Persius/hicric huggingface dataset:
ALMS1
Alstrom syndrome 1 also known as ALMS1 is a protein which in humans is encoded by the ALMS1 gene.

# Molecular biology
The gene is located on the short arm of chromosome 2 (2p13.2) on the plus (Watson) strand. It is 224,161 bases in length organised into 23 exons. The encoded protein has 4,167 amino acids and molecular weight of 460,937 Da. Three isofoms are known. The protein itself has a large tandem-repeat domain comprising 34 imperfect repetitions of 47 amino acids. Mutations associated with disease are usually found in exons 8, 10 and 16.
The gene is expressed in fetal tissues including the aorta, brain, eye, kidney, liver, lung, olfactory bulb, pancreas, skeletal muscle, spleen and testis. The protein is found in the cytoplasm, centrosome, cell projections and cilium basal body. During mitosis it localizes to both spindle poles.

# Function
Knockdown of Alms1 by short interfering RNA in mouse inner medullary collecting duct cells caused defective ciliogenesis. Cilia were stunted and treated cells lacked the ability to increase calcium influx in response to mechanical stimuli.

# Disease association
Mutations in the ALMS1 gene have been found to be causative for Alstrom syndrome with a total of 81 disease-causing mutations.
Multiple mutations are known: the current (2007) total is 79. These include both nonsense and frameshift mutations. Most of the mutations have been found in exons 8,10 and 16.

# Discovery
The Jackson Laboratory in Bar Harbor, Maine, USA with the University of Southampton, UK isolated ALMS1 as the single gene responsible for Alstrom syndrome.
AMELX
Amelogenin, X isoform is a protein that in humans is encoded by the AMELX (amelogenin, X isoform) gene.
The protein Amelogenin, X isoform is an isoform of amelogenin that comes from the X chromosome. The protein Amelogenin is a type of extracellular matrix protein, and is involved in the process of amelogenesis, the formation of enamel on teeth. Amelogenin X is a member of the amelogenin family of extracellular matrix proteins.  When alternative splicing occurs, it results in multiple transcript variants encoding different isoforms, which in humans results in amelogenin genes on both the X and Y chromosomes.

# Function
AMELX is involved in biomineralization during tooth enamel development. The AMELX gene encodes for the structural modeling protein, amelogenin, which works with other amelogenesis-related proteins to direct the mineralisation of enamel. This process involves the organization of enamel rods, the basic unit of tooth enamel, as well as the inclusion and growth of hydroxyapatite crystals.

# Clinical significance
Mutations in the AMELX gene can result in amelogenesis imperfecta, which refers to the collection of enamel defects resulting from either genetic or environmental causes. It has been shown that mice with a knocked-out AMELX gene will present disorganized and hypoplastic enamel.
AMPD3
AMP deaminase 3 is an enzyme that in humans is encoded by the AMPD3 gene.
This gene encodes a member of the AMP deaminase gene family. The encoded protein is a highly regulated enzyme that catalyzes the hydrolytic deamination of adenosine monophosphate to inosine monophosphate, a branch point in the adenylate catabolic pathway. This gene encodes the erythrocyte (E) isoforms, whereas other family members encode isoforms that predominate in muscle (M) and liver (L) cells. Mutations in this gene lead to the clinically asymptomatic, autosomal recessive condition erythrocyte AMP deaminase deficiency. Alternatively spliced transcript variants encoding different isoforms of this gene have been described.

# Model organisms
Model organisms have been used in the study of AMPD3 function. A conditional knockout mouse line, called Ampd3tm2a(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 eight tests were carried out on mutant mice and four significant abnormalities were observed. Mutant animals had increased IgG1 levels, increased trabecular bone thickness, decreased B cell numbers / increased granulocyte number and unusual brain histopathology (the thickness of the stratum radiatum was reduced and the dorsal 3rd ventricle area was increased).
ANKK1
Ankyrin repeat and kinase domain containing 1 (ANKK1) also known as protein kinase PKK2 or sugen kinase 288 (SgK288) is an enzyme that in humans is encoded by the ANKK1 gene.  The ANKK1 is a member of an extensive family of the Ser/Thr protein kinase family, and protein kinase superfamily  involved in signal transduction pathways.

