Persius/hicric huggingface dataset:
CAPN3
Calpain-3 is a protein that in humans is encoded by the CAPN3 gene.

# Function
Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed.
In melanocytic cells CAPN3 gene expression may be regulated by MITF.

# Interactions
CAPN3 has been shown to interact with Titin.
CARD9
Caspase recruitment domain-containing protein 9 is an adaptor protein which in humans is encoded by the CARD9 gene.It mediates signals from pattern recognition receptors to activate pro-inflammatory and anti-inflammatory cytokines,   regulating inflammation and cell apoptosis. Homozygous mutations in CARD9 are associated with defective innate immunity against yeasts, like Candida and dermatophytes.

# Function
CARD9 is a member of the CARD protein family, which is defined by the presence of a characteristic caspase-associated recruitment domain (CARD). CARD is a protein interaction domain known to participate in activation or suppression of CARD containing members of the caspase family, and thus plays an important regulatory role in cell apoptosis. This protein was identified by its selective association with the CARD domain of BCL10, a positive regulator of apoptosis and NF-B activation.It is thought to function as a molecular scaffold for the assembly of a BCL10 signaling complex that activates NF-B. Several alternatively spliced transcript variants have been observed, but their full-length nature is not clearly defined.

# Clinical significance
In 2006, it became clear that Card9 plays important roles within the innate immune respons against yeasts. Card9 mediates signals from so called pattern recognition receptors (Dectin-1) to downstream signalling pathways such as NF-B and by this activates pro-inflammatory cytokines (TNF, IL-23, IL-6, IL-2) and an anti-inflammatory cytokine (IL-10) and subsequently an appropriate innate and adaptive immune response to clear an infection.
An autosomal recessive form of susceptibility to chronic mucocutaneous candidiasis was found in 2009 to be associated with homozygous mutations in CARD9.
Deep dermatophytosis and Card9 deficiency reported in an Iranian family led to its discovery in 17 people from Tunisian, Algerian, and Moroccan families with deep dermatophytosis.
CARD9 mutations have been associated with inflammatory diseases such as ankylosing spondylitis and inflammatory bowel disease (Crohn's Disease and Ulcerative Colitis).

# Model organisms
Model organisms have been used in the study of CARD9 function. A conditional knockout mouse line called Card9tm1a(EUCOMM)Hmgu 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 - in-depth bone and cartilage phenotyping
CARKD
Carbohydrate kinase domain containing protein (abbreviated as CARKD), encoded by CARKD gene, is a human protein of unknown function. The CARKD gene encodes proteins with a predicted mitochondrial propeptide (mCARKD), a signal peptide (spCARKD) or neither of them (cCARKD). Confocal microscopy analysis of transfected CHO (Chinese-hamster ovary) cells indicated that cCARKD remains in the cytosol, whereas mCARKD and spCARKD are targeted to the mitochondria and the endoplasmic reticulum respectively. The protein is conserved throughout many species, and has predicted orthologs through eukaryotes, bacteria, and archea.

# Structure

## Gene
Human CARKD gene has 10 exons and resides on Chromosome 13 at q34. The following genes are near CARKD on the chromosome:
- COL4A2: A2 Subunit of type IV collagen
- RAB20: Potential regulator of Connexin 43 trafficking.
- CARS2: Mitochondrial Cystienyl-tRNA Synthetase 2
- ING1: Tumor-Suppressor Protein

## Protein
This protein is part of the phosphomethylpyrimidine kinase: ribokinase / pfkB superfamily. This family is characterized by the presence of a domain shared by the family. CARKD contains a carbohydrate kinase domain (Pfam PF01256). This family is related to Pfam PF02210 and Pfam PF00294 implying that it also is a carbohydrate kinase.

## Predicted properties
The following properties of CARKD were predicted using bioinformatic analysis:
- Molecular Weight: 41.4 KDal
- Isoelectric point: 9.377
CARKD orthologs have highly variable isoelectric points.
- CARKD orthologs have highly variable isoelectric points.
- Post-translational modification: Three post-translational modifications are predicted:
Modified Phosphotyrosine Residue
Two N-Linked Glycosylation Sites
- Modified Phosphotyrosine Residue
- Two N-Linked Glycosylation Sites
- A Signal Peptide and signal peptide cleavage site was predicted.

