Persius/hicric huggingface dataset:
HAVCR2
Hepatitis A virus cellular receptor 2 (HAVCR2), also known as T-cell immunoglobulin and mucin-domain containing-3 (TIM-3), is a protein that in humans is encoded by the HAVCR2 gene. HAVCR2 was first described in 2002 as a cell surface molecule expressed on IFN producing CD4+ Th1 and CD8+ Tc1 cells. Later, the expression was detected in Th17 cells, regulatory T-cells, and innate immune cells (dendritic cells, NK cells, monocytes).

# Structure
HAVCR2 belongs to TIM family cell surface receptor proteins. These proteins share a similar structure, in which the extracellular region consists of membrane distal single variable immunoglobulin domain (IgV) and a glycosylated mucin domain of variable length located closer to the membrane. Intracellular domain of HAVCR2 is called C-terminal cytoplasmic tail. It contains five conserved tyrosine residues that interact with multiple components of T-cell receptor (TCR) complex and negatively regulates its function.

# Function
HAVCR2 is an immune checkpoint and together with other inhibitory receptors including programmed cell death protein 1 (PD-1) and lymphocyte activation gene 3 protein (LAG3) mediate the CD8+ T-cell exhaustion.  HAVCR2 has also been shown as a CD4+ Th1-specific cell surface protein that regulates macrophage activation and enhances the severity of experimental autoimmune encephalomyelitis in mice.
HAVCR2 is primarily activated by galectin-9. The engagement leads to stimulation of an influx of calcium to intracellular space and induction of programmed cell death, apoptosis. As a consequence, a suppression of Th1 and Th17 responses and induction of immune tolerance occurs. In addition to galectin-9, a couple other ligands have been identified, such as phospatidyl serine (PtdSer), High Mobility Group Protein 1 (HMGB1) and Carcinoembryonic Antigen Related Cell Adhesion Molecule 1 (CEACAM1). The binding of PtdSer has been shown to cause an uptake of apoptotic cells and reduced cross presentation of dying cell-associated antigens by dendritic cells. The binding of HMGB1 can interfere with nucleic acid stimulation and suppresses activation of innate immune response. The role of CEACAM1 engagement is still not clear.

# Clinical significance
HAVCR2 expression is up regulated in tumor-infiltrating lymphocytes in lung, gastric, head and neck cancer, schwannoma, melanoma and follicular B-cell non-Hodgkin lymphoma.
The HAVCR2 pathway may interact with the PD-1 pathway in the dysfunctional CD8+ T cells and Tregs in cancer. HAVCR2 is mainly expressed on activated CD8+ T cells and suppresses macrophage activation following PD-1 inhibition. Upregulation was observed in tumors progressing after anti-PD-1 therapy. This seems to be a form of adaptive resistance to immunotherapy. Multiple phase 1/2 clinical trials with anti-HAVCR2 monoclonal antibodies (LY3321367, Eli Lilly and Company; MBG453, Novartis Pharmaceuticals; TSR-022, Tesaro, Inc.) in combination with anti-PD-1 or anti-PD-L1 therapies are ongoing.
The role of HAVCR2 in the T-cell dysfunction has been investigated in chronic viral infections.
HDAC10
Histone deacetylase 10 is an enzyme that in humans is encoded by the HDAC10 gene.
Acetylation of histone core particles modulates chromatin structure and gene expression. The opposing enzymatic activities of histone acetyltransferases and histone deacetylases, such as HDAC10, determine the acetylation status of histone tails (Kao et al., 2002).

# Interactions
HDAC10 has been shown to interact with Histone deacetylase 2 and Nuclear receptor co-repressor 2.
HDAC11
Histone deacetylase 11 is a 39kDa histone deacetylase enzyme that in humans is encoded by the HDAC11 gene on chromosome 3 in humans and chromosome 6 in mice.
It is the only Class IV HDAC since it is not highly homologous with either Rpd3 or hda1 yeast enzymes and so does not fit into either Class I or Class II. It is the smallest HDAC isoform and it was first described in 2002.

