Persius/hicric huggingface dataset:
S-layer
An S-layer (surface layer) is a part of the cell envelope commonly found in bacteria, as well as among archaea. It consists of a monomolecular layer composed of identical proteins or glycoproteins. This two dimensional structure is built via self-assembly and encloses the whole cell surface. Thus, the S-layer protein can represent up to 10-15% of the whole protein content of a cell
. S-layer proteins are poorly or not conserved at all and can differ markedly even between related species.
Depending on species the S-layers have a thickness between 5 and 25 nm and possess identical pores with 2-8 nm in diameter . S-layers exhibit either an oblique (p1, p2), square (p4) or hexagonal (p3, p6) lattice symmetry. Depending on the lattice symmetry the S-layer is composed of one (P1), two (P2), three (P3), four (P4) or six (P6) identical protein subunits, respectively. The centre to centre spacings (or unit cell dimensions) between these subunits range between 2.5 and 35 nm.

# Fixation of S-layers in the cell wall
- In Gram-negative bacteria S-layers are associated to the LPS via ionic, carbohydrate-carbohydrate, protein carbohydrate interactions and/or protein-protein interactions.
- In Gram-positive bacteria whose S-layers contain surface layer homology (SLH) domains the binding occurs to the peptidoglycan and to a secondary cell wall polymer (e.g. teichuronic acids). In the absence of SLH domains the binding occurs via electrostatic interactions between the positively charged N-terminus of the S-layer protein and a negatively charged secondary cell wall polymer.
- In Gram-negative archaea S-layer proteins possess a hydrophobic anchor that is associated with the underlying lipid membrane.
- In Gram-positive archaea the S-layer proteins bind pseudomurein or to methanochondritin.

# Biological functions of the S-layer
As for many bacteria the S-layer represents the outermost interaction zone with their respective environment, its functions are very diverse and vary from species to species.
In Gram-negative archaea the S-layer is the only cell wall component and therefore is important for mechanical stabilisation. Additional functions associated with S-layers include:
- protection against bacteriophages and phagocytosis
- resistance against low pH
- barrier against high molecular weight substances (e.g. lytic enzymes)
- adhesion (for glycosylated S-layers)
- stabilisation of the membrane
- provide adhesion sites for exoproteins
- provide a periplasmic compartment in Gram-positive prokaryotes together with the peptidoglycan and the cytoplasmic membrane
S100A11
S100 calcium-binding protein A11 (S100A11) is a protein that in humans is encoded by the S100A11 gene.

# Function
The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100A11 is localized in the cytoplasm of resting human keratinocytes in vitro.
S100A11, along with all 13 members of the S100 family, are located as a cluster on chromosome 1q21. The protein may function in motility, invasion, and tubulin polymerization. Chromosomal rearrangements and altered expression of this gene have been implicated in tumor metastasis.
Suppression of S100A11 by small interfering RNA caused cells to apoptosis, and overexpression of S100A11 has been found to inhibit apoptosis in tumor cells. Furthermore, the knock-down of S100A11 via siRNA reduces the sister-chromatid exchange and the viability of cells.
IL-8 and TNF-alpha induce S100A11 expression and release in chondrocytes in culture and exogenous S100A11 causes chondrocyte hypertrophy.
It has been shown that S100A11 enhances the recombination activity of human RAD51 in vitro. A knock-down leads to diffuse distribution of RAD54B.  These finding suggest a potential role of S100A11 in the process of homologous recombination repair of double-strand breaks.

# Interactions
S100A11 has been shown to interact with Nucleolin, S100B and RAD54B.
S100A13
S100 calcium-binding protein A13 (S100A13) is a protein that in humans is encoded by the S100A13 gene.

# Function
The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein is widely expressed in various types of tissues with a high expression level in thyroid gland. In smooth muscle cells, this protein co-expresses with other family members in the nucleus and in stress fibers, suggesting diverse functions in signal transduction. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene.

# Interactions
S100A13 has been shown to interact with SYT1 and FGF1.

# Pathology
Up-regulation of S100A13 was detected in cystic papillary thyroid carcinoma and association of S100A13 expression and chemotherapy resistance was shown in proteomics study of melanoma.
SAPS II

# Overview
SAPS II is a severity of disease classification system (Le Gall, Lemeshow, Saulnier, 1993). Its name stands for "Simplified Acute Physiology Score", and is one of several ICU scoring systems.