# Function

## Tissue distribution
CARKD appears to be ubiquitously expressed at high levels. Expression data in the human protein, and the mouse ortholog, indicate its expression in almost all tissues. One peculiar expression pattern of CARKD is its differential expression through the development of oligodendrocytes. Its expression is lower in oligodendrocyte progenitor cells than in mature oligodendrocytes.

## Binding partners
The human protein apolipoprotein A-1 binding precursor (APOA1BP) was predicted to be a binding partner for CARKD. This prediction is based on co-occurrence across genomes and co-expression. In addition to these data, the orthologs of CARKD  in E. coli contain a domain similar to APOA1BP. This indicates that the two proteins are likely to have originated from a common evolutionary ancestor and, according to Rosetta stone analysis theory, are likely interaction partners even in species such as humans where the two proteins are not produced as a single polypeptide.

# Clinical significance
Based on allele-specific expression of CARKD,  CARKD may play a role in acute lymphoblastic leukemia. In addition, microarray data indicates that CARKD is up-regulated in Glioblastoma multiforme tumors.
CARM1
CARM1 (coactivator-associated arginine methyltransferase 1), also known as PRMT4 (protein arginine N-methyltransferase 4), is an enzyme (EC 2.1.1.125) encoded by the CARM1 gene found in human beings, as well as many other mammals. It has a polypeptide (L) chain type that is 348 residues long, and is made up of alpha helices and beta sheets. Its main function includes catalyzing the transfer of a methyl group from S-adenosyl-L-methionine to the side chain nitrogens of arginine residues within proteins to form methylated arginine derivatives and S-adenosyl-L-homocysteine. CARM1 is a secondary coactivator through its association with p160 family (SRC-1, GRIP1, AIB) of coactivators.  It is responsible for moving cells toward the inner cell mass in developing blastocysts.

# Clinical significance
CARM1 plays an important role in androgen receptors and may play a role in prostate cancer progression.
CARM1 exerts both oncogenic and tumor-suppressive functions. In breast cancer, CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. In pancreatic cancer, CARM1 methylates and inhibits MDH1 by disrupting its dimerization, which represses mitochondria respiration and inhibits glutamine utilization. CARM1-mediated MDH1 methylation reduces cellular NADPH level and sensitizes cells to oxidative stress, thereby suppressing cell proliferation and colony formation.
CASC5
CASC5 is a protein that is encoded by the CASC5 gene in humans.

# Function
CASC5 is part of the kinetochore. It is involved in microtubule attachment to chromosome centromeres and in the activation of the spindle checkpoint during mitosis. The CASC5 gene is upregulated in the areas of cell proliferation surrounding the ventricles during fetal brain development.

# Interactions
CASC5 has been shown to interact with MIS12, BUB1, BUBR1 and ZWINT-1.

# Polymorphisms
Homozygous polymorphisms in the CASC5 gene have been seen in patients with autosomal recessive primary microcephaly (MCPH). The mutation resulted in the skipping of exon 18 transcription, causing a frameshift and the production of a truncated protein. This truncation inhibits the binding ability of MIS12.
CASPR
CASPR also known as Contactin associated protein 1, Paranodin and CASPR1 is a protein that in humans is encoded by the CNTNAP1 gene.
CASPR is a part of the neurexin family of proteins, hence its another name "Neurexin IV". CASPR is a membrane protein found in the neuronal membrane in the paranodal section of the axon in myelinated neurons, between the Nodes of Ranvier containing Na+ channels, and juxtaparanode, which contains K+ channels. During myelination, caspr associates with contactin in a cis complex, though its precise role in myelination is not yet understood.

# Function
The gene product was initially identified as a 190-kD protein associated with the contactin-PTPRZ1 complex. The 1,384-amino acid protein, also designated p190 or CASPR for 'contactin-associated protein,' includes an extracellular domain with several putative protein-protein interaction domains, a putative transmembrane domain, and a 74-amino acid cytoplasmic domain. Northern blot analysis showed that the gene is transcribed predominantly in brain as a transcript of 6.2 kb, with weak expression in several other tissues tested. The architecture of its extracellular domain is similar to that of neurexins, and this protein may be the signaling subunit of contactin, enabling recruitment and activation of intracellular signaling pathways in neurons. .
Mutations in CNTNAP1 cause                 arthrogryposis multiplex congenita            .
CCBE1
Collagen and calcium-binding EGF domain-containing protein 1 is a protein that in humans is encoded by the CCBE1 gene.

