protein encoded by this gene is the catalytic subunit of mitochondrial DNA polymerase.  Defects in this gene are a cause of progressive external ophthalmoplegia with mitochondrial DNA deletions 1 (PEOA1), sensory ataxic neuropathy dysarthria and ophthalmoparesis (SANDO), Alpers-Huttenlocher syndrome (AHS), and mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE).

# Structure
POLG is located on the q arm of chromosome 15 in position 26.1 and has 23 exons. The POLG gene produces a 140 kDa protein composed of 1239 amino acids. POLG, the protein encoded by this gene, is a member of the DNA polymerase type-A family. It is a mitochondrion nucleiod with an Mg2+ cofactor and 15 turns, 52 beta strands, and 39 alpha helixes. POLG contains a polyglutamine tract near its N-terminus that may be polymorphic. Two transcript variants encoding the same protein have been found for this gene. 

# Function
POLG is a gene that codes for the catalytic subunit of the mitochondrial DNA polymerase, called DNA polymerase gamma. The human POLG cDNA and gene were cloned and mapped to chromosome band 15q25.  In eukaryotic cells, the mitochondrial DNA is replicated by DNA polymerase gamma, a trimeric protein complex composed of a catalytic subunit, POLG, and a dimeric accessory subunit of 55 kDa encoded by the POLG2 gene.  The catalytic subunit contains three enzymatic activities, a DNA polymerase activity, a 3-5 exonuclease activity that proofreads misincorporated nucleotides, and a 5-dRP lyase activity required for base excision repair.

## Catalytic activity
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

# Clinical significance
Mutations in the POLG gene are associated with several mitochondrial diseases, progressive external ophthalmoplegia with mitochondrial DNA deletions 1 (PEOA1), sensory ataxic neuropathy dysarthria and ophthalmoparesis (SANDO), Alpers-Huttenlocher syndrome (AHS), and mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE). Pathogenic variants have also been linked with fatal congenital myopathy and gastrointestinal pseudo-obstruction and fatal infantile hepatic failure. A list of all published mutations in the POLG coding region and their associated disease can be found at the Human DNA Polymerase Gamma Mutation Database.

# Interactions
POLG has been shown to have 50 binary protein-protein interactions including 32 co-complex interactions. POLG appears to interact with POLG2, Dlg4, Tp53, and Sod2.
POLH
Polymerase (DNA directed), eta, also known as POLH, is a protein which in humans is encoded by the POLH gene.

# Function
This gene encodes a member of the Y family of specialized DNA polymerases. It copies undamaged DNA with a lower fidelity than other DNA-directed polymerases. However, it accurately replicates UV-damaged DNA; when thymine dimers are present, this polymerase inserts the complementary nucleotides in the newly synthesized DNA, thereby bypassing the lesion and suppressing the mutagenic effect of UV-induced DNA damage. This polymerase is thought to be involved in hypermutation during immunoglobulin class switch recombination. Mutations in this gene result in XPV, a variant type of xeroderma pigmentosum.

# Clinical significance
Xeroderma pigmentosum (XP) is an autosomal recessive human disease characterized by sunlight sensitivity, cutaneous and ocular deterioration, and premature malignant skin neoplasms after exposure to sunlight. XP has been classified into eight complementation groups, XP-A to XP-G and XP-V. Cells from XP-A to XP-G patients have defects in the process of nucleotide excision repair (NER), which eliminates a wide variety of structurally unrelated lesions, including ultraviolet light (UV)-induced cyclobutane pyrimidine dimers (CPD) and (6-4) photoproducts, as well as certain chemical adducts. The genes and proteins of XP groups A, B, C, D, F and G have been isolated and found to represent some of the subunits of the core NER machinery. In contrast, cells belonging to the eighth group, XP variant (XP-V), are NER-proficient but display abnormal DNA replication, including reduced ability to elongate nascent DNA strands on UV-irradiated DNA. Thus, the XP-V gene product is likely to be involved in the process of DNA replication on damaged DNA known as post-replication repair, but not in NER
POT1
Protection of telomeres protein 1 is a protein that in humans is encoded by the POT1 gene.

