Persius/hicric huggingface dataset:
PADI4
Peptidyl arginine deiminase, type IV, also known as PADI4, is a human protein which in humans is encoded by the PADI4 gene.

# Molecular biology
The human gene is found on the short arm of Chromosome 1 near the telomere (1p36.13). It is located on the Watson (plus) strand and is 55,806 bases long. The protein is 663 amino acids long with a molecular weight of 74,095 Da.

# Function
This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. PADI4 plays a role in the epigenetics, the deimination of arginines on histones 3 and 4 can act antagonistically to arginine methylation (Chromatin modifications and their function, Kouzarides 2007, Cell, review)
The protein may be found in oligomers and binds 5 calcium ions per subunit. It catalyses the reaction:
- Protein L-arginine + H2O = protein L-citrulline + NH3

# Subcellular and tissue distribution
It is normally found in the cytoplasm, nucleus and in cytoplasmic granules of eosinophils and neutrophils. It is not expressed in peripheral monocytes or lymphocytes. It is also expressed in rheumatoid arthritis synovial tissues.
PALB2
Partner and localizer of BRCA2, also known as PALB2 or FANCN, is a protein which in humans is encoded by the PALB2 gene.

# Function
This gene encodes a protein that functions in genome maintenance (double strand break repair). This protein binds to and colocalizes with the breast cancer 2 early onset protein (BRCA2) in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. PALB2 binds the single strand DNA and directly interacts with the recombinase RAD51 to stimulate strand invasion, a vital step of homologous recombination, (see Figure "Homologous recombinational repair of DNA double-strand damage"). PALB2 can function synergistically with a BRCA2 chimera (termed piccolo, or piBRCA2) to further promote strand invasion.

# Clinical significance
Variants in the PALB2 gene are associated with an increased risk of developing breast cancer  of magnitude similar to that associated with BRCA2 mutations  and PALB2-deficient cells are sensitive to PARP inhibitors.
PALB2 was recently identified as a susceptibility gene for familial pancreatic cancer by scientists at the Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins.  This has paved for the way for developing a new gene test for families where pancreatic cancer occurs in multiple family members. Tests for PALB2 have been developed by Ambry Genetics  and Myriad Genetics that are now available. The PALB2 Interest Group (PALB2.org) is an international consortium of scientists and clinicians who coordinate research into this gene. They are keen to hear from women and men with PALB2 mutations.
Biallelic mutations in PALB2 (also known as FANCN), similar to biallelic BRCA2 mutations, cause Fanconi anemia.

# Meiosis
PALB2 mutant male mice have reduced fertility.  This reduced fertility appears to be due to germ cell attrition resulting from a combination of unrepaired DNA breaks during meiosis and defective synapsis of the X and Y chromosomes.  The function of homologous recombination during meiosis appears to be repair of DNA damages, particularly double-strand breaks (also see Origin and function of meiosis).  The PALB2-BRCA1 interaction is likely important for repairing such damages during male meiosis.
PAM16
Mitochondrial import inner membrane translocase subunit TIM16 also known as presequence translocated-associated motor subunit PAM16, mitochondria-associated granulocyte macrophage CSF-signaling molecule, or presequence translocated-associated motor subunit PAM16 is a protein that in humans is encoded by the PAM16 gene.

# Structure
The PAM16 gene is located on the p arm of chromosome 16 at position 13.3 and it spans 11,150 base pairs. The PAM16 gene produces a 15.1 kDa protein composed of 137 amino acids. The structure has been found to contain a 21-residue mitochondrial targeting leader sequence.

# Function
The PAM16 gene encodes for a mitochondrial protein with mutltiple functions. It is responsible for the regulation of ATP-dependent protein translocation into the mitochondrial matrix, inhibition of DNAJC19 stimulation of HSPA9/Mortalin ATPase activity, and granulocyte-macrophage colony-stimulating factor (GM-CSF) signaling. Furthermore, PAM16 plays a role in the import of nuclear-encoded mitochondrial proteins into the mitochondrial matrix and may be important in reactive oxygen species (ROS) homeostasis.