# Function
CCBE1 is a regulator of the development and growth of the lymphatic system. CCBE1 is necessary for the proteolytic activation of VEGF-C by ADAMTS3, which is the main growth factor for the lymphatic system .

# Clinical significance
Hennekam syndrome type I (a generalized lymphatic dysplasia in humans) is associated with mutations in the CCBE1 gene, and the molecular etiology of the disease has been elucidated.
CCDC8
Coiled-coil domain containing 8 is a protein that in humans is encoded by the CCDC8 gene.

# Function
This gene encodes a coiled coil domain-containing protein. The encoded protein functions as a cofactor required for p53-mediated apoptosis following DNA damage, and may also play a role in growth through interactions with the cytoskeletal adaptor protein obscurin-like 1.

# Clinical relevance
Mutations in this gene have been shown to cause 3-M syndrome.
CCL11
C-C motif chemokine 11 also known as eosinophil chemotactic protein and eotaxin-1 is a protein that in humans is encoded by the CCL11 gene. This gene is encoded on three exons and is located on chromosome 17.

# Function
CCL11 is a small cytokine belonging to the CC chemokine family. CCL11 selectively recruits eosinophils by inducing their chemotaxis, and therefore, is implicated in allergic responses. The effects of CCL11 are mediated by its binding to a G-protein-linked receptor known as a chemokine receptor.  Chemokine receptors for which CCL11 is a ligand include CCR2, CCR3 and CCR5.  However, it has been found that eotaxin-1 (CCL11) has high degree selectivity for its receptor, such that they are inactive on neutrophils and monocytes, which do not express CCR3.

# Clinical significance
Increased CCL11 levels in blood plasma are associated with aging in mice and humans.  Additionally, it has been demonstrated that exposing young mice to CCL11 or the blood plasma of older mice decreases their neurogenesis and cognitive performance on behavioural tasks thought to be dependent on neurogenesis in the hippocampus.
Higher plasma concentrations of CCL11 have been found in current cannabis users compared to past users and those who had never used.  CCL11 has also been found in higher concentrations in people suffering from schizophrenia; cannabis is a known trigger of schizophrenia.
It's also a biomarker for CTE or punch-drunk syndrome.
During periods of bone inflammation, CCL11 and CCR3 are upregulated. This is associated with an increase in osteoclast activity.
CCL16
Chemokine (C-C motif) ligand 16 (CCL16) is a small cytokine belonging to the CC chemokine family that is known under several pseudonyms, including Liver-expressed chemokine (LEC) and Monotactin-1 (MTN-1).  This chemokine is expressed by the liver, thymus, and spleen and is chemoattractive for monocytes and lymphocytes. Cellular expression of CCL16 can be strongly induced in monocytes by IL-10, IFN- and bacterial lipopolysaccharide. Its gene is located on chromosome 17, in humans, among a cluster of other CC chemokines. CCL16 elicits its effects on cells by interacting with cell surface chemokine receptors such as CCR1, CCR2, CCR5 and CCR8.
C-C motif chemokine ligand 16 has been found in high levels in the blood plasma of humans.
CCL16 may be useful for trafficking eosinophils. This ligand has been found to have a functional affinity for H4 receptors that are expressed by eosinophils and mast cells. 
This chemokine has been shown to suppress rapid proliferation of myeloid progenitor cells.
CCL19
Chemokine (C-C motif) ligand 19 (CCL19) is a protein that in humans is encoded by the CCL19 gene.
This gene is one of several CC cytokine genes clustered on the p-arm of chromosome 9. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene may play a role in normal lymphocyte recirculation and homing. It also plays an important role in trafficking of T cells in thymus, and in T cell and B cell migration to secondary lymphoid organs. It specifically binds to chemokine receptor CCR7.
Chemokine (C-C motif) ligand 19 (CCL19) is a small cytokine belonging to the CC chemokine family that is also known as EBI1 ligand chemokine (ELC) and macrophage inflammatory protein-3-beta (MIP-3-beta). CCL19 is expressed abundantly in thymus and lymph nodes, with moderate levels in trachea and colon and low levels in stomach, small intestine, lung, kidney and spleen. The gene for CCL19 is located on human chromosome 9. This chemokine elicits its effects on its target cells by binding to the chemokine receptor chemokine receptor CCR7. It attracts certain cells of the immune system, including dendritic cells and antigen-engaged B cells, CCR7+ central-memory T-Cells.
CCL20
Chemokine (C-C motif) ligand 20 (CCL20) or liver activation regulated chemokine (LARC) or Macrophage Inflammatory Protein-3 (MIP3A)  is a small cytokine belonging to the CC chemokine family.  It is strongly chemotactic for lymphocytes and weakly attracts neutrophils. CCL20 is implicated in the formation and function of mucosal lymphoid tissues via chemoattraction of lymphocytes and dendritic cells towards the epithelial cells surrounding these tissues.  CCL20 elicits its effects on its target cells by binding and activating the chemokine receptor CCR6.
Gene expression of CCL20 can be induced by microbial factors such as lipopolysaccharide (LPS), and inflammatory cytokines such as tumor necrosis factor and interferon-, and down-regulated by IL-10. CCL20 is expressed in several tissues with highest expression observed in peripheral blood lymphocytes, lymph nodes, liver, appendix, and fetal lung and lower levels in thymus, testis, prostate and gut. The gene for CCL20 (scya20) is located on chromosome 2 in humans.
Recent research  in an animal model of multiple sclerosis known as experimental autoimmune encephalitis (EAE) demonstrated that regional neural activation can create "gates" for pathogenic CD4+ T cells to enter the CNS by increasing CCL20 expression, especially at L5. Sensory nerve stimulation, elicited by using muscles in the leg or electrical stimulation as in Arima et al., 2012, activates sympathetic neurons whose axons run through the dorsal root ganglia containing cell bodies of the stimulated afferent sensory nerve. Sympathetic neuronal activity activates IL-6 amplifier resulting in increased regional CCL20 expression and subsequent pathogenic CD4+ T cell accumulation at the same spinal cord level. CCL20 expression was observed to be dependent on IL-6 amplifier activation, which is dependent on NF-B and STAT3 activation. This research provides evidence for a critical role for CCL20 in autoimmune pathogenesis of the central nervous system.
CCL24
Chemokine (C-C motif) ligand 24 (CCL24) also known as myeloid progenitor inhibitory factor 2 (MPIF-2) or eosinophil chemotactic protein 2 (eotaxin-2) is a protein that in humans is encoded by the CCL24 gene. This gene is located on human chromosome 7.

