Persius/hicric huggingface dataset:
CD81
CD81 molecule, also known as CD81 (Cluster of Differentiation 81), is a protein which in humans is encoded by the CD81 gene. It is also known as 26 kDa cell surface protein, TAPA-1 (Target of the Antiproliferative Antibody 1), and Tetraspanin-28 (Tspan-28).

# Gene
The gene is located on the Watson (plus) strand of the short arm of chromosome 11 (11p15.5). It is 20,103 bases in length and encodes a protein of  236 amino acids (predicted molecular weight 25.809 kDa).
The protein does not appear to be post translationally modified and has four transmembrane domains. Both the N-terminus and C-terminus lie on the intracellular side of the membrane.
The gene is expressed in hemopoietic, endothelial, and epithelial cells. It is absent from erythrocytes, platelets, and neutrophils.

# Function
The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. This protein appears to promote muscle cell fusion and support myotube maintenance. Also it may be involved in signal transduction. This gene is localized in the tumor-suppressor gene region and thus it is a candidate gene for malignancies.
The tetraspanin family includes CD9, CD37, CD53, CD63, CD81 (this protein), CD82 and CD151.
CD81 interacts directly with immunoglobulin superfamily member 8 (IGSF8, CD316) and CD36. It forms a signal transduction complex with CD19, CD21 and Leu-13 (CD225) on the surface of the B cell.  On T cells CD81 associates with CD4 and CD8 and provides a costimulatory signal with CD3.

# Clinical significance
This protein plays a critical role in Hepatitis C attachment and/or cell entry by interacting with virus' E1/E2 glycoproteins heterodimer. The large extracellular loop(LEL) of CD81 binds the hepatitis E2 glycoprotein dimer.  HCV-E2 and CD81 binding Kd is 1.8 nM.  HCV-E2 engaged CD81 is only 30% internalized after 12hr, suggesting CD81 may be primarily an attachment receptor for HCV.
It also appears to play a role in liver invasion by Plasmodium species. CD81 is required for Plasmodium vivax sporozoite entry into human hepatocytes and for Plasmodium yoelii sporozoite entry into murine hepatocytes.
HIV gag proteins use tetraspanin enriched microdomains (containing minimally CD81, CD82, CD63) as a platform for virion assembly and release.  Purified HIV produced by MOLT\HIV cells contains CD81.  Anti-CD81 antibodies downregulate HIV production 3 fold, however the CD81 protein free virus is more infectious. Engagement of CD81 lowers the signaling threshold required to trigger T-Cell\CD3 mediated proviral DNA in CD4+ T cells.
CD81 appears to play a role in the pathogenesis of influenza.

# Interactions
CD81 has been shown to interact with TSPAN4, CD19, CD9, PTGFRN, CD117 and CD29.

## Ligands
Benzyl salicylate and terfenadine have been shown to bind to CD81.
CD98
CD98 is a glycoprotein that is a heterodimer composed of SLC3A2 and SLC7A5 that forms the large neutral amino acid transporter (LAT1).  LAT1 is a heterodimeric membrane transport protein that preferentially transports branched-chain (valine, leucine, isoleucine) and aromatic (tryptophan, tyrosine) amino acids.  LAT is highly expressed in brain capillaries (which form the bloodbrain barrier) relative to other tissues.
A functional LAT1 transporter is composed of two proteins encoded by two distinct genes:
- 4F2hc/CD98 heavy subunit protein encoded by the SLC3A2 gene 
- CD98 light subunit protein encoded by the SLC7A5 gene
CD99
CD99 antigen (Cluster of differentiation 99), also known as MIC2 or single-chain type-1 glycoprotein, is a heavily O-glycosylated transmembrane protein that is encoded by the CD99 gene in humans. The protein has a mass of 32 kD.  Unusually for a gene present on the X chromosome, the CD99 gene does not undergo X inactivation, and it was the first such pseudoautosomal gene to be discovered in humans.