# Application
SAPS II was designed to measure the severity of disease for patients admitted to Intensive care units aged 15 or more.
24 hours after admission to the ICU, the measurement has been completed and resulted in an integer point score between 0 and 163 and a predicted mortality between 0% and 100%. No new score can be calculated during the stay. If a patient is discharged from the ICU and readmitted, a new SAPS II score can be calculated.
This scoring system is mostly used to:
- describe the morbidity of a patient when comparing the outcome with other patients.
- describe the morbidity of a group of patients when comparing the outcome with another group of patients

# Calculation
The point score is calculated from 12 routine physiological measurements during the first 24 hours, information about previous health status and some information obtained at admission. The calculation method is optimized for paper schemas. In contrast to APACHE II, the resulting value is much better at comparing patients with different diseases.
The calculation method results in a predicted mortality, that is pure statistics. It does not tell the individual patient's chance of survival. The main purpose of this calculation is to provide a value that can be averaged for a group of patients, since it gives very unprecise values to calculate an average of the scores of a group of patients.
SCGB1D2
Secretoglobin family 1D member 2 is a protein that in humans is encoded by the SCGB1D2 gene.

# Function
The protein encoded by this gene is a member of the lipophilin subfamily, part of the uteroglobin superfamily, and is an ortholog of prostatein, the major secretory glycoprotein of the rat ventral prostate gland. Lipophilin gene products are widely expressed in normal tissues, especially in endocrine-responsive organs. Assuming that human lipophilins are the functional counterparts of prostatein, they may be transcriptionally regulated by steroid hormones, with the ability to bind androgens, other steroids and possibly bind and concentrate estramustine, a chemotherapeutic agent widely used for prostate cancer. Although the gene has been reported to be on chromosome 10, this sequence appears to be from a cluster of genes on chromosome 11 that includes mammaglobin 2.
SCGB1D2 expression is high in mammary tissue, and is sometimes used for identification and detection of disseminated breast cancer cells.
SEQUEST
SEQUEST is a tandem mass spectrometry data analysis program used for protein identification.  Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.

# Applications
This tool is most useful in the context of proteomics. Starting with a complex mixture of proteins, this strategy typically employs trypsin to digest proteins. These peptides are separated by liquid chromatography en route to a tandem mass spectrometer. The mass spectrometer then isolates ions of a particular peptide, subjects them to collision-induced dissociation, and records the produced fragments in a tandem mass spectrum. This process, repeated for several hours, will produce thousands of tandem mass spectra. Identifying such a data collection requires automation, and Sequest was the first software to fill that need.
Sequest identifies each tandem mass spectrum individually.  The software evaluates protein sequences from a database to compute the list of peptides that could result from each.  The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those which are near the mass of the observed peptide ion.  For each candidate peptide, Sequest projects a theoretical tandem mass spectrum, and Sequest compares these theoretical spectra to the observed tandem mass spectrum by the use of cross correlation.  The candidate sequence with the best matching theoretical tandem mass spectrum is reported as the best identification for this spectrum.
SH3KBP1
SH3 domain-containing kinase-binding protein 1 (synonyms - CIN85, in rodents - Ruk) is an adaptor protein that in humans is encoded by the SH3KBP1 gene.

# Function
CBL (MIM 165360) constitutively interacts with SH3 domain-containing proteins and, upon tyrosine phosphorylation, with SH2 domain-containing proteins. The SH3KBP1 gene encodes an 85-kD CBL-interacting protein that enhances tumor necrosis factor (MIM 191160)-mediated apoptotic cell death (Narita et al., 2001).

# Interactions
SH3KBP1 has been shown to interact with B-cell linker, Grb2, SH3GLB2, SH3GL3, SH3GL2, BCAR1, Epidermal growth factor receptor, CBLB, Cbl gene, SOS1, CRK and PAK2.
SHROOM3
Protein shroom3 also known as shroom-related protein is a protein that in humans is encoded by the SHROOM3 gene.
Protein shroom3 is a PDZ domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues.

# Clinical relevance
Mutations in this gene have been shown to cause heterotaxy. A similar protein in mice is required for proper neurulation, eye, and gut development.
SLC10A1
Sodium/bile acid cotransporter also known as the Na+-taurocholate cotransporting polypeptide (NTCP) or liver bile acid transporter (LBAT) is a protein that in humans is encoded by the SLC10A1  (solute carrier family 10 member 1) gene.

# Structure
Sodium/bile acid cotransporters are integral membrane glycoproteins. Human NTCP contains 349 amino acids and has a mass of 56 kDa.