# Function
Histone deacetylases, such as HDAC11, control DNA expression by modifying the core histone octamers that package DNA into dense chromatin structures and repress gene expression.
HDAC11 expression is normally found in brain and testis tissue, but upregulation of HDAC11 expression has also been seen in various cancer cells.
HDAC11 has been shown to be a negative regulator of IL-10 production in antigen presenting cells. It has also been shown that inhibition of HDAC11 results in increased expression of OX40L in Hodgkin lymphoma cells.

# Interactions
HDAC11 has been shown to interact with HDAC6.
HGSNAT
Heparan--glucosaminide N-acetyltransferase (also called "acetyl-CoA:heparan--D-glucosaminide N-acetyltransferase" and "acetyl-CoA:alpha-glucosaminide N-acetyltransferase") is an enzyme that in humans is encoded by the HGSNAT gene.
In enzymology, this enzyme belongs to the family of transferases, specifically those acyltransferases transferring groups other than aminoacyl groups. It is catalysed in the chemical reaction:
This enzyme participates in glycosaminoglycan degradation and glycan structures degradation. Mutations in the gene encoding this enzyme cause mucopolysaccharidosis IIIC.
HLA-A1
HLA-A1 (A1) is an HLA-A serotype. The serotype identifies the more common HLA-A*01 gene products. A1 is more common in Europe than elsewhere, it is part of a long haplotype that appears to have been frequent in the ancient peoples
-f Northwestern Europe. Part of this haplotype is A1-Cw7-B8 (its serotype name), which has a frequency mode in Ireland where it is the highest frequency A-Cw-B type in Europe.

# Serotype
The serotyping capability of the A1 serotype is excellent. For the A1 group there are 24 alleles, 7 nulls, 14 protein variants. Two alleles, A*0101 and A*0102, comprise the overwhelming majority of alleles.

# Disease Associations

### By allele
A*0101 appears to alter risk for type 1 diabetes. Because A*0101 is linked to DR3-DQ2.5 (see below), and because this class II haplotype has a bearing on diabetes risk (2nd most potent risk factor) some of this risk could be due to linkage with DR3.

### By haplotype
A1-B58 (A1-B17 where B58 is dominant) is associated with antineutrophil cytoplasmic antibodies (ANCA)

# A-B Haplotypes
- A1-B7 Armenia, Austria, NW Europe (regional recombinant between A1-B8 and A2/A3-B7)
- A1-B13 Uralic
- A1-B35 (Albania, Belgium, Italy, Greece, France - Eastern mediterranian in origin)
- A1-B37 Yakuts, Tribal-India, Iyers-India, Mongolian, Indian, Orochon, Romanian, Yugoslavia, Korean, Albania, French, German, Manchu
- A1-B51 Yugoslavia, Germany, Iberia, Italy
- A1-B52 Bharghavas-India, Tribal-India, Italy, Iberia, France
- A1-B57 (See tables on discussion page)
- A1-B58 (See tables on discussion page)

## A1-Cw7-B8
A1-Cw7-B8 is the multi-serotype designation for the haplotype HLA-A*0101:C*0701:B*0801, the class I portion, of the "Super B8 Haplotype" ancetral "Ancestral Haplotype" (A1-B8-DR17(3)-DQ2.5). The full haplotype is (for relative distances see Human leukocyte antigens:
A*0101 : C*0701 : B*0801 : DRB1*0301 : DQA1*0501 : DQB1*0201
The frequency node for this haplotype is in Western Ireland. Where as the most allelic diversity (variations of A*01 or B*08 are within East Africa.  The Cw7 locus carries several variants Europe (Cw*0701) Africa (Cw*0701 & Cw*0704)
It suprisingling maintains DR linkage, over 2 million nt distance is still shows relative linkage disequilibrium with DR3. In NW Europe linked to DRB1*0301 and in  SE Europe DRB1*0301/*0302. It is also disequilibrated in its linkage to DQ2, and in NW Europe it is linked to DQA1*0501:DQB1*0201. Because of the incredible linkage disequilibrium this haplotype is believed to have been under positive selection in Europe's
prehistoric period. When DR or DQ typing is not present for a population this haplotype can substitute as a marker for DQ2.5 abundance and coeliac disease risk, as in the case for Ireland.
The rightmost column in the table on the right shows the rank of A1-B8 in A-B haplotypes, it is the most common top ranked haplotype in Western Europe, in fact it is one of the more common A-B haplotypes in the world.
HLA-A3
HLA-A3 (A3) is an HLA-A serotype. The serotype identifies the more common HLA-A*03 gene products. A3 is more common in Northwestern and Central Europe, Central Asia, India and Arabia. It is less common on the West Pacific Rim, Africa or indigenous populations of the New World.