# Function
This gene is a member of the telombin family and encodes a nuclear protein involved in telomere maintenance. Specifically, this protein functions as a member of a multi-protein complex known as shelterin, that binds to the TTAGGG repeats of telomeres, regulating telomere length and protecting chromosome ends from illegitimate recombination, catastrophic chromosome instability, and abnormal chromosome segregation. Alternatively spliced transcript variants have been described.
The absence of POT1 in mouse embryonic fibroblasts and chicken cells leads to a detrimental DNA damage response on telomeres resulting in telomere dysfunction-induced foci (TIFs). POT1 is required for telomere protection because it allows for telomere inhibition of DNA damage response factors. The protein also serves a role in the regulation of telomerase activity on telomeres. In vitro experiments utilizing human POT1 have shown that reduction in POT1 levels result in the elongation of telomeres.

# Interactions
POT1 has been shown to interact with ACD and TINF2.

# Pathology
- Increased transcriptional expression of this gene is associated with stomach carcinogenesis and its progression.
- Mutations in this gene have also been associated to the acquisition of the malignant features of chronic lymphocytic leukemia.
- POT1 loss-of-function variants predispose to familial melanoma and glioma.
PPAN
Suppressor of SWI4 1 homolog is a protein that in humans is encoded by the PPAN gene.
The protein encoded by this gene is an evolutionarily conserved protein similar to yeast SSF1 as well as to the gene product of the Drosophila gene peter pan (PPAN). SSF1 is known to be involved in the second step of mRNA splicing. Both SSF1 and PPAN are essential for cell growth and proliferation. This gene was found to cotranscript with P2RY11/P2Y(11), an immediate downstream gene on the chromosome that encodes an ATP receptor. The chimeric transcripts of this gene and P2RY11 were found to be ubiquitously present and regulated during granulocytic differentiation. Exogenous expression of this gene was reported to reduce the anchorage-independent growth of some tumor cells.
One of the introns of PPAN encodes the Small nucleolar RNA SNORD105.
PPID
PPID may also refer to Private Personal Identifier, a standard SAML assertion.
Peptidylprolyl isomerase D (cyclophilin D), also known as PPID, is a human gene.
The protein encoded by this gene is a member of the peptidyl-prolyl cis-trans isomerase (PPIase) family. PPIases catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and accelerate the folding of proteins. This protein has been shown to possess PPIase activity and, similar to other family members, can bind to the immunosuppressant cyclosporin A.
PPT1
Palmitoyl-protein thioesterase 1 (PPT-1), also known as palmitoyl-protein hydrolase 1, is an enzyme that in humans is encoded by the PPT1 gene.

# Function
PPT-1 a member of the palmitoyl protein thioesterase family.  PPT-1 is a small glycoprotein involved in the catabolism of lipid-modified proteins during lysosomal degradation. This enzyme removes thioester-linked fatty acyl groups such as palmitate from cysteine residues.

# Clinical significance
Defects in this gene are a cause of neuronal ceroid lipofuscinosis type 1 (CLN1).
<ref Genetic basis and phenotypic correlations of the neuronal ceroid lipofusinoses. 
Warrier V; Vieira M; Mole SE.
Biochimica et Biophysica Acta. 1832(11):1827-30, 2013>
PSPH
Phosphoserine phosphatase is an enzyme that in humans is encoded by the PSPH gene.

# Function
The protein encoded by this gene belongs to a subfamily of the phosphotransferases. This encoded enzyme is responsible for the third and last step in L-serine formation. It catalyzes magnesium-dependent hydrolysis of L-phosphoserine and is also involved in an exchange reaction between L-serine and L-phosphoserine. Deficiency of this protein is thought to be linked to Williams syndrome.

# Clinical significance
Homozygous or compound heterozygous mutations in PSPH cause Neu-Laxova syndrome and Phosphoserine phosphatase deficiency.

# Model organisms
Model organisms have been used in the study of PSPH function. A conditional knockout mouse line called Psphtm1a(EUCOMM)Hmgu was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed:  - In-depth immunological phenotyping
PTK6
Tyrosine-protein kinase 6 is an enzyme that in humans is encoded by the PTK6 gene.