# Function
CCL24 is a small cytokine belonging to the CC chemokine family. CCL24 interacts with chemokine receptor CCR3 to induce chemotaxis in eosinophils.  This chemokine is also strongly chemotactic for resting T lymphocytes and slightly chemotactic for neutrophils.

# Clinical significance
Elevated levels of eotaxin-2 has been seen in patients with aspirin-exacerbated respiratory disease (AERD), such as asthma. People with lower plasma levels of eotaxin-2 have not been showing tendency to develop aspirin inducible asthma.
CCL28
Chemokine (C-C motif) ligand 28 (CCL28), also known as mucosae-associated epithelial chemokine (MEC), CCK1 and SCYA28, is a chemokine. CCL28 regulates the chemotaxis of cells that express the chemokine receptors CCR3 and CCR10.
CCL28 is expressed by columnar epithelial cells in the gut, lung, breast and the salivary glands and drives the mucosal homing of T and B lymphocytes that express CCR10, and the migration of eosinophils expressing CCR3.  This chemokine is constitutively expressed in the colon, but its levels can be increased by pro-inflammatory cytokines and certain bacterial products implying a role in effector cell recruitment to sites of epithelial injury. CCL28 has also been implicated in the migration of IgA-expressing cells to the mammary gland, salivary gland, intestine and other mucosal tissues.  It has also been shown as a potential antimicrobial agent effective against certain pathogens, such as Gram negative and Gram positive bacteria and the fungus Candida albicans.
Human CCL28 is encoded by an RNA transcript of 373 nucleotides and a gene with four exons. The gene codes for a 127-amino acid CCL28 protein with a 22-amino acid N-terminal signal peptide.  It shares 76% nucleic acid identity and 83% amino acid similarity to the equivalent molecule in mouse. Sequence analysis has revealed CCL28 to be most similar to another CC chemokine called CCL27.

# Gene neighbourhood
The gene C5orf34 is found downstream of CCL28 and is a predicted to be in the Polo-like Kinase family. C5orf34 extends from base pair 43,486,701 to base pair 43,515,445.
CCR10
C-C chemokine receptor type 10 is a protein that in humans is encoded by the CCR10 gene.

