Persius/hicric huggingface dataset:
CHKA
Choline kinase alpha is an enzyme that in humans is encoded by the CHKA gene.
The major pathway for the biosynthesis of phosphatidylcholine occurs via the CDP-choline pathway. The protein encoded by this gene is the initial enzyme in the sequence and may play a regulatory role. The encoded protein also catalyzes the phosphorylation of ethanolamine. Two transcript variants encoding different isoforms have been found for this gene.
In melanocytic cells CHKA gene expression may be regulated by MITF.
CHL1
Neural cell adhesion molecule L1-like protein also known as close homolog of L1 (CHL1) is a protein that in humans is encoded by the CHL1 gene.
CHL1 is a cell adhesion molecule closely related to the L1. In melanocytic cells CHL1 gene expression may be regulated by MITF, and can act as a helicase protein during the interphase stage of mitosis.
The protein, however, has dynamic localisation, meaning that it has not only multiple roles in the cell, but also various locations.
CHOP
CHOP is the acronym for a chemotherapy regimen used in the treatment of non-Hodgkin lymphoma.  CHOP stands for Cytoxan, Hydroxydaunorubicin (Adriamycin), Oncovin (Vincristine), Prednisone/Prednisolone.

# Uses and indications
CHOP consists of:
- Cyclophosphamide
- Hydroxydaunorubicin (alternative name) -  doxorubicin
- Oncovin (brand name) -  vincristine
- Prednisone or Prednisolone.
This regimen can also be combined with the monoclonal antibody rituximab if the lymphoma is of B cell origin (R-CHOP or CHOP-R). Typically, courses are administered at an interval of three weeks. A staging CT scan is generally performed after three cycles to assess whether the disease is responding to treatment.
In patients with a history of cardiovascular disease, the doxorubicin (which is cardiotoxic) is often deemed to be too great a risk and is omitted from the regimen. The combination is then referred to as COP or CVP.

# Side-effects and complications
The combination is generally well tolerated. Chemotherapy-induced nausea and vomiting may require antiemetics (such as ondansetron), and hemorrhagic cystitis is prevented with administration of mesna. Alopecia (hair loss) is common.
Neutropenia generally develops in the second week. During this period, many clinicians recommend prophylactic use of ciprofloxacin. If a fever develops in the neutropenic period, urgent medical assessment is required for neutropenic sepsis, as infections in patients with low neutrophil counts may progress rapidly.
Allopurinol is typically co-administered prophylactically to prevent tumor lysis syndrome, the result of rapid death of tumor cells.

# History
A pivotal study published in 1993 compared CHOP to several other chemotherapy regimens (e.g. m-BACOD, ProMACE-CytaBOM, MACOP-B). CHOP emerged as the regimen with the least toxicity but similar efficacy.
CIB1
Calcium and integrin-binding protein 1 is a protein that in humans is encoded by the CIB1 gene.
The protein encoded by this gene is a member of the calcium-binding protein family.  The specific function of this protein has not yet been determined; however this protein is known to interact with DNA-dependent protein kinase and may play a role in kinase-phosphatase regulation of DNA end-joining.  This protein also interacts with integrin alpha(IIb)beta(3), which may implicate this protein as a regulatory molecule for alpha(IIb)beta(3).

# Interactions
CIB1 has been shown to interact with RAC3, PSEN2, DNA-PKcs, UBR5 and CD61.
CISH
Cytokine-inducible SH2-containing protein is a protein that in humans is encoded by the CISH gene. CISH orthologs  have been identified in most mammals with sequenced genomes. CISH controls T cell receptor (TCR) signaling, and variations of CISH with certain SNPs are associated with susceptibility to bacteremia, tuberculosis and malaria.