# Serotype
A3 is primarily composed of A*0301 and *0302 which serotype well with anti-A3 antibodies. 
There are 26 non-synonymous variants of A*03, 4 nulls, and 22 protein variants.

# Disease Associations

### By serotype
A3 serotype is a secondary risk factor for myasthenia gravis, lower CD8+ levels in hemochromatosis patients

### By allele
A*0301 modulates increased risk for Multiple Sclerosis

# A3-B Haplotypes
A3-B8  (Romania, svanS) 
A3-B35 (Bulgaria, Croatia, E. Black Sea)
A3-B55 (E. Black Sea)

## A3-Cw7-B7
A3-B7 is bimodal in frequency in Europe with one node in Ireland and the other in Switzerland, relatively speaking Switzerland appears to be higher. A3-Cw7-B7 is one of the most common multigene haplotypes in the western world, particularly in Central and Eastern Europe.
A*0301 : C*0702 : B*0702 : DRB1*1501 : DQA1*0102 : DQB1*0602
HLA-DO
Human leukocyte histocompatibility complex DO (HLA-DO) is an intracellular, dimeric non-classical Major Histocompatibility Complex (MHC) class II protein composed of - and -subunits which interact with HLA-DM in order to fine tune immunodominant epitope selection. As a non-classical MHC class II molecule, HLA-DO is a non-polymorphic accessory protein that aids in antigenic peptide chaperoning and loading, as opposed to it classical counterparts, which are polymorphic and involved in antigen presentation. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian bodynamely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cellsindicate that it may be of physiological importance and has inspired further research. Moreover, HLA-DO is stable in complex with HLA-DM, and its exhibited instability in the absence of HLA-DM, as well as its evolutionary conservation, further denote its biological significance and potential to confer evolutionary benefits to its host.

# Discovery
Studies on HLA-DO transfected fibroblast cells lines and on the HLA-DO mouse homolog, H-2O, provide most of the current knowledge on the protein. In 1985, the - and -chains were separately discovered, and in 1990, both chains were found to be co-expressed in one protein in H-2O. In contrast to other molecules of MHC class II, interferon gamma does not induce HLA-DO expression.

# Function
The binding of HLA-DO at the MHC class II peptide-exchange catalysis site suggested that it acts as a competitive inhibitor, although biochemical studies have established its complementary function to HLA-DM in fine tuning epitope selection.
During infection, exogenous antigen is internalized by phagocytosis or receptor-mediated endocytosis, and processed in hydrolytic enzyme-containing compartments of increasing acidity. Once the degraded antigen is 13-18 residues, it is ready to bind to MHC class II molecules. To bind to the MHC-class II protein, HLA-DM catalyzes the exchange of CLIP, a protein occupying the binding groove of MHC class II, with the antigenic oligopeptide. HLA-DO is strongly associated with HLA-DM throughout the catalyzed exchange.

# Structure
Before the three-dimensional structure of complexed HLA-DO was elucidated by X-ray crystallography, its crystal structure was modeled after homology studies to classical MHC class II proteins. Following crystallization of the protein, HLA-DO was found to be conformationally similar to classical MHC class II protein, with alterations in the N-terminus. The structure of the free HLA-DO protein, however, remains to be elucidated.
HNRNPC
Heterogeneous nuclear ribonucleoproteins C1/C2 is a protein that in humans is encoded by the HNRNPC gene.
It is abnormally expressed in fetuses of both IVF and ICSI, which may contribute to the increase risk of birth defects in these ART.

# Function
This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing(reference: Koenig J. nature structural and Molecular Biology 2010: iCLIP) and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. Transcriptional regulation by hormonal 1,25-dihydroxyvitamin D(3) (calcitriol) involves occupancy of vitamin D response elements (VDREs) by HNRNPC or 1,25(OH)(2)D(3)-bound vitamin D receptor (VDR). This relationship is disrupted by elevated HNRNPC, causing a form of hereditary vitamin D-resistant rickets (HVDRR) in both humans and non-human primates. The protein encoded by this gene can act as a tetramer and is involved in the assembly of 40S hnRNP particles. Species-specific tetramerization of HNRNPC subunits is important to its nucleic acid binding, whereby over-expression of major human HNRNPC subunits in mouse osteoblastic cells confers vitamin D resistance. Multiple transcript variants encoding at least two different isoforms have been described for this gene.