# Clinical Significance
Mutations in the PAM16 gene has been shown to cause mitochondrial deficiencies and associated disorders. It is mainly associated with Megarbane-Dagher-Melike type spondylometaphyseal dysplasia, which is an autosomal recessive disease characterized by pre- and postnatal short stature, developmental delay, dysmorphic facial appearance, narrow chest, prominent abdomen, platyspondyly, short limbs, and other abnormalities of the skeleton.

# Interactions
PAM16 has been known to interact with PAM18, DNAJC19, TIMM17A, FEZ1, TRIM25, MARC1, and other proteins.
PANX1
Pannexin 1 is a protein in humans that is encoded by the PANX1 gene.
The protein encoded by this gene belongs to the innexin family. Innexin family members are the structural components of gap junctions. This protein and pannexin 2 are abundantly expressed in central nerve system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 2 may form cell type-specific gap junctions with distinct properties.

# Clinical relevance
Truncating mutations in this gene have been shown to promote breast cancer metastasis to the lungs by allowing cancer cells to survive mechanical stretch in the microcirculation.
Disruptions of this gene have been associated to melanoma tumor progression.
Pannexin 1 is also an important component of membrane channels involved in the formation of thin plasma membrane extensions called apoptopodia and beaded apoptopodia during apoptosis.
PARP2
Poly  polymerase 2 is an enzyme that in humans is encoded by the PARP2 gene. It is one of the PARP family of enzymes.

# Function
This gene encodes poly(ADP-ribosyl)transferase-like 2 protein, which contains a catalytic domain and is capable of catalyzing a poly(ADP-ribosyl)ation reaction. This protein has a catalytic domain which is homologous to that of poly (ADP-ribosyl) transferase, but lacks an N-terminal DNA binding domain which activates the C-terminal catalytic domain of poly (ADP-ribosyl) transferase. The basic residues within the N-terminal region of this protein may bear potential DNA-binding properties, and may be involved in the nuclear and/or nucleolar targeting of the protein. Two alternatively spliced transcript variants encoding distinct isoforms have been found.
In the plant species Arabidopsis thaliana, PARP2 plays more significant roles than PARP1 in protective responses to DNA damage and bacterial pathogenesis.  The plant PARP2 carries N-terminal SAP DNA binding motifs rather than the Zn-finger DNA binding motifs of plant and animal PARP1 proteins.

# PARP inhibitor drugs
Some PARP inhibitor anti-cancer drugs (primarily aimed at PARP1) also inhibit PARP2, e.g. niraparib.

# Interactions
PARP2 has been shown to interact with XRCC1.
PBRM1
Protein polybromo-1 (PB1) also known as BRG1-associated factor 180 (BAF180) is a protein that in humans is encoded by the PBRM1 gene.

# Structure and function
Component of the SWI/SNF-B (PBAF) chromatin-remodeling complex, which contains at least SMARCA4/BRG1, SMARCB1/SNF5/INI1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, and actin.
Chicken PB1 possesses 5 bromodomains, 2 bromo-adjacent homology (BAH) domains, and 1 truncated high-mobility group (HMG) motif. cPB1 is also homologous to yeast Rsc1, Rsc2, and Rsc4, essential proteins that are required for cell cycle progression through mitosis.

# Clinical significance
PBRM1 is a tumor suppressor gene in many cancer subtypes.  Mutations are especially prevalent in clear cell renal cell carcinoma.
PCBP2
Poly(rC)-binding protein 2 is a protein that in humans is encoded by the PCBP2 gene.