# Function
The protein encoded by this gene contains a SH2 domain and a SOCS box domain. The protein thus belongs to the cytokine-induced STAT inhibitor (CIS), also known as suppressor of cytokine signaling (SOCS) or STAT-induced STAT inhibitor (SSI), protein family. CIS family members are known to be cytokine-inducible negative regulators of cytokine signaling.
The expression of this gene can be induced by IL-2, IL-3, GM-CSF and EPO in hematopoietic cells. Proteasome-mediated degradation of this protein has been shown to be involved in the inactivation of the erythropoietin receptor.
CISH is induced by T cell receptor (TCR) ligation and negatively regulates it by targeting the critical signaling intermediate PLC-gamma-1 for degradation. The deletion of Cish in effector T cells has been shown to augment TCR signaling and subsequent effector cytokine release, proliferation and survival. The adoptive transfer of tumor-specific effector T cells knocked out or knocked down for CISH resulted in a significant increase in functional avidity and long-term tumor immunity. There are no changes in activity or phosphorylation of Cish's purported target, STAT5 in either the presence or absence of Cish.

# Model organisms
Model organisms have been used in the study of CISH function. A conditional knockout mouse line, called Cishtm1a(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  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty four tests were carried out on mutant mice, however no significant abnormalities were observed.

# Interactions
CISH has been shown to interact with IL2RB and Growth hormone receptor. and PLCG1.
CIZ1
Cip1-interacting zinc finger protein is a protein that in humans is encoded by the CIZ1 gene.

# Function
The protein encoded by this gene is a zinc finger DNA binding transcription factor that interacts with CIP1 (p21 / CDKN1A), part of a complex with cyclin E. The encoded protein may regulate the cellular localization of CIP1.

# Clinical significance
An altered circulating form of the Ciz1 protein is synthesized by lung cancer cells, even when they are at a very early stage. Hence detection of this protein variant in blood could be used as a biomarker for early detection of lung cancer.

# Interactions
CIZ1 has been shown to interact with P21.
CLN3
Battenin is a protein that in humans is encoded by the CLN3 gene located on chromosome 16. Battenin is not clustered into any Pfam clan, but it is included in the TCDB suggesting that it is a transporter. In humans, it belongs to the atypical SLCs due to its structurally and phylogenetically similarity to other SLC transporters.

# Function
Battenin is involved in lysosomal function. Many alternatively spliced transcript variants have been found for this gene.
Battenin is a transmembrane protein predicted to be composed of 11 transmembrane helices, yet no crystal structure is available.

# Clinical significance
Mutations in this gene, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease, also known as Juvenile Neuronal Ceroid Lipofuscinosis (JNCL) or Juvenile Batten disease.
CLN8
Protein CLN8 is a protein that in humans is encoded by the CLN8 gene.

# Molecular biology
This gene encodes a transmembrane protein that localizes to the endoplasmic reticulum (ER) and recycles between the ER and the Golgi apparatus via COPII- and COPI-coated vesicles. CLN8 protein functions as a cargo receptor for lysosomal soluble proteins in the ER.

# Clinical
Mutations in this gene are associated with progressive epilepsy with mental retardation (EPMR), a subtype of neuronal ceroid lipofuscinosis (NCL). Patients with mutations in this gene have altered levels of sphingolipid and phospholipids in the brain.
COA3
Cytochrome c oxidase assembly factor 3, also known as Coiled-coil domain-containing protein 56, or Mitochondrial translation regulation assembly intermediate of cytochrome c oxidase protein of 12 kDa is a protein that in humans is encoded by the COA3 gene. This gene encodes a member of the cytochrome c oxidase assembly factor family. Studies of a related gene in fly suggest that the encoded protein is localized to mitochondria and is essential for cytochrome c oxidase function.

# Structure
The COA3 gene is located on the q arm of chromosome 17 at position 21.2 and it spans 1,107 base pairs. The COA3 gene produces a 7.8 kDa protein composed of 71 amino acids. COA3 is a component of the enzyme MITRAC (mitochondrial  translation regulation assembly intermediate of cytochrome c oxidase complex) complex, and the structure contains a C-terminal coiled-coil domain as well as a central single pass transmembrane domain.

# Function
The COA3 gene encodes for a Core protein of the MITRAC (mitochondrial  translation regulation assembly intermediate of cytochrome c oxidase complex) complex. The MITRAC complex is essential in the assembly of cytochrome c oxidase (complex IV) of the mitochondrial respiratory chain, which is responsible for the catalysis of oxidation of cytochrome c by  molecular oxygen. The MITRAC complex regulates both translation of mitochondrial encoded components and assembly of nuclear-encoded components imported in mitochondrion. In addition, COA3 is required for efficient translation of MT-CO1 and assembly of the mitochondrial respiratory chain complex IV.