# Function
Bile acid:sodium symporters participate in the enterohepatic circulation of bile acids. Two homologous transporters are involved in the reabsorption of bile acids.  One of these absorbs bile acids from the intestinal lumen, the bile duct, and the kidney with an apical localization (ileal sodium/bile acid cotransporter).  The other is this protein and is expressed in the basolateral membranes of hepatocytes (NTCP).
As a cotransporter, NTCP binds two sodium ions and one (conjugated) bile salt molecule, thereby providing an hepatic influx of bile salts. Other transported molecules include steroid hormones, thyroid hormones and various xenobiotics:

## Hepatitis virus entry
NTCP is a cell surface receptor necessary for the entry of hepatitis B and hepatitis D virus. This entry mechanism is inhibited by myrcludex B, cyclosporin A, progesterone, propranolol, bosentan, ezetimibe, as well as NTCP substrates like taurocholate, tauroursodeoxycholate and bromosulfophthalein.
SLC10A2
The SLC10A2 (solute carrier family 10 member 2) gene in humans encodes the bile acid:sodium symporter known as the apical sodiumbile acid transporter (ASBT) or as the ileal bile acid transporter (IBAT).
ASBT/IBAT is  most highly expressed in the ileum, where it is found on the brush border membrane of enterocytes.  It is responsible for the initial uptake of bile acids, particularly conjugated bile acids, from the intestine as part of their enterohepatic circulation.

# As a drug target
Several medications to inhibit IBAT are under development. They include elobixibat, under development for the treatment of constipation and irritable bowel syndrome, and volixibat, under development for the treatment of nonalcoholic steatohepatitis.
SLC13A5
Solute carrier family 13 (sodium-dependent citrate transporter), member 5 also known as the Na+/citrate cotransporter is a protein that in humans is encoded by the SLC13A5 gene.

# Function
SLC13A5 is a tricarboxylate plasma transporter with a preference for citrate.

# Clinical significance
In 2014, by means of exome sequencing it was determined that a genetic mutation of the SLC13A5 gene is the cause of an extremely rare citrate transporter disorder.
Mutations in SLC13A5 cause autosomal recessive epileptic encephalopathy with seizure onset in the first days of life.  Those afflicted suffer from seizures, global developmental delay, movement disorder and hypotonia.
The site www.citratetransporterdisorders.org aims to unite families, doctors and researchers in their efforts to find treatment options.
SLC17A5
Solute carrier family 17 (anion/sugar transporter), member 5, also known as SLC17A5 or sialin, is a protein which in humans is encoded by the SLC17A5 gene.

# Clinical significance
A deficiency of this protein causes Salla disease. and Infantile Sialic Acid Storage Disease (ISSD).
The gene for HP59 contains, entirely within its coding region, the Sialin Gene SLC17A5. Member 5, also known as SLC17A5 or sialin is a lysosomal membrane sialic acid transport protein which in humans is encoded by the SLC17A5 gene on Chromosome 6
SLC17A8
Solute carrier family 17 member 8 (SLC17A8) also known as the vesicular glutamate transporter 3 (VGluT3) is a protein that in humans is encoded by the SLC17A8 gene.

# Function
This gene encodes a vesicular glutamate transporter. The encoded protein transports the neurotransmitter glutamate into synaptic vesicles before it is released into the synaptic cleft.

# Clinical significance
Mutations in this gene are the cause of autosomal-dominant nonsyndromic deafness type 25 (DFNA25).
SLC19A1
Solute carrier family 19 (folate transporter), member 1, also known as SLC19A1 or RFC1, is a protein which in humans is encoded by the SLC19A1 gene.

# Function
Transport of folate compounds into mammalian cells can occur via receptor-mediated (see folate receptor 1) or carrier-mediated mechanisms. A functional coordination between these 2 mechanisms has been proposed to be the method of folate uptake in certain cell types. Methotrexate (MTX) is an antifolate chemotherapeutic agent that is actively transported by the carrier-mediated uptake system. RFC1 plays a role in maintaining intracellular concentrations of folate.

# Clinical significance
Individuals carrying a specific polymorphism of SLC19A1 (c.80GG) have lower levels of folate. Other studies have also shown that individuals carrying the c.80AA polymorphism who are treated with methotrexate have higher levels of this anti-folate chemotherapeutic agent. Personalized dosing of the drug depending on the patient's genotype may therefore be required.
SLC19A2
Thiamine transporter 1, also known as thiamine carrier 1 (TC1) or solute carrier family 19 member 2 (SLC19A2) is a protein that in humans is encoded by the SLC19A2 gene. SLC19A2 is a thiamine transporter. Mutations in this gene cause thiamine-responsive megaloblastic anemia syndrome (TRMA), which is an autosomal recessive disorder characterized by diabetes mellitus, megaloblastic anemia and sensorineural deafness.

# Structure
The SLC19A2 gene is located on the q arm of chromosome 1 in position 24.2 and spans 22,062 base pairs. The gene produces a 55.4 kDa protein composed of 497 amino acids. In the encoded protein (TC1), a multi-pass membrane protein located in the cell membrane, the N-terminus and C-terminus face the cytosol. This gene has 6 exons while the protein has 12 putative transmembrane domains, with 3 phosphorylation sites in putative intracellular domains, 2 N-glycolysation sites in putative extracellular domains, and a 17-amino acid long G protein-coupled receptor signature sequence. The thiamine transporter protein encoded by SLC19A2 has a 40% shared amino acid identity with the folate transporter SLC19A1. The N-terminal domain and the sequence between the C-terminal domain and sixth transmembrane domain are required for proper localization of this protein to the cell membrane.