# Function
The protein encoded by this gene appears to be multifunctional. It along with PCBP-1 and hnRNPK corresponds to the major cellular poly(rC)-binding proteins. It contains three K-homologous (KH) domains which may be involved in RNA binding. This encoded protein together with PCBP-1 also functions as translational coactivators of poliovirus RNA via a sequence-specific interaction with stem-loop IV of the IRES and promote poliovirus RNA replication by binding to its 5'-terminal cloverleaf structure. It has also been implicated in translational control of the 15-lipoxygenase mRNA, human Papillomavirus type 16 L2 mRNA, and hepatitis A virus RNA. The encoded protein is also suggested to play a part in formation of a sequence-specific alpha-globin mRNP complex which is associated with alpha-globin mRNA stability. This multiexon structural mRNA is thought to be retrotransposed to generate PCBP-1 intronless gene which has similar functions. This gene and PCBP-1 has paralogues PCBP3 and PCBP4 which is thought to arose as a result of duplication events of entire genes. It also has two processed pseudogenes PCBP2P1 and PCBP2P2. There are presently two alternatively spliced transcript variants described for this gene.
In humans, the PCBP2 gene overlaps with TUC338, a transcribed ultra-conserved element implicated in Hepatocellular carcinoma.

# Interactions
PCBP2 has been shown to interact with HNRPK, PTBP1, and HNRNPL.
PCDHY
PCDH11Y is a gene unique to human males that encodes Protocadherin 11Y, a protein that guides the development of nerve cells.  PCDH11X, located on the X chromosome, is common, in both sexes, to humans and our nearest relative, the chimpanzee; however, PCDH11Y, located on the Y chromosome, is unique to males.
In terms of human evolution, it has been estimated that pcdh11x "gene jumped" from X to Y around three million years ago; coincident with increased human brain size and the first use of tools. Furthermore,  around 120,000 to 200,000 years ago, the PCDH11Y gene was able to further transform, splitting in half and reversing its position.
PCDH11X/Y are cadherin family genes. They make proteins, involved in signalling, that attach to the surface of nerve cells. PCDH11X and PCDH11Y, respond in different ways to Retinoic acid, a chemical involved in the development of embryos.  The acid stimulates the  activity of PCDH11Y but suppresses PCDH11X.  This is likely one of the explanations for the differences between the brains of men and women.
Psychiatrist, professor Tim Crow, also believes the gene explains lateralisation. Humans have "lateralised" brains, in which the different sides became specialised for particular jobs. For instance 90% of people will use their right hands for fiddly tasks. A chimpanzee is just as likely to use either hand. It also explains why, for right-handed people, linguistic functions are concentrated on the left side of the brain.
PCSK5
Proprotein convertase subtilisin/kexin type 5 is an enzyme that in humans is encoded by the PCSK5 gene, found in chromosome 9q21.3  Two alternatively spliced transcripts are described for this gene but only one has its full length nature known.

# Function
The protein encoded by this gene belongs to the subtilisin-like proprotein convertase family. The members of this family are proprotein convertases that process latent precursor proteins into their biologically active products. This encoded protein mediates posttranslational endoproteolytic processing for several integrin alpha subunits. It is thought to process prorenin, pro-membrane type-1 matrix metalloproteinase and HIV-1 glycoprotein gp160.

# Clinical significance
Mutations in this gene have been associated with Currarino syndrome-like malformations.
PCSK6
Proprotein convertase subtilisin/kexin type 6 is an enzyme that in humans is encoded by the PCSK6 gene. PCSK6 is a protease that cleaves NODAL into an active form to help trigger the development of left/right (LR) asymmetry. It may also be involved in left and right handedness in humans.

# Function
The protein encoded by this gene belongs to the subtilisin-like proprotein convertase family. The members of this family are proprotein convertases that process latent precursor proteins into their biologically active products. This encoded protein is a calcium-dependent serine endoprotease that can cleave precursor protein at their paired basic amino acid processing sites. Some of its substrates are - transforming growth factor beta related proteins, proalbumin, and von Willebrand factor. Alternatively spliced transcript variants encoding different isoforms have been identified.
PCSK6 also cleaves and activates corin, a serine protease that regulates sodium homeostasis and blood pressure.