# Clinical significance
Variants of COA3 have been associated with the mitochonrdial Complex IV deficiency, a deficiency in an enzyme complex of the mitochondrial respiratory chain which catalyzes the oxidation of cytochrome c utilizing  molecular oxygen. The deficiency is characterized by heterogeneous phenotypes ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. Other Clinical Manifestations include hypertrophic cardiomyopathy, hepatomegaly and liver dysfunction, hypotonia, muscle weakness, exercise intolerance, developmental delay, delayed motor development and mental retardation. A missense mutation of c.215A>G in the COA3 gene has been found to result in a severe decrease in protein levels with symptoms of exercise intolerance and peripheral neuropathy.

# Interactions
Like COX14, COA3 is a key component of the MITRAC (mitochondrial  translation regulation assembly intermediate of cytochrome c oxidase complex) complex. In addition, it has interactions with proteins such as MT-CO1, COX1, SMIM20, SURF1, TIMM21, and others.
COA5
Cytochrome c oxidase assembly factor 5 is a protein that in humans is encoded by the COA5 gene. This gene encodes an ortholog of yeast Pet191, which in yeast is a subunit of a large oligomeric complex associated with the mitochondrial inner membrane, and required for the assembly of the cytochrome c oxidase complex. Mutations in this gene are associated with mitochondrial complex IV deficiency.

# Structure
The COA5 gene is located on the q arm of chromosome 2 at position 11.2 and it spans 9,195 base pairs. The COA5 gene produces an 8 kDa protein composed of 73 amino acids. The structure of the protein contains the twin CX9C motif of yeast Pet191, which is conserved in the 74-amino acid deduced human protein. An example of the twin CX9C would be a repeated motif of 2 cysteines.

# Function
The COA3 gene encodes for a protein involved in an early step of the complex IV assembly process. The conserved cysteines in the twin CX9C motif, which is a part of the COA3 protein, has been shown to be essential in cell viability as well as the proper function and assembly of the cytochrome c oxidase complex.

# Clinical Significance
Variants of COA5 have been mainly associated with a mitochondrial complex IV deficiency, a deficiency of the enzyme complex Complex IV, which is responsible for the catalysis of oxidation of cytochrome c using molecular oxygen. The deficiency is characterized by heterogeneous phenotypes ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. Other phenotypes include hypertrophic cardiomyopathy, hepatomegaly and liver dysfunction, hypotonia, muscle weakness, exercise intolerance, developmental delay, delayed motor development and mental retardation. Mutations in COA5 has also known to be associated with Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 3 (CEMCOX3). CEMCOX3 is an infantile disorder associated with a severely fatal course during the first weeks of life. It is characterized by hypertrophic cardiomyopathy and is caused by mitochondrial complex IV deficiency. Postmortem microscopic investigations have shown accumulation of lipid droplets in cardiomyocytes and mitochondrial proliferation. A homozygous mutation of 157G>C has resulted in decreased complex IV in fibroblasts and heart muscle.

# Interactions
COA5 has been known to have unique proteinprotein interactions with APP, KRT31, and CHCHD4.
COA6
Cytochrome c oxidase assembly factor 6 is a protein that in humans is encoded by the COA6 gene. Mitochondrial respiratory chain Complex IV, or cytochrome c oxidase, is the component of the respiratory chain that catalyzes the transfer of electrons from intermembrane space cytochrome c to molecular oxygen in the matrix and as a consequence contributes to the proton gradient involved in mitochondrial ATP synthesis. The COA6 gene encodes an assembly factor for mitochondrial complex IV and is a member of the cytochrome c oxidase subunit 6B family. This protein is located in the intermembrane space, associating with SCO2 and COX2. It stabilizes newly formed COX2 and is part of the mitochondrial copper relay system. Mutations in this gene result in fatal infantile cardioencephalomyopathy.