# Function
Tyrosine-protein kinase 6 (also known as Breast Tumor Kinase, Brk) is a cytoplasmic non-receptor protein kinase which may function as an intracellular signal transducer in epithelial tissues. The encoded protein has been shown to undergo autophosphorylation.

# Clinical significance
Overexpression of this gene in mammary epithelial cells leads to sensitization of the cells to epidermal growth factor and results in a partially transformed phenotype.  Expression of this gene has been detected at low levels in some breast tumors but not in normal breast tissue.

# Interactions
PTK6 has been shown to interact with STAP2 and KHDRBS1.
PTK7
Tyrosine-protein kinase-like 7 also known as colon carcinoma kinase 4 (CCK4) is a receptor tyrosine kinase that in humans is encoded by the PTK7 gene.

# Function
Receptor protein tyrosine kinases transduce extracellular signals across the cell membrane. A subgroup of these kinases lack detectable catalytic tyrosine kinase activity but retain roles in signal transduction. The protein encoded by this gene an intracellular domain with tyrosine kinase homology and may function as a cell adhesion molecule. This gene is thought to be expressed in colon carcinomas but not in normal colon, and therefore may be a marker for or may be involved in tumor progression. Four transcript variants encoding four different isoforms have been found for this gene.
PTK7 serves as a context-dependent signalling switch for the Wnt pathways (particularly in planar cell polarity related functions such as convergent extension and neural crest cell migration) and appears to have similar functions for plexin and Flt-1 pathways. PTK7 was identified to be highly expressed in colon cancer by Saha et al. using serial analysis of gene expression (LongSAGE). Pfizer is targeting PTK7 for cancer by generating an antibody-drug conjugate against the PTK7 receptor.
PTRF
Polymerase I and transcript release factor, also known as Cavin1, Cavin-1 or PTRF, is a protein which in humans is encoded by the PTRF gene.

# Function
PTRF (Cavin1) has been shown to be crucial for caveola formation and function. 
Termination of RNA polymerase I catalyzed transcription is a 2-step process that involves pausing of transcription elongation and release of both the pre-ribosomal RNA and Pol I from the DNA template. The pausing is mediated by TTF1 and PTRF.
PTRF is a soluble protein containing putative leucine zipper, nuclear localization signal, and PEST domains.

# Interactions
PTRF (Cavin1) forms trimers with Cavin2 and Cavin3 in caveola formation and has been shown to interact with other membrane associating proteins such as EHD2 and caveolins. 
PTRF has been shown to interact with ZNF148.
PUVA

# Overview
PUVA is a psoralen + UVA treatment for eczema, psoriasis, graft-versus-host disease, vitiligo, mycosis fungoides, large-plaque parapsoriasis and cutaneous T-cell lymphoma. The psoralen is applied or taken orally to sensitize the skin, then the skin is exposed to UVA.
Photodynamic therapy is the general use of nontoxic light-sensitive compounds that are exposed selectively to light, whereupon they become toxic to targeted malignant and other diseased cells. Still, PUVA therapy is often classified as a separate technique from photodynamic therapy.

# Procedure
Psoralens are photosensitizing agents found in plants. Psoralens are taken systemically or can be applied directly to the skin. The psoralens allow a relatively lower dose of UVA to be used. When they are combined with exposure to UVA in PUVA, they are highly effective at clearing psoriasis and vitiligo. Like UVB light treatments, the reason remains unclear, though investigators speculate there may be similar effects on cell turnover and the skin's immune response.
Choosing the proper dose for PUVA is similar to the procedure followed with UVB. The physician can choose a dose based on the patient's skin type. The dose will increase in every treatment until the skin starts to respond.
Some clinics test the skin before the treatments, by exposing a small area of the patient's skin to UVA, after ingestion of psoralen. The dose of UVA that produces uniform redness 72 hours later, called the minimum phototoxic dose (MPD), becomes the starting dose for treatment.
At the very least for vitiligo, narrowband ultraviolet B (UVB) phototherapy is now used more commonly than PUVA since it does not require the use of the Psoralen. As with PUVA, treatment is carried out twice weekly in a clinic or every day at home, and there is no need to use psoralen.
Narrowband UVB does not cure the legs and hands, compared to the face and neck. To the hands and legs PUVA may be more effective. The reason can be because UVA penetrates deeper in the skin, and the melanocytes in the skin of the hands and legs is deeper in the skin. The Narrowband UVB does not reach the melanocytes.