# Clinical significance
This gene contains a single nucleotide polymorphism that causes an amino acid substitution within the 11th of 12 ankyrin repeats of ANKK1 (Glu713Lys of 765 residues). This polymorphism, which is commonly referred to Taq1A, was previously believed to be located in the promoter region of the DRD2 gene, since the polymorphism is proximal to the DRD2 gene and can influence DRD2 receptor expression. It is now known to be located in the coding region of the ANKK1 gene which controls the synthesis of dopamine in the brain. The A1 allele is associated with increased activity of striatal L-amino acid decarboxylase.

## A1+ allele
- Hepatitis C infection
- Antisocial personality disorder
- Borderline personality traits
- Schizoid/avoidant behavior
Given that the A1+ allele is associated with antisocial personality disorder, one may infer that the allele is also associated with narcissistic personality disorder and histrionic personality disorder. However, these predictions have not yet been empirically verified.

## A1+ genotype frequencies
European population estimates for A1+ genotype frequencies range from 20.8 to 43.4% (National Center of Biotechnology Information (NCBI), identification number rs1800497).

## Addictive behaviors
The ANKK1 gene is closely linked to dopamine receptor D2 (DRD2) on chromosome band 11q23.1. The A1 allele of the Taq1A polymorphism (rs1800497T), is located 10kb downstream of the dopamine receptor DRD2 gene. Dopamine (DA) is a neurotransmitter in the brain, which controls feelings of wellbeing. This sensation results from the interaction of dopamine and other neurotransmitters such as serotonin, the opioids, and other brain chemicals. Dopamine increases the motivation for food cravings and appetite mediation.
The Reward Deficiency Syndrome (RDS) involves the pleasures or reward mechanisms that rely on dopamine. The result of this deficiency is based on the genetic makeup; this helps explain how certain simple genetic anomalies can give rise to complex aberrant behaviours as the ones mentioned previously. The A1 allelic prevalence has been reported to be significantly higher in obese individuals than in lean subjects, moreover, individuals with increased body mass index (BMI) (BMI >30 kg/m2) have fewer DRD2 dopamine receptors. Investigators have also suggested that hormonal mechanism may underline a gender difference in the ability to suppress hunger in relation to this SNP, which may contribute to the greater incidence of obesity in women compared to men. However, authors have pointed out that A1 carriers have difficulty in learning from negative feedback in a reinforcement-learning task and are less efficient at learning to avoid actions that have negative consequences.
Aorta
The aorta (generally pronounced et or "ay-orta") is the largest artery in the human body, originating from the left ventricle of the heart and bringing oxygenated blood to all parts of the body in the systemic circulation.

# The course of the aorta
The aorta is usually divided into five segments/sections    
- Ascending aorta  the section between the heart and the arch of aorta
- Arch of aorta  the peak part that looks somewhat like an inverted "U"
- Descending aorta  the section from the arch of aorta to the point where it divides into the common iliac arteries
Thoracic aorta  the half of the descending aorta above the diaphragm
Abdominal aorta  the half of the descending aorta below the diaphragm
- Thoracic aorta  the half of the descending aorta above the diaphragm
- Abdominal aorta  the half of the descending aorta below the diaphragm

# Features
The aorta is an elastic artery, and as such is quite distensible. When the left ventricle contracts to force blood into the aorta, the aorta expands. This stretching gives the potential energy that will help maintain blood pressure during diastole, as during this time the aorta contracts passively.

# Diseases/pathology
- Aneurysm of sinus of Valsalva
- Aortic aneurysm - myotic, bacterial (e.g. syphilis), senile, genetic, associated with valvular heart disease
Dissecting aortic aneurysm
- Dissecting aortic aneurysm
- Aortic coarctation - pre-ductal, post-ductal
- Atherosclerosis
- Marfan syndrome
- Trauma, such as traumatic aortic rupture, most often thoracic and distal to the left subclavian artery and frequently quickly fatal
- Aorta (Image courtesy of radiopaedia.org)
AP1S1
AP-1 complex subunit sigma-1A is a protein that in humans is encoded by the AP1S1 gene.

# Function
The protein encoded by this gene is part of the clathrin coat assembly complex which links clathrin to receptors in coated vesicles. These vesicles are involved in endocytosis and Golgi processing. This protein, as well as beta-prime-adaptin, gamma-adaptin, and the medium (mu) chain AP47, form the AP-1 assembly protein complex located at the Golgi vesicle. Two alternatively spliced transcript variants of this gene, which encode distinct isoforms, have been reported.
A mutation in the AP1S1 causes the rare familial  MEDNIK syndrome  described in 2008.