# Expression
It is expressed on all leukocytes but highest on thymocytes and is believed to augment T-cell adhesion  and apoptosis of double positive t cells. It has been found in endothelial cells and in the periodontium, including gingival fibroblasts and gingival epithelial cells. It also participates in migration and activation. There is also experimental evidence that it binds to cyclophilin A.
It is found on the cell surface of Ewing's sarcoma tumors  and is positive in granulosa cell tumors. It is more expressed in malignant gliomas than in the brain, and such overexpression results in higher levels of invasiveness and lower rates of survival. Antibodies to CD99 are used in diagnostic immunohistochemistry to distinguish Ewing's sarcoma from other tumours of similar histological appearance, as well as for the identification of thymic tumours, and of spindle cell tumours, such as synovial sarcoma, haemangiopericytoma, and meningioma. EWS/FLI is thought to regulate CD99, but knockdown of EWS/FLI results in only a modest reduction in CD99. When CD99 expression is knocked down in human cells with Ewing's sarcoma and those cells are grafted onto mice, tumor and bone metastasis development is reduced.
Reducing CD99 expression results in higher -III tubulin expression and more neurite outgrowth.
Upregulating CD99 expression in the cell line L428, a Hodgkin's lymphoma line, resulted in those cells redifferentiating towards B cells.  Consequently, the loss of B-cell differentiation in Hodgkin's lymphoma may be due to CD99 downregulation.
Men appear to express higher levels of CD99 than women.

# Prognostic Value
In patients with diffuse large B-cell lymphoma (DLBCL) with the germinal center B-cell (GCB, classified according to the Muris algorithm) subtype, positive expression of CD99 resulted in better 2-year event free survival (EFS) and 2-year overall survival (OS) compared to negative expression of CD99.  In patients with DLBCL with non-GCB, however, negative expression of CD99 resulted in better 2-year EFS and 2-year OS.
In patients with non-small cell lung cancer (NSCLC), higher CD99 expression in the stroma results in better prognosis.

# Interactions
There is evidence that through suppressing 1 integrin affinity, CD99 inhibits cell-extracellular matrix adhesion.
Cdk1
Cell division cycle 2, G1 to S and G2 to M, also known as Cdk1 (CDC2), is a human gene. The protein encoded by this gene is called p34cdk1 and is a cyclin-dependent kinase in the Ser/Thr protein kinase family. This protein is a catalytic subunit of the highly conserved protein kinase complex known as maturation promoting factor (MPF), which is essential for G1/S and G2/M phase transitions of eukaryotic cell cycle. Mitotic cyclins stably associate with this protein and function as regulatory subunits. The kinase activity of this protein is controlled by cyclin accumulation and destruction through the cell cycle. The phosphorylation and dephosphorylation of this protein also play important regulatory roles in cell cycle control.
Cdk1 is one of the components of the maturation promoting factor (MPF) which controls the cell division cycle in yeast. Cdk1 is a cyclin-dependent kinase (CDK) which, when bound to cyclin B, allows a dividing cell to enter into mitosis from G2 (in the absence of inhibitory proteins such as Wee1). Cdk1 also permits the transition from G1 through S in conjunction with cyclin A and cyclin E.
In humans, the functions of cdc2 are divided between its homologues. Some important ones are Cdk1, Cdk2, Cdk4, and Cdk6 (See cyclin-dependent kinase), which associate with different cyclins and regulate stage transitions during the cell cycle.
Other "Cell division cycle" genes (cdc's) are also involved in complex regulatory pathways during the cell cycle. Cdc's were originally discovered in Saccharomyces cerevisiae, and are followed by a number which signifies the order in which they were discovered (e.g. cdc2, cdc20, cdc25, etc).
CDC6
Cell division control protein 6 homolog is a protein that in humans is encoded by the CDC6 gene.
The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Cdc6, a protein essential for the initiation of DNA replication. This protein functions as a regulator at the early steps of DNA replication. It localizes in the cell nucleus during cell cycle phase G1, but translocates to the cytoplasm at the start of S phase. The subcellular translocation of this protein during the cell cycle is regulated through its phosphorylation by cyclin-dependent kinases. Transcription of this protein was reported to be regulated in response to mitogenic signals through a transcriptional control mechanism involving E2F proteins.

