Persius/hicric huggingface dataset:
CDCA8
Borealin is a protein that in humans is encoded by the CDCA8 gene.

# Function
CDCA8 is a component of a chromosomal passenger complex required for stability of the bipolar mitotic spindle.

# Interactions
CDCA8 has been shown to interact with INCENP, Survivin and Aurora B kinase.
CDCP1
CUB domain-containing protein 1 (CDCP1) is a protein that in humans is encoded by the CDCP1 gene. CDCP1 has also been designated as CD318 (cluster of differentiation 318) and Trask (Transmembrane and associated with src kinases). Alternatively spliced transcript variants encoding distinct isoforms have been reported.

# Function
CDCP1/Trask  is not important for the development of the mouse. Adult mice lacking CDCP1 do not exhibit gross morphologic, reproductive or behavioral abnormalities compared with wild-type mice, and histologic examination of multiple organ systems has shown no significant pathology and no observed histologic differences. CDCP1 is a ligand for CD6, a receptor molecule expressed on certain T-cells and may play a role in their migration and chemotaxis. As such CDCP1 may contribute to autoimmune diseases such as encephalomyelitis, multiple sclerosis and inflammatory arthritis.
CDCP1 is a 140 kD transmembrane glycoprotein with a large extracellular domain (ECD) containing two CUB domains, and a smaller intracellular domain (ICD). CDCP1 is cleaved by serine proteases at the extracellular domain next to Arg368 to generate a truncated molecule of 80 kDa size. Different cell lines express different amounts of p140 and p80, depending on the activity of endogenous serine proteases. In vivo, CDCP1 is not cleaved during normal physiological circumstances, but its cleavage can be induced during tumorigenesis or tissue injury.
The intracellular domain of CDCP1 contains five tyrosine residues - Y707, Y734, Y743, Y762 and Y806. Phosphorylation of CDCP1 is exclusively mediated by Src kinases and depends on the adherence state of the cells. The tyrosine phosphorylation of CDCP1 in cultured cells occurs when cells are induced to detach by trypsin or EDTA, or seen spontaneously during mitotic detachment. The loss of anchorage or cellular detachment is associated with the phosphorylation of CDCP1 as well as the concomitant dephosphorylation of focal adhesion proteins, consistent with the dismantling of focal adhesions. Contrary, during cellular attachment CDCP1 is dephosphorylated, allowing the phosphorylation of focal adhesion proteins. The anti-adhesion and anti-migratory functions of CDCP1 are mediated through negative regulation on integrin receptors.

# Clinical significance
The phosphorylation of CDCP1 is seen in many cancers, including some pre-invasive cancers as well as in invasive tumors and in tumor metastases.
CDCa1
CDCa1 is a protein product of the human genome.  The gene that codes for this protein is found on chromosome 1, from 150,076,963-150,079,657. The gene contains 2 exons and encodes 353 amino acids.  Synonyms for CDCa1 are "hypothetical protein LOC100191040" and NP_001129475.  CDCa1 contains a conserved metal binding domain that is a known as Protein kinase C conserved region 2, subgroup 1. This motif is known to be a member of the C2 superfamily, which is present in phospholipases, protein kinases C, and synaptotagmins.  The amino acid sequence of CDCa1 can be accessed at  Prior to any post translational modification, CDCa1 has a molecular weight of 37.6 kdal.  Although scientists have not yet determined where CDCa1 functions within the cell, CDCa1 has a predicted isoelectric point of 11.636 which severely limits the places in which it can be effective. In addition, CDCa1 does not contain any predicted transmembrane domains or any predicted signal peptides.

# Expression
According to the National Center for Biotechnology Information, CDCa1 has only been found to be expressed in adult individuals with some form of cancer.  CDCa1 is not ubiquitously expressed, and thus far scientists have only found CDCa1 expressed in the tissues of the brain, intestine, and mammary gland.

# Evolutionary conservation
There are 52 known mammalian orthologs for CDCa1, found in at least 10 species including Pan troglodytes, Ornithorhynchus anatinus, and Sus scrofa.  There are a total of 38 completely conserved residues across these 10 species, corresponding to 10.76% conservation.  Within vertebrates conservation remains high at 33 residues, corresponding to 9.3%.  However, outside of vertebrates, conservation drops to a maximum of 1.98%, or 3 residues.
CDEPT

# Overview
Clostridial-directed enzyme prodrug therapy (CDEPT) is the use of Clostridia to convert prodrugs into active drug agents. It is comparable to a more popular strategy, called ADEPT.