# Clinical significance
This gene is thought to play a role in tumor progression.
PCSK6 deficiency causes salt-sensitive hypertension in mice.
PDCD2
Programmed cell death protein 2 is a protein that in humans is encoded by the PDCD2 gene.

# Function
This gene encodes a nuclear protein expressed in a variety of tissues. The rat homolog, Rp8, is transiently expressed in immature thymocytes and is thought to be involved in programmed cell death. Expression of the human gene has been shown to be repressed by BCL6, a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on PDCD2. This gene is closely linked on chromosome 6 to the gene for TBP, the TATA binding protein. Six transcripts encoding different proteins have been identified.

# Interactions
PDCD2 has been shown to interact with Host cell factor C1 and Parkin (ligase).

# Model organisms
Model organisms have been used in the study of PDCD2 function. A conditional knockout mouse line called Pdcd2tm1b(EUCOMM)Wtsi 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
PDCD4
Programmed cell death protein 4 is a protein that in humans is encoded by the PDCD4 gene. It is one of the targets of an oncomiR, MIRN21.

# Function
This gene encodes a protein localized to the nucleus in proliferating cells. Expression of this gene is modulated by cytokines in natural killer and T cells. The gene product is thought to play a role in apoptosis but the specific role has not yet been determined. Two transcripts encoding different isoforms have been identified.

# Interactions
PDCD4 has been shown to interact with RPS13 and Ribosomal protein L5.
PDCD6
Programmed cell death protein 6 is a protein that in humans is encoded by the PDCD6 gene.
This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant.

# Interactions
PDCD6 has been shown to interact with ASK1, PDCD6IP, Fas receptor, ANXA11 and PEF1.
PDE4A
cAMP-specific 3',5'-cyclic phosphodiesterase 4A is an enzyme that in humans is encoded by the PDE4A gene.

# Function
The protein encoded by this gene belongs to the cyclic nucleotide phosphodiesterase (PDE) family, and PDE4 subfamily. This PDE hydrolyzes the secondary messenger, cAMP, which is a regulator and mediator of a number of cellular responses to extracellular signals. Thus, by regulating the cellular concentration of cAMP, this protein plays a key role in many important physiological processes.  Recently, it has been shown through the use of PDE4A knock out mice that PDE4A may play a role in the regulation of anxiety and emotional memory.

# Clinical significance
PDE4A is a target of a number of drugs including:
- rolipram (antidepressant and antiinflammatory) and cilomilast (antiinflammatory)  inhibits PDE4A isoforms 1, 2, 6, and 7
- roflumilast (antiinflammatory)  inhibits PDE4A isoforms 1, 2, and 6
PDE4B
cAMP-specific 3',5'-cyclic phosphodiesterase 4B is an enzyme that in humans is encoded by the PDE4B gene.
This gene is a member of the type IV, cyclic AMP (cAMP)-specific, cyclic nucleotide phosphodiesterase (PDE) family. Cyclic nucleotides are important second messengers that regulate and mediate a number of cellular responses to extracellular signals, such as hormones, light, and neurotransmitters. The cyclic nucleotide phosphodiesterases (PDEs) regulate the cellular concentrations of cyclic nucleotides and thereby play a role in signal transduction. This gene encodes a protein that specifically hydrolyzes cAMP. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.

# Clinical relevance
Altered activity of this protein has been associated with schizophrenia and bipolar disorder. PDE4B is believed to be the PDE4 subtype involved in the antipsychotic effects of PDE4 inhibitors such as rolipram. PDE4B is involved in dopamine-associated and stress-related behaviours. It has also recently been found to modulate cognition, as reduction in PDE4B activity improves memory and long-term plasticity in mouse models, possibly supporting further therapeutic applications.