# Interactions
AP1S1 has been shown to interact with AP1G1 and RAB10.
AP2M1
AP-2 complex subunit mu is a protein that in humans is encoded by the AP2M1 gene.

# Function
This gene encodes a subunit of the heterotetrameric coat assembly protein complex 2 (AP2), which belongs to the adaptor complexes medium subunits family. The encoded protein is required for the activity of a vacuolar ATPase, which is responsible for proton pumping occurring in the acidification of endosomes and lysosomes. The encoded protein may also play an important role in regulating the intracellular trafficking and function of CTLA-4 protein. Two transcript variants encoding different isoforms have been found for this gene.

# Interactions
AP2M1 has been shown to interact with CTLA-4 and Alpha-1B adrenergic receptor.
AP4B1
AP-4 complex subunit beta-1 is a protein that in humans is encoded by the AP4B1 gene.

# Function
The heterotetrameric adaptor protein (AP) complexes sort integral membrane proteins at various stages of the endocytic and secretory pathways. AP4 is composed of 2 large chains, beta-4 (AP4B1, this protein) and epsilon-4 (AP4E1), a medium chain, mu-4 (AP4M1), and a small chain, sigma-4 (AP4S1)

# Interactions
AP4B1 has been shown to interact with AP4M1.

# Clinical relevance
AP4-complex-mediated trafficking plays a crucial role in brain development and functioning.
AP4E1
AP-4 complex subunit epsilon-1 is a protein that in humans is encoded by the AP4E1 gene.

# Function
The heterotetrameric adaptor protein (AP) complexes sort integral membrane proteins at various stages of the endocytic and secretory pathways. AP4 is composed of 2 large chains, beta-4 (AP4B1) and epsilon-4 (AP4E1; this gene), a medium chain, mu-4 (AP4M1), and a small chain, sigma-4 (AP4S1).

# Clinical relevance
It is currently hypothesized that AP4-complex-mediated trafficking plays a crucial role in brain development and functioning.

# Model organisms
Model organisms have been used in the study of AP4E1 function. A conditional knockout mouse line, called Ap4e1tm1a(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 homozygous mutant mice and four significant abnormalities were observed. Females displayed decreased vertical activity in an open field test, had an abnormal complete blood count, hypoferremia, and a decreased corpus callosum size and enlarged lateral ventricles.
AP4M1
AP-4 complex subunit mu-1 is a protein that in humans is encoded by the AP4M1 gene.

# Function
This gene encodes a subunit of the heterotetrameric AP-4 complex. The encoded protein belongs to the adaptor complexes medium subunits family. This AP-4 complex is involved in the recognition and sorting of cargo proteins with tyrosine-based motifs from the trans-golgi network to the endosomal-lysosomal system.

# Interactions
AP4M1 has been shown to interact with AP4B1.

# Clinical relevance
The AP4-complex-mediated trafficking plays a crucial role in brain development and functioning.
AP4S1
AP-4 complex subunit sigma-1 is a protein that in humans is encoded by the AP4S1 gene.

# Function
The heterotetrameric adaptor protein (AP) complexes sort integral membrane proteins at various stages of the endocytic and secretory pathways. AP4 is composed of 2 large chains, beta-4 (AP4B1) and epsilon-4 (AP4E1), a medium chain, mu-4 (AP4M1), and a small chain, sigma-4 (AP4S1, this gene).

# Clinical relevance
It is currently hypothesized that AP4-complex-mediated trafficking plays a crucial role in brain development and functioning.
APAF1
Apoptotic protease activating factor 1, also known as APAF1, is a human homolog of C. elegans CED-4 gene.

# Function
This gene encodes a cytoplasmic protein that forms one of the central hubs in the apoptosis regulatory network. This protein contains (from the N terminal) a caspase recruitment domain (CARD), an ATPase domain (NB-ARC), few short helical domains and then several copies of the WD40 repeat domain. Upon binding cytochrome c and dATP, this protein forms an oligomeric apoptosome. The apoptosome binds and cleaves Procaspase-9 protein, releasing its mature, activated form.  The precise mechanism for this reaction is still debated though work published by Guy Salvesen suggests that the apoptosome may induce caspase-9 dimerization and subsequent autocatalysis. Activated caspase-9 stimulates the subsequent caspase cascade that commits the cell to apoptosis.
Alternative splicing results in several transcript variants encoding different isoforms.