# Interactions
CDC6 has been shown to interact with ORC1L, ORC2L, Cyclin A2, PPP2R3B, MCM3, PPP2R3A, MCM7 and PSKH1.
CDK9
CDK9 or cyclin-dependent kinase 9 is a cyclin-dependent kinase associated with P-TEFb.
The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and known as important cell cycle regulators. This kinase was found to be a component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II-directed transcription and functions by phosphorylating the C-terminal domain of the largest subunit of RNA polymerase II. This protein forms a complex with and is regulated by its regulatory subunit cyclin T or cyclin K. HIV-1 Tat protein was found to interact with this protein and cyclin T, which suggested a possible involvement of this protein in AIDS. 
CDK9 is also known to associate with other proteins such as TRAF2, and be involved in differentiation of skeletal muscle.
CDON
Cell adhesion molecule-related/down-regulated by oncogenes is a protein that in humans is encoded by the CDON gene.
CDON and BOC are cell surface receptors of the immunoglobulin (Ig)/fibronectin type III (FNIII) repeat family involved in myogenic differentiation. CDON and BOC are coexpressed during development, form complexes with each other in a cis fashion, and are related to each other in their ectodomains, but each has a unique long cytoplasmic tail.

# Structure and function
Cell adhesion molecule-related/down-regulated by oncogenes (CDON) is a conserved transmembrane glycoprotein belonging to a subgroup of the immunoglobulin superfamily of cell adhesion molecules. It is highly expressed in both the somites and dorsal lips of the neural tube of embryonic day 8.5 mice. It is expressed in proliferating and differentiating myoblast cell lines, there is evidence showing its role in mediating the effects of cellcell interactions between muscle precursors that are critical in myogenesis. It is also expressed in neural crest precursor cells, it regulates the localization of N-cadherin providing a mechanism for directed neural crest migration. CDON protein was shown to bind to all three mammalian isoforms of hedgehog proteins: Sonic Hh, Indian Hh, and Desert Hh.

# Clinical significance
CDON mutations are thought to diminish sonic hedgehog (SHH)-pathway activity which is important in stimulating cell proliferation, differentiation, and tissue patterning at multiple points in animal development. CDON was shown to play a role in differentiation of midbrain dopaminergic neurons through the interference with of Shh signaling pathway. Mutations in CDON gene has been associated with Holoprosencephaly which is structural anomaly of the brain, in which the developing forebrain fails to correctly separate into right and left hemispheres. CDON mutations synergistically interact with prenatal alcohol exposure to increase susceptibility to Holoprosencephaly.

# Gene knockdown studies
CDON knockdown using morpholinos in zebra fish altered the eye development, CDON was shown important in restraining the size of the optic stalk and ventral retina in chick embryos. Additionally, double CDON knock out mice display optic nerve hypoplasia (ONH), a prominent feature of septo-optic dysplasia  (SOD), the same phenotype shown by treating mice prenatally with ethanol. CDON/ animals also show cardiac dysfunction with increased fibrosis, those cardiac effects are mediated through hyperactivation of WNT/-catenin signaling.

# Interactions
CDON has been shown to interact with CDH1 and BOC.
CDS2
Phosphatidate cytidylyltransferase 2 is an enzyme that in humans is encoded by the CDS2 gene.
Breakdown products of phosphoinositides are ubiquitous second messengers that function downstream of many G protein-coupled receptors and tyrosine kinases regulating cell growth, calcium metabolism, and protein kinase C activity. This gene encodes an enzyme which regulates the amount of phosphatidylinositol available for signaling by catalyzing the conversion of phosphatidic acid to CDP-diacylglycerol. This enzyme is an integral membrane protein localized to two subcellular domains, the matrix side of the inner mitochondrial membrane where it is thought to be involved in the synthesis of phosphatidylglycerol and cardiolipin. and the cytoplasmic side of the endoplasmic reticulum where it functions in phosphatidylinositol biosynthesis. Two genes encoding this enzyme have been identified in humans, one mapping to human chromosome 4q21 (CDS1) and a second (this gene) to 20p13.