# Function
The encoded protein is a high-affinity transporter specific to the intake of thiamine. Thiamine transport is not inhibited by other organic cations nor affected by sodium ion concentration; it is stimulated by a proton gradient directed outward, with an optimal pH between 8.0 and 8.5. TC1 is transported to the cell membrane by intracellular vesicles via microtubules.

# Clinical significance
Mutations in the SLC19A2 gene can cause thiamine-responsive megaloblastic anemia syndrome (TRMA), which is an autosomal recessive disease characterized by megaloblastic anemia, diabetes mellitus, and sensorineural deafness. Onset is typically between infancy and adolescence, but all of the cardinal findings are often not present initially. The anemia, and sometimes the diabetes, improves with high doses of thiamine. Other more variable features include optic atrophy, congenital heart defects, short stature, and stroke.
A 3.8 kb transcript is expressed variably in most tissues, highest in skeletal and cardiac muscle, followed by medium expression placenta, heart, liver, kidney cells and low expression in lung cells. In melanocytic cells SLC19A2 gene expression may be regulated by MITF.

# Interactions
This protein interacts with CERS2.
SLC19A3
Thiamine transporter 2 (ThTr-2), also known as solute carrier family 19 member 3, is a protein that in humans is encoded by the SLC19A3 gene. SLC19A3 is a thiamine transporter.

# Function
ThTr-2 is a ubiquitously expressed transmembrane thiamine transporter that lacks folate transport activity.
It is specifically inhibited by chloroquine.

# Clinical significance
Mutations in this gene cause biotin-responsive basal ganglia disease (BBGD); a recessive disorder manifested in childhood that progresses to chronic encephalopathy, dystonia, quadriparesis, and death if untreated. Patients with BBGD have bilateral necrosis in the head of the caudate nucleus and in the putamen. Administration of high doses of biotin in the early progression of the disorder eliminates pathological symptoms while delayed treatment results in residual paraparesis, mild mental retardation, or dystonia. Administration of thiamine is ineffective in the treatment of this disorder. Experiments have failed to show that this protein can transport biotin. Mutations in this gene also cause a Wernicke's-like encephalopathy.
SLC20A2
Sodium-dependent phosphate transporter 2 is a protein that in humans is encoded by the SLC20A2 gene.

# Genomics
This gene is found on the short arm of chromosome 8 (8p12-p11) on the minus (Crick) strand. It is 123,077 bases in length. The encoded protein has 652 amino acids and the predicted molecular weight of the protein is 70.392 kiloDaltons.

# Function
The protein acts as a homodimer and is involved in phosphate transport by absorbing phosphate from interstitial fluid for normal cellular functions such as cellular metabolism, signal transduction, and nucleic acid and lipid synthesis.

# Clinical significance
Mutations in the  SLC20a2 gene are associated with idiopathic basal ganglia calcification (Fahr's syndrome). This association suggests that familial idiopathic basal ganglia calcification is caused by changes in phosphate homeostasis, since this gene encodes for PIT-2, an inorganic phosphate transporter.
SLC22A1
Solute carrier family 22 member 1 is a protein that in humans is encoded by the gene SLC22A1.

# Function
Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter.
It is also required for the uptake of metformin by cells.
SLC22A3
Solute carrier family 22 member 3 (SLC22A3) also known as the organic cation transporter 3 (OCT3) or extraneuronal monoamine transporter (EMT) is a protein that in humans is encoded by the SLC22A3 gene.
Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein.

# Distribution
OCT3 is widely distributed in brain tissue. It is not yet completely clear whether its location is primarily neuronal or glial. Areas of the brain in which it has been reported include: hippocampus, retrosplenial cortex, visual cortex, hypothalamus, amygdala, nucleus accumbens, thalamus, raphe nucleus, subiculum, superior and inferior colliculi, and islands of Calleja.

# Pharmacology
Organic cation transporter 3 is a polyspecific transporter whose transport is independent of sodium. Known substrates for transport include: histamine, serotonin, norepinephrine, dopamine and MPP+. Capacity for transport and affinity for these substrates may vary between rat and human isoforms however.
Transport activity of OCT3 is inhibited by recreational and pharmaceutical drugs, including MDMA, phencyclidine (PCP), MK-801, amphetamine, methamphetamine and cocaine. Transport is also inhibited by the chemical decynium-22 and physiological concentrations of corticosterone and cortisol. Ki values for decynium-22 and corticosterone inhibition of OCT3 transport are respectively 10 and 100 times lower than Ki values of OCT1 and OCT2.