# Function
Chemokines are a group of small (approximately 8 to 14 kD), mostly basic, structurally related molecules that regulate cell trafficking of various types of leukocytes through interactions with a subset of 7-transmembrane, G protein-coupled receptors. Chemokines also play fundamental roles in the development, homeostasis, and function of the immune system, and they have effects on cells of the central nervous system as well as on endothelial cells involved in angiogenesis or angiostasis. Chemokines are divided into 2 major subfamilies, CXC and CC, based on the arrangement of the first 2 of the 4 conserved cysteine residues; the 2 cysteines are separated by a single amino acid in CXC chemokines and are adjacent in CC chemokines.
CCR10 is a chemokine receptor. Its ligands are CCL27 and CCL28. This receptor is normally expressed by melanocytes, plasma cells and skin-homing T cells. B16 melanoma cell transduction of CCR10 significantly increases the development of lymph node metastasis in mice after inoculation in the skin, suggesting a role for the receptor in directing metastasis. CCR10-CCL27 interactions are involved in T cell-mediated skin inflammation.
ITGAE
Integrin, alpha E (ITGAE) also known as CD103 (cluster of differentiation 103) is an integrin protein that in human is encoded by the ITGAE gene. CD103 binds integrin beta 7 (7 ITGB7) to form the complete heterodimeric integrin molecule E7, which has no distinct name. The E7 complex is often referred to as "CD103" though this appellation strictly refers only to the E chain. Note that the 7 subunit can bind with other integrin  chains, such as 4 (CD49d).

# Tissue distribution
CD103 is expressed widely on intraepithelial lymphocyte (IEL) T cells (both  T cells and  T cells) and on some peripheral regulatory T cells (Tregs). It has also been reported on lamina propria T cells. A subset of dendritic cells in the gut mucosa and mesenteric lymph nodes, known as CD103 dendritic cells, also expresses this marker.
It is useful in identifying hairy cell leukemia which is positive for this marker in contrast to most other hematologic malignancies which are negative for CD103 except enteropathy-associated T cell lymphoma.

# Function
The chief ligand for E7 is E-cadherin, an adhesion molecule (CAM) found on epithelial cells. It is probably important for T cell homing to the intestinal sites.
Tregs are important for decreasing the immune response and appear to play a crucial role in the prevention of autoimmune diseases. Tregs are defined as CD4+/CD25+/Foxp3+ cells. Some CD4+/FoxP3 cells also express CD103 and have been attributed regulatory activity. It is unclear whether the presence of CD103 on Treg cells represents a specialized feature for Treg, or Treg differentiation of IEL T cells.
CD11a
Integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide), also known as ITGAL, is a human gene which functions in the immune system. It is involved in cellular adhesion and costimulatory signaling. It is the target of the drug efalizumab.

# Function
ITGAL encodes the integrin alpha L chain. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This I-domain containing alpha integrin combines with the beta 2 chain (ITGB2) to form the integrin lymphocyte function-associated antigen-1 (LFA-1), which is expressed on all leukocytes. LFA-1 plays a central role in leukocyte intercellular adhesion through interactions with its ligands, ICAMs 1-3 (intercellular adhesion molecules 1 through 3), and also functions in lymphocyte costimulatory signaling.
CD11a is one of the two components, along with CD18, which form lymphocyte function-associated antigen-1.
Efalizumab acts as an immunosuppressant by binding to CD11a but was withdrawn in 2009 because it was associated with severe side effects.

# Interactions
CD11a has been shown to interact with ICAM-1.
CD11c
CD11c, also known as Integrin, alpha X (complement component 3 receptor 4 subunit) (ITGAX), is a gene that encodes for CD11c  .
CD11c is an integrin alpha X chain protein. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as inactivated-C3b (iC3b) receptor 4 (CR4). The alpha X beta 2 complex seems to overlap the properties of the alpha M beta 2 integrin in the adherence of neutrophils and monocytes to stimulated endothelium cells, and in the phagocytosis of complement coated particles.
CD11c is a type I transmembrane protein found at high levels on most human dendritic cells, but also on monocytes, macrophages, neutrophils, and some B cells that induces cellular activation and helps trigger neutrophil respiratory burst; expressed in hairy cell leukemias, acute nonlymphocytic leukemias, and some B-cell chronic lymphocytic leukemias.