# Model organisms
Model organisms have been used in the study of CDS2 function. A conditional knockout mouse line, called Cds2tm1a(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 six tests were carried out and two phenotypes were reported. 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 significant abnormalities were observed in these animals.
CDX1
Homeobox protein CDX-1 is a protein in humans that is encoded by the CDX1 gene. CDX1 is expressed in the developing endoderm and its expression persists in the intestine throughout adulthood. CDX1 protein expression varies along the intestine, with high expression in intestinal crypts and diminishing expression along intestinal villi.

# Function
This gene is a member of the caudal-related homeobox transcription factor family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity.
CDX1 has also been shown to play an important role in embryonic epicardial development. It has been demonstrated that CDX proteins suppress cardiac differentiation in both zebrafish and mouse embryonic stem cells, but the overall mechanism for how this happens is poorly understood. However, CDX1 has been shown to be transiently expressed in the embryonic heart 11.5 days post coitum (dpc). This transient expression is thought to induce epicardial epithelial-to-mesynchemal transition and thus proper cardiovascular formation. It has been shown that low-dose CDX1 induction caused enhanced migration and differentiation of epicardium-derived cells into vascular smooth muscle, where as continued high dose induction of CDX1 or CDX1 deficiency diminished the ability of these cells to migrate and differentiate into smooth muscle by the actions of TGF-1. Furthermore, CDX1 induction also altered transcript expression of genes related to cell adhesions for EMT and angiogenesis. Therefore, along with its known roles in intestinal patterning and differentiation, CDX1 is also shown to be important in epicardial development.
CDX2
Homeobox protein CDX-2 is a protein that in humans is encoded by the CDX2 gene. This gene is a member of the caudal-related homeobox transcription factor family that is expressed in the nuclei of intestinal epithelial cells.

# Function
Cdx2 is the gene that directs early embryogenesis in mice. It is required to form the placenta.
Ectopic expression of CDX2 was reported in more than 85% of the human patients with acute myeloid leukemia (AML). Ectopic expression of Cdx2 in murine bone marrow induced AML in mice and upregulate Hox genes in bone marrow progenitors. CDX2 is also implicated in the pathogenesis of Barrett's esophagus where it has been shown that components from gastroesophageal reflux such as bile acids are able to induce the expression of an intestinal differentiation program through up-regulation of NF-B and CDX2.

# Biomarker for intestinal cancer
CDX2 is also used in diagnostic surgical pathology as a marker for gastrointestinal differentiation, especially colorectal.

# Possible use in stem cell research
This gene (or, more specifically, the equivalent gene in humans) has come up in the proposal by the President's Council on Bioethics, as a solution to the stem cell controversy. According to one of the plans put forth, by deactivating the gene, it would not be possible for a properly organized embryo to form, thus providing stem cells without requiring the destruction of an embryo. Other genes that have been proposed for this purpose include Hnf4, which is required for gastrulation.

# Interactions
CDX2 has been shown to interact with EP300, and PAX6.
CHD1
Chromodomain-helicase-DNA-binding protein 1 is an enzyme that in humans is encoded by the CHD1 gene.
The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains.  CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.

# Interactions
CHD1 has been shown to interact with Nuclear receptor co-repressor 1.
CHD2
Chromodomain-helicase-DNA-binding protein 2 is an enzyme that in humans is encoded by the CHD2 gene.