# Side effects and complications
Some patients experience nausea and itching after ingesting the psoralen compound. For these patients PUVA bath therapy may be a good option.
Long term use of PUVA therapy has been associated with higher rates of skin cancer.
The most significant complication of PUVA therapy for psoriasis is squamous cell skin cancer. Two carcinogenic components of the therapy include the nonionizing radiation of UVA light as well as the psoralen intercalation with DNA. Both processes negatively impact overall genome instability.

# History
Psoralens have been known since ancient Egypt but have only been available in a chemically synthesized form since the 1970s.
PXDN
Peroxidasin homolog is a protein that in humans is encoded by the PXDN gene.
Peroxidasin requires ionic bromine as a co-factor, making bromine an essential element for human life.

# Clinical significance
Mutations in PXDN are associated with                 microphthalmia            .
Piwi
The piwi (sometimes also PIWI; originally P-element induced wimpy testis in Drosophila) class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells. Piwi proteins are highly conserved across evolutionary lineages and are present in both plants and animals. One of the major human homologs, whose upregulation is implicated in the formation of tumors such as seminomas, is called hiwi; other variants on the theme include the miwi protein in mice.

# Role in RNA interference
The piwi domain is a protein domain homologous to piwi proteins and present in a large number of nucleic acid-binding proteins, especially those that bind and cleave RNA. The best-studied such family of proteins is the argonaute family; argonautes are RNase H-like enzymes that carry out the catalytic functions of the RNA-induced silencing complex (RISC). In the well-known cellular process of RNA interference, the argonaute protein in the RISC complex binds small interfering RNA (siRNA) generated from exogenous double-stranded RNA or microRNA (miRNA) generated from endogenous non-coding RNA, both the ribonuclease dicer. The RNA-RISC complex binds and cleaves complementary base pairing messenger RNA, destroying it and preventing its translation into a protein. Crystallized piwi domains have a conserved basic binding site for the 5' end of bound RNA; in the case of argonaute proteins binding siRNA strands, the last unpaired nucleotide base of the siRNA is also stabilized by base stacking interactions between the base and neighboring tyrosine residues.
Recent evidence suggests that the germ-line determination function of piwi proteins relies on their interaction with miRNAs, which are known to play a key role in early development and morphogenesis of Drosophila melanogaster embryos, in which germ-line maintenance has been extensively studied.

# piRNAs and transposon silencing
Recently, a novel class of longer-than-average miRNAs known as Piwi-interacting RNAs (piRNAs) has been defined in mammalian cells, about 26-31 nucleotides long as compared to the more typical miRNA or siRNA of about 21 nucleotides. These piRNAs are expressed specifically in spermatogenic cells in the testes of mammals. piRNAs have been identified in the genomes of mice, rats, and humans, with an unusual "clustered" genomic organization that may originate from repetitive regions of the genome such as retrotransposons or regions normally organized into heterochromatin, and which are normally derived exclusively from the antisense strand of double-stranded RNA. piRNAs have thus been classified as repeat-associated small interfering RNAs (rasiRNAs). Although their biogenesis is not yet well understood, piRNAs and Piwi proteins are thought to form an endogenous system for silencing the expression of selfish genetic elements such as retrotransposons and thus preventing the gene products of such sequences from interfering with germ cell formation.
Puto
This article is about the Filipino food. For the Spanish homophobic epithet, see Spanish Profanity, or faggot for the English equivalent.
Puto is a type of fermented rice cake eaten in the Philippines.
It is produced by fermenting a mixture of soaked ground rice and sugar with a culture of bacteria such as Leuconostoc mesenteroides and Streptococcus faecalis.