# Structure
APAF1 contains a CARD domain with a Greek key motif composed of six helices, a Rossman fold nucleotide binding domains, a short helical motif and a winged-helix domain.

# Interactions
APAF1 has been shown to interact with:
- APIP,
- BCL2-like 1
- Caspase-9,
- HSPA4, and
- NLRP1.
APBA1
Amyloid beta A4 precursor protein-binding family A member 1 is a protein that in humans is encoded by the APBA1 gene.

# Function
The protein encoded by this gene is a member of the X11 protein family. It is a neuronal adaptor protein that interacts with the Alzheimer's disease amyloid precursor protein (APP). It stabilises APP and inhibits production of proteolytic APP fragments including the A beta peptide that is deposited in the brains of Alzheimer's disease patients. This gene product is believed to be involved in signal transduction processes. It is also regarded as a putative vesicular trafficking protein in the brain that can form a complex with the potential to couple synaptic vesicle exocytosis to neuronal cell adhesion.

# Interactions
APBA1 has been shown to interact with KCNJ12, CCS, CASK and Amyloid precursor protein.
APBA2
Amyloid beta A4 precursor protein-binding family A member 2 is a protein that in humans is encoded by the APBA2 gene.

# Function
The protein encoded by this gene is a member of the X11 protein family. It is a neuronal adaptor protein that interacts with the Alzheimer's disease amyloid precursor protein (APP). It stabilises APP and inhibits production of proteolytic APP fragments including the A beta peptide that is deposited in the brains of Alzheimer's disease patients. This gene product is believed to be involved in signal transduction processes. It is also regarded as a putative vesicular trafficking protein in the brain that can form a complex with the potential to couple synaptic vesicle exocytosis to neuronal cell adhesion.

# Interactions
APBA2 has been shown to interact with CLSTN1, RELA and Amyloid precursor protein.
APBB1
Amyloid beta A4 precursor protein-binding family B member 1 is a protein that in humans is encoded by the APBB1 gene.

# Function
The protein encoded by this gene is a member of the Fe65 protein family. It is an adaptor protein localized in the nucleus. It interacts with the Alzheimer's disease amyloid precursor protein (APP), transcription factor CP2/LSF/LBP1 and the low-density lipoprotein receptor-related protein. APP functions as a cytosolic anchoring site that can prevent the gene product's nuclear translocation. This encoded protein could play an important role in the pathogenesis of Alzheimer's disease. It is thought to regulate transcription. Also it is observed to block cell cycle progression by downregulating thymidylate synthase expression. Multiple alternatively spliced transcript variants have been described for this gene but some of their full length sequence is not known.

# Interactions
APBB1 has been shown to interact with APLP2, TFCP2, LRP1 and Amyloid precursor protein.
APEX1
DNA-(apurinic or apyrimidinic site) lyase is an enzyme that in humans is encoded by the APEX1 gene.
Apurinic/apyrimidinic (AP) sites (also called "abasic sites") occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication. All cells, from simple prokaryotes to humans, have evolved systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site, thereby initiating a process known as base excision repair (BER). The APEX gene (alternatively named APE1, HAP1, APEN) encodes the major AP endonuclease in human cells. Splice variants have been found for this gene; all encode the same protein.

# Interactions
APEX1 has been shown to interact with MUTYH, Flap structure-specific endonuclease 1 and XRCC1.
APLP1
Amyloid-like protein 1, also known as APLP1, is a protein that in humans is encoded by the APLP1 gene. APLP1 along with APLP2 are important modulators of glucose and insulin homeostasis.

# Function
This gene encodes a member of the highly conserved amyloid precursor protein gene family. The encoded protein is a membrane-associated glycoprotein that is cleaved by secretases in a manner similar to amyloid beta A4 precursor protein cleavage. This cleavage liberates an intracellular cytoplasmic fragment that may act as a transcriptional activator. The encoded protein may also play a role in synaptic maturation during cortical development. Alternatively spliced transcript variants encoding different isoforms have been described.
APLP1 and APLP2 double knockout mice display hypoglycemia and hyperinsulinemia indicating that these two proteins are important modulators of glucose and insulin homeostasis.
APOA2
Apolipoprotein A-II is a protein that in humans is encoded by the APOA2 gene.

# Function
This gene encodes apolipoprotein (apo-) A-II, which is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia.

# Interactions
APOA2 has been shown to interact with PLTP.

# Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles. 
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