# Structure
The COA6 gene is located on the q arm of chromosome 1 in position 42.2 and spans 10,612 base pairs. The gene produces a 14.1 kDa protein composed of 125 amino acids. The COA6 protein is found a complex with TMEM177, COX20, MT-CO2/COX2, COX18, SCO1 and SCO2. This protein localizes to the intermembrane space, associating with the inner membrane and transmembrane proteins such as SCO2 and COX2.

# Function
The COA6 encodes a protein which is an assembly factor for Complex IV. This protein is specifically required for COX2 biogenesis and stability; the absence of this protein will cause fast turnover of newly synthesized COX2. As a constituent of mitochondrial copper relay system, this protein possibly relays copper ions from SCO2 to COX2.

# Clinical Significance
Two mutations have been identified in this protein: W66R and W59C. The latter mutation results in the protein being mistargeted to the mitochondrial matrix, resulting in the loss of interaction with SCO2 and COX2. Inheritance of this mutation is autosomal recessive and results in a phenotype of fatal infantile cardioencephalomyopathy due to Complex IV deficiency. Symptoms include hypertrophic cardiomyopathy, left ventricular non-compaction, lactic acidosis, and metabolic hypotonia.

# Interactions
This protein interacts transiently with the copper-containing catalytic domain of newly synthesized COX2 via its C-terminal tail exposed to the intermembrane space. It also interacts selectively with the copper metallochaperone SCO2 in a COX2-dependent manner and with COX20 in a COX2- and COX18-dependent manner. Additionally, this protein interacts with COA1, SCO1, COX16, TTC19, DTX2, NADSYN1, GABARAP, AIFM1, COX4I1, CD81, COX14, SFXN1, and PLGRKT.
COA7
Cytochrome c oxidase assembly factor 7 (putative) (COA7), also known as Beta-lactamase hap-like protein, Respiratory chain assembly factor 1 (RESA1), Sel1 repeat-containing protein 1 (SELRC1), or C1orf163 is a protein that in humans is encoded by the COA7 gene. The protein encoded by COA7 is an assembly factor important for the mitochondrial respiratory chain. Mutations in COA7 have been associated with cytochrome c oxidase deficiency resulting in spinocerebellar ataxia with axonal neuropathy type 3 and mitochondrial myopathy.

# Structure
COA7 is located on the p arm of chromosome 1 in position 32.3 and has 3 exons. The COA7 gene produces a 25.7 kDa protein composed of 231 amino acids. COA7, the protein encoded by this gene, is a member of the hcp beta-lactamase family. This protein has a series of 5 Sel1-like tetratricopeptide repeat domains. It is also believed to be a soluble mitochondrial protein that contains large amounts of cysteine. Additionally, COA7 contains an N-acetylalanine amino acid modification at position 2.

# Function
COA7 is a protein assembly factor that is important for normal mitochondrial respiratory chain activity. It is believed to be involved in the assembly of cytochrome c oxidase (complex IV), but may also have effects on complex I and even complex III as well. It has been suggested that COA7 is a mitochondrial soluble intermembrane space protein, however, others have indicated that this soluble protein may actually be localized to the mitochondrial matrix.

# Clinical significance
Mutations in COA7 have been associated with spinocerebellar ataxia with axonal neuropathy type 3 and mitochondrial myopathy resulting from cytochrome c oxidase (complex IV) deficiency. Complex IV deficiency is a disorder of the mitochondrial respiratory chain with heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. In cases of pathogenic COA7 mutations, patient clinical manifestations can include sensory disturbance, decreased deep tendon reflexes, dysarthria, peripheral neuropathy, axonal sensorimotor neuropathy, ataxia, cerebellar and spinal cord atrophy, leukoencephalopathy, elevated serum creatine kinase levels, ragged-red fibers, and cognitive impairment. COA7 loss-of-function has been shown to lead to the disruption of oxidative phosphorylation, with cytochrome c oxidase activity being the most affected complex. Pathogenic variations have been known to include D6G, S149I, G144fs, and Y137C amino acid changes in addition to a c.115C>T exon 2 deletion.