# Interactions
HNRNPC has been shown to interact with Grb2.
HNRPDL
Heterogeneous nuclear ribonucleoprotein D-like, also known as HNRPDL, is a protein which in humans is encoded by the HNRPDL gene.

# Function
This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two RRM domains that bind to RNAs. Two alternatively spliced transcript variants have been described for this gene. One of the variants is probably not translated because the transcript is a candidate for nonsense-mediated mRNA decay. The protein encoded by this gene is similar to its family member HNRPD.

# Clinical Significance
Heterozygous nonsense mutations in HNRNPDL has been identified as the cause of the autosomal disorder, Limb-girdle muscular dystrophy.
HOMER1
Homer protein homolog 1 or Homer1 is a neuronal protein that in humans is encoded by the HOMER1 gene.  Other names are Vesl and PSD-Zip45.

# Structure
Homer1 protein has an N-terminal EVH1 domain, involved in protein interaction, and a C-terminal coiled-coil domain involved in self association.  It consists of two major splice variants, short-form (Homer1a) and long-form (Homer1b and c).  Homer1a has only EVH1 domain and is monomeric while Homer1b and 1c have both EVH1 and coiled-coil domains and are tetrameric.  The coiled-coil can be further separated into N-terminal half and C-terminal half.  The N-terminal half of the coiled-coil domain is predicted to be a parallel dimer while the C-terminus half is a hybrid of dimeric and anti-parallel tetrameric coiled-coil.  As a whole, long Homer is predicted to have a dumbbell-like structure where two pairs of EVH1 domains are located on two sides of long (~50 nm) coiled-coil domain.  Mammals have Homer2 and Homer3, in addition to Homer1, which have similar domain structure.  They also have similar alternatively spliced forms.

# Tissue distribution
Homer1 is expressed widely in the central nervous system as well as peripheral tissue including heart, kidney, ovary, testis, and skeletal muscle.  Subcellularly in neurons, Homer1 is concentrated in postsynaptic structures and constitutes a major part of the postsynaptic density.

# Function
EVH1 domain interacts with PPXXF motif.  This sequence motif exists in group 1 metabotrophic glutamate receptor (mGluR1 and mGluR5), IP3 receptors (IP3R), Shank, transient receptor potential canonical (TRPC) family channels, drebrin, oligophrenin, dynamin3, CENTG1, and ryanodin receptor.  Through its tetrameric structure, long forms of Homer (such as Homer1b and Homer1c) are proposed to cross link different proteins.  For example, group 1 mGluR is crossed linked with its signaling downstream, IP3 receptor.  Also, through crosslinking another multimeric protein Shank, it is proposed to comprise a core of the postsynaptic density.
Notably, the expression of Homer1a is induced by neuronal activity while that of Homer1b and 1c are constitutive.  Thus Homer1a is classified as an immediate early gene.  Homer1a, acts as a natural dominant negative form that blocks interaction between long-forms and their ligand proteins by competing with the EVH1 binding site on the ligand proteins.  In this way, the short form of Homer uncouples mGluR signaling and also shrinks dendritic spine structure.  Therefore, the short form of Homer is considered to be a part of a mechanism of homeostatic plasticity that dampens the neuronal responsiveness when input activity is too high. The long form Homer1c plays a role in synaptic plasticity and the stabilization of synaptic changes during long-term potentiation.
The coiled-coil domain is reported to interact with syntaxin13 and activated Cdc42.  The interaction with Cdc42 inhibit the activity of Cdc42 to remodel dendritic spine structure.
HOT-17
HOT-17, or 2,5-dimethoxy-4-(-isobutylthio)-N-hydroxyphenethylamine, is a psychedelic phenethylamine of the 2C family.  It was presumably first synthesized by Alexander Shulgin and reported in his book, PIHKAL.