# Inhibitors
AN2728, a boron-containing drug candidate that as of 2015 was under development by Anacor Pharmaceuticals for the topical treatment of psoriasis and atopic dermatitis (atopic eczema). mainly acting on PDE4B.
PDE4D
cAMP-specific 3',5'-cyclic phosphodiesterase 4D is an enzyme that in humans is encoded by the PDE4D gene.

# Function
The PDE4D gene is complex and has at least 9 different isoforms that encode functional proteins. These proteins degrade the second messenger cAMP, which is a key signal transduction molecule in multiple cell types, including vascular cells (Dominiczak and McBride, 2003).

# Interactions
PDE4D has been shown to interact with myomegalin and GNB2L1.

# Clinical relevance
Mutations in this gene have been associated to cases of acrodysostosis.
This is the subtype of PDE4 that appears to be involved in the emetic and antidepressant effects of PDE4 inhibitors.
Furthermore, changes in expression of the isoform PDE4D7 have been proposed as prostate cancer biomarker.
PDGFB
Platelet-derived growth factor subunit B is a protein that in humans is encoded by the PDGFB gene.

# Function
The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a motif of eight cysteines. This gene product can exist either as a homodimer (PDGF-BB) or as a heterodimer with the platelet-derived growth factor alpha (PDGFA)  polypeptide (PDGF-AB), where the dimers are connected by disulfide bonds.

# Clinical significance
Mutations in this gene are associated with meningioma. Reciprocal translocations between chromosomes 22 and 17, at sites where this gene and that for COL1A1 are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans resulting from unregulated expression of growth factor. Two splice variants have been identified for this gene.
PDGFC
Platelet-derived growth factor C, also known as PDGF-C, is a 345-amino acid protein that in humans is encoded by the PDGFC gene. Platelet-derived growth factors are important in connective tissue growth, survival and function, and consist of disulphide-linked dimers involving two polypeptide chains, PDGF-A and PDGF-B.  PDGF-C is a member of the PDGF/VEGF family of growth factors with a unique two-domain structure and expression pattern.  PDGF-C was not previously identified with PDGF-A and PDGF-B, possibly because it may be that it is synthesized and secreted as a latent growth factor, requiring proteolytic removal of the N-terminal CUB domain for receptor binding and activation.

# Function
The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines. This gene product appears to form only homodimers. It differs from the platelet-derived growth factor alpha and beta polypeptides in having an unusual N-terminal domain, the CUB domain.
PDGF-C is a key component of the PDGFR- signaling pathway and has a specific role in palatogenesis and the morphogenesis of the integumentary tissue. The phenotypes of compound mutants imply that PDGF-C and PDGF-A may function as principal ligands for PDGFR-.
Mouse knockout studies show that PDGF-C is required for palatogenesis. Although human studies support an etiologic role for several genes in cleft lip and palate etiology (PVRL1, IRF6, and MSX1), expression levels of the mouse homologs of these genes were unaltered in Pdgfc/ mutant embryos that develop clefts, suggesting that their activity is not related to PDGF-C signaling in palatogenesis, so PDGF-C signaling is a new pathway in palatogenesis.

# Interactions
PDGFC has been shown to interact with PDGFRA.
PDGF-C is a latent growth factor with proteolytic activation, and the processing enzyme might be controlled by the other CLP-associated genes that may indirectly connect to PDGF-C signaling. Notably, a 30-cM region on human chromosome 4, where the PDGFC gene maps, shows strong linkage association with CLP26, and clinical genetic data further suggest a potential link between PDGFC gene polymorphism and cleft lip and palate.
PDS5B
Sister chromatid cohesion protein PDS5 homolog B is a protein that in humans is encoded by the PDS5B gene.

# Model organisms
Model organisms have been used in the study of PDS5B function. A conditional knockout mouse line, called Pds5btm1a(EUCOMM)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  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. 
Twenty three tests were carried out and two phenotypes were reported. Almost all homozygous mutant animals died prior to birth, and therefore they did not survive until weaning. The remaining tests were carried out on heterozygous mutant mice, and no significant abnormalities were observed.