# Function
The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. CHD2 catalyzes the assembly of chromatin into periodic arrays; and the N-terminal region of CHD2, which contains tandem chromodomains, serves an auto-inhibitory role in both the DNA-binding and ATPase activities of CHD2.  Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

# Clinical significance
De Novo Mutations and deletions in this gene have been associated with cases of epileptic encephalopathies.
CHD2 epilepsy is increasingly being identified as a subpopulation of Lennox-Gastaut Syndrome.
Recently, de novo mutations or deletions in CHD2 has been linked to intellectual disability and to autism. Researchers found 27 genes which abolish function of the corresponding protein  in at least two people with autism, and 6 genes are mutated in three or more people with autism. These six genes  CHD8, DYRK1A, ANK2, GRIN2B, DSCAM and CHD2  are the strongest autism candidates identified so far.

# Family support
Syndromes associated with mutations or deletions in CHD2 can be devastating. Families of individuals with CHD2 mutations or deletions can join a research and support group.
CHD3
Chromodomain-helicase-DNA-binding protein 3 is an enzyme that in humans is encoded by the CHD3 gene.

# Function
This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described.
Mutations in CHD3 cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.

# Interactions
CHD3 has been shown to interact with:
- HDAC1,
- Histone deacetylase 2  and
- SERBP1.
CHD4
Chromodomain-helicase-DNA-binding protein 4 is an enzyme that in humans is encoded by the CHD4 gene.

# Function
The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis develop antibodies against this protein.

# Interactions
CHD4 has been shown to interact with HDAC1, Histone deacetylase 2, MTA2, SATB1 and Ataxia telangiectasia and Rad3 related.
CHD7
Chromodomain-helicase-DNA-binding protein 7 also known as ATP-dependent helicase CHD7 is an enzyme that in humans is encoded by the CHD7 gene.
CHD7 is an ATP-dependent chromatin remodeler homologous to the Drosophila trithorax-group protein Kismet. Mutations in CHD7 are associated with CHARGE syndrome.

# Model organisms
Model organisms have been used in the study of CHD7 function. A conditional knockout mouse line, called Chd7tm2a(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.
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 five 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. Male heterozygotes displayed abnormal pelvic elevation in a modified SHIRPA test and have a high incidence of Bergmeister's papilla in both eyes.  When the brains of heterozygous animals were studied, an absence of corpus callosum was observed.
CHD8
Chromodomain-helicase-DNA-binding protein 8 is an enzyme that in humans is encoded by the CHD8 gene.

# Function
The gene CHD8 encodes the protein chromodomain helicase DNA binding protein 8, which is a chromatin regulator enzyme that is essential during fetal development. CHD8 is an ATP dependent enzyme.
The protein contains an Snf2 helicase domain that is responsible for the hydrolysis of ATP to ADP. CHD8 encodes for a DNA helicase that function as a transcription repressor by remodeling chromatin structure by altering the position of nucleosomes. CHD8 negatively regulates Wnt signaling. Wnt signaling is important in the vertebrate early development and morphogenesis. It is believed that CHD8 also recruits the linker histone H1 and causes the repression of -catenin and p53 target genes. The importance of CHD8 can be observed in studies where CHD8-knockout mice died after 5.5 embryonic days because of widespread p53 induced apoptosis.

# Clinical significance
Mutations in this gene have been linked to a subset of autism cases.
Mutations in CHD8 could lead to upregulation of -catenin-regulated genes, in some part of the brain this upregulation can cause brain overgrowth also known as macrocephaly, which occurs in 15-35% of autistic children.
Some studies have determined the role of CHD8 in autism spectrum disorder (ASD). CHD8 expression significantly increases during human mid-fetal development. The chromatin remodeling activity and its interaction with transcriptional regulators have shown to play an important role in ASD aetiology. The developing mammalian brain has a conserved CHD8 target regions that are associated with ASD risk genes. The knockdown of CHD8 in human neural stem cells results in dysregulation of ASD risk genes that are targeted by CHD8.