# Chemistry
HOT-17's full chemical name is 2-[4-(2-isobutylthio)-2,5-dimethoxyphenyl-N-hydroxyethanamine.  It has structural properties similar to 2C-T-17 and to other drugs in the HOT- series, with the most closely related compounds being HOT-2 and HOT-7.

# General Information
The dosage range of HOT-17 is typically 70-120 mg and its duration is approximately 12-18 hours according to Shulgin.  HOT-17 produces time distortion and general psychedelia.  It also has little to no body load.

# Categorization
HOTAIR
HOTAIR (for HOX transcript antisense RNA) is a human gene located on chromosome 12. It is the first example of an RNA expressed on one chromosome that has been found to influence transcription on another chromosome.

# Gene and transcribed RNA product
The HOTAIR gene contains 6,232 bp and encodes 2.2 kb long noncoding RNA molecule, which controls gene expression.  Its source DNA is located within a HOXC gene cluster.  It is shuttled from chromosome 12 to chromosome 2 by the Suz-Twelve protein.

# Function
The 5' end of HOTAIR interacts with a Polycomb-group protein Polycomb Repressive Complex 2 (PRC2) and as a result regulates chromatin state. It is required for gene-silencing of the HOXD locus by PRC2. The 3' end of HOTAIR interacts with the histone demethylase LSD1.
It is an important factor in the epigenetic differentiation of skin over the surface of the body. Skin from various anatomical positions is distinct, e.g. the skin of the eyelid differs markedly from that on the sole of the foot.

# Clinical significance
HOTAIR is highly expressed in metastatic breast cancers. High levels of expression in primary breast tumours are a significant predictor of subsequent metastasis and death. This is partially due to HOTAIR-mediated overexpression of the HER2 oncogene through sequestration of miR-133-3p, which is a negative regulator of HER2 expression. In cells, especially those that over express PRC2, the prevention of HOTAIR expression leads to a reduction in invasive potential of that cell.  It is also involved in esophageal squamous cell carcinoma.
HOXA13
Homeobox protein Hox-A13 is a protein that in humans is encoded by the HOXA13 gene.

# Function
In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation.

# Clinical significance
Expansion of a polyalanine tract in the encoded protein can cause                  hand-foot-genital syndrome            , also known as hand-foot-uterus syndrome.
HOXB13
Homeobox protein Hox-B13 is a protein that in humans is encoded by the HOXB13 gene.

# Function
This gene encodes a transcription factor that belongs to the homeobox gene family. Genes of this family are highly conserved among vertebrates and essential for vertebrate embryonic development. This gene has been implicated in fetal skin development and cutaneous regeneration. In mice, a similar gene was shown to exhibit temporal and spatial colinearity in the main body axis of the embryo, but was not expressed in the secondary axes, which suggests functions in body patterning along the axis. This gene and other HOXB genes form a gene cluster on chromosome 17 in the 17q21-22 region.
Men who inherit a rare (<0.1% in a selected group of patients without clinical signs of prostate cancer) genetic variant in HOXB13 (G84E or rs138213197) have a 10-20-fold increased risk of prostate cancer.
HOXC10
Homeobox protein Hox-C10 is a protein that in humans is encoded by the HOXC10 gene.

# Function
This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The protein level is controlled during cell differentiation and proliferation, which may indicate this protein has a role in origin activation.

# Pathology
- HOXC10 is overexpressed in breast cancer and transcriptionally regulated by estrogen via involvement of histone methylases MLL3 and MLL4.
- Methylation of the estrogen-repressed gene HOXC10 in breast cancer determines resistance to aromatase inhibitors. This epigenetic reprogramming of HOXC10 is observed in endocrine-resistant breast cancer.
HOXD10
Homeobox D10, also known as HOXD10, is a protein which in humans is encoded by the HOXD10 gene.

# Function
This gene is a member of the Abd-B homeobox family and encodes a protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox D genes located on chromosome 2. The encoded nuclear protein functions as a sequence-specific transcription factor that is expressed in the developing limb buds and is involved in differentiation and limb development.

# Clinical significance
Mutations in this gene have been associated with Wilms' tumor and congenital vertical talus (also known as "rocker-bottom foot" deformity or congenital convex pes valgus) and/or a foot deformity resembling that seen in Charcot-Marie-Tooth disease.

# Regulation
The HOXD10 gene is repressed by the microRNAs miR-10a and miR-10b.