# Interactions
COA7 has been shown to have 27 binary protein-protein interactions including 16 co-complex interactions. COA7 appears to interact with EFHC1, SNRPB, SUOX, AES, ENKD1, and GPSM3.
COG2
Conserved oligomeric Golgi complex subunit 2 is a protein that in humans is encoded by the COG2 gene.
Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Several complexes have been identified, including the Golgi transport complex (GTC), the LDLC complex, which is involved in glycosylation reactions, and the SEC34 complex, which is involved in vesicular transport. These 3 complexes are identical and have been termed the conserved oligomeric Golgi (COG) complex, which includes COG2 (Ungar et al., 2002).

# Model organisms
Model organisms have been used in the study of COG2 function. A conditional knockout mouse line, called Cog2tm1a(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 five were carried out on mutant mice and one significant abnormality was observed: no homozygous mutant mice survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice; no additional significant abnormalities were observed in these animals.

# Interactions
COG2 has been shown to interact with COG4 and COG3.
COG4
Conserved oligomeric Golgi complex subunit 4 is a protein that in humans is encoded by the COG4 gene.
Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Several complexes have been identified, including the Golgi transport complex (GTC), the LDLC complex, which is involved in glycosylation reactions, and the SEC34 complex, which is involved in vesicular transport. These 3 complexes are identical and have been termed the conserved oligomeric Golgi (COG) complex, which includes COG4 (Ungar et al., 2002).

# Interactions
COG4 has been shown to interact with COG7, COG2, COG1 and COG5.
COQ6
Coenzyme Q6 monooxygenase is a protein that in humans is encoded by the COQ6 gene.

# Function
The protein encoded by this gene belongs to the ubiH/COQ6 family. It is an evolutionarily conserved monooxygenase required for the biosynthesis of coenzyme Q10 (or ubiquinone), which is an essential component of the mitochondrial electron transport chain, and one of the most potent lipophilic antioxidants implicated in the protection of cell damage by reactive oxygen species. knockdown of this gene in mouse and zebrafish results in decreased growth due to increased apoptosis.

# Clinical significance
Mutations in this gene are associated with autosomal recessive coenzyme Q10 deficiency-6 (COQ10D6), which manifests as nephrotic syndrome with sensorineural deafness. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.
COQ7
The clk-1 (clock-1) gene encodes an enzyme (demethoxyubiquinone monooxygenase) that is necessary for ubiquinone biosynthesis in the worm Caenorhabditis elegans and other eukaryotes. The mouse version of the gene is called mclk-1 and the human, fruit fly and yeast homolog COQ7 (coenzyme Q biosynthesis protein 7).
CLK-1 is not to be confused with the unrelated human protein CLK1 which plays a role in RNA splicing.

# Structure
The protein has two repeats of approximately 90 amino acids, that contain two conserved motifs predicted to be important for coordination of iron. The structure and function of the gene are highly conserved among different species.
The C. elegans protein contains 187 amino acid residues (20 kilodaltons), the human homolog 217 amino acid residues (24 kilodaltons, gene consisting of  six exons spanning 11 kb and located on chromosome 16).

# Mitochondrial function
Ubiquinone is a small redox active lipid that is found in most cellular membranes where it acts as a cofactor in numerous cellular redox processes, including mitochondrial electron transport. As a cofactor, ubiquinone is often involved in processes that produce reactive oxygen species (ROS). In addition, ubiquinone is one of the main endogenous antioxidants of the cell. The CLK-1 enzyme is responsible for the  hydroxylation of 5-demethoxyubiquinone to 5-hydroxyubiquinone.
It has been shown that mutations in the gene are associated with increased lifespan. Defects of the gene slow down a variety of developmental and physiological processes, including the cell cycle, embryogenesis, post-embryonic growth, rhythmic behaviors and aging.

# Nuclear function
CLK-1 and COQ7 predominantly localise to mitochondria to participate in the ubiquinone biosynthetic pathway which is found there. However, a small pool of CLK-1 and COQ7 translocates to the nucleus in response to the production of ROS by normally functioning mitochondria in both worms and human cells, respectively. Translocation of CLK-1 and COQ7 represents a mitochondrial to nuclear retrograde signalling pathway that acts to suppress mitochondrial stress responses. The mitochondrial and nuclear pools of CLK-1 are thought to contribute independently to worm lifespan regulation. The nuclear form of CLK-1 and COQ7 is thought to regulate gene expression through an unidentified mechanism.