# The CDEPT strategy
Perhaps the most challenging issue in cancer treatment is how to reduce the side effects of the injected anti-cancer agents, which are of a high cytotoxicity potential. A widely used solution is to use enzymes which are able to convert a relatively non-toxic prodrug precursor into the active drug form(s). Clostridial-directed enzyme prodrug therapy (CDEPT) is one of the possible approaches.
Solid tumors, in contrast to normal tissues, grow rapidly. As a result, the cancerous tissues may suffer from inadequate blood and oxygen supply. Therefore, clostridia can grow in tumor and destroy it specifically. (Originally, Parker and co-workers showed that the injection of Clostridium histolyticum spores to the transplanted sarcomas of mice results in significant tumour lysis. Soon after, it was shown that a direct injection is not necessary, and that tumour colonization was readily obtained after intravenous administration of spores).
In CDEPT, a prodrug-converting enzyme expressed by a clostridial expression plasmid converts a prodrug into an active drug form within the tumor. While the prodrug is the inactive form and can be administrated to the blood, the  products of the prodrug cleavage are highly cytotoxic and show their effect only in the vicinity of tumor cells.
Difficulties in the engineering of clostridial strains have restricted the application of other enzyme prodrug systems. So far, two enzymes have been applied in CDEPT: cytosine deaminase and nitroreductase. It has been recently suggested that -lactamases, which are naturally found in Clostridia, can facilitate the application of the method significantly.
CDH11
Cadherin-11 is a protein that in humans is encoded by the CDH11 gene.

# Function
This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Expression of this particular cadherin in osteoblastic cell lines, and its upregulation during differentiation, suggests a specific function in bone development and maintenance. The mammalian CDH-11 homologues are termed calsyntenin.

# Relevance to cancer
CDH11 is overexpressed in 15% of breast cancers and seems essential to tumour progression in some other cancer types.

# Drug interactions
Arthritis drug celecoxib binds to CDH11.

# Interactions
CDH11 has been shown to interact with CDH2.
CDH23
Cadherin-23 is a protein that in humans is encoded by the CDH23 gene.

# Function
This gene is a member of the cadherin superfamily, genes encoding calcium dependent cell-cell adhesion glycoproteins. The protein encoded by this gene is a large, single-pass transmembrane protein composed of an extracellular domain containing 27 repeats that show significant homology to the cadherin ectodomain. Expressed in the neurosensory epithelium, the protein is thought to be involved in stereocilia organization and hair bundle formation. Specifically, it is thought to interact with protocadherin 15 to form tip-link filaments.

# Clinical significance
The gene is located in a region containing the human                 deafness             loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this novel cadherin-like gene.
The gene is associated with kidney function decline.

# Interactions
CDH23 has been shown to interact with USH1C.
CDKL5
CDKL5 is a gene that provides instructions for making a protein called cyclin-dependent kinase-like 5 also known as serine/threonine kinase 9 (STK9) that is essential for normal brain development with mutations causing deficiencies in the protein level. It regulates neuronal morphology through cytoplasmic signaling and controlling gene expression. The CDKL5 protein acts as a kinase, which is an enzyme that changes the activity of other proteins by adding a cluster of oxygen and phosphorus atoms (a phosphate group) at specific positions. Researchers are currently working to determine which proteins are targeted by the CDKL5 protein.

# Mutations
CDKL5 Deficiency had been thought of as a variant of Rett's Syndrome due to some similarities in the clinical presentation, but it is now known to be an independent clinical entity caused by mutations in a distinct X-linked gene, and is considered separate to Rett Syndrome rather than a variant of it. While CDKL5 is primarily associated with girls, it has been seen in boys as well.  This disorder includes many of the features of classic Rett syndrome (including developmental problems, loss of language skills, and repeated hand wringing or hand washing movements), but also causes recurrent seizures beginning in infancy. Some CDKL5 mutations change a single protein building block (amino acid) in a region of the CDKL5 protein that is critical for its kinase function. Other mutations lead to the production of an abnormally short, nonfunctional version of the protein.
Further confirmation that CDKL5 is an independent disorder with its own characteristics is provided by this study, published in April 2016, which concluded 'There were differences in the presentation of clinical features occurring in the CDKL5 disorder and in Rett syndrome, reinforcing the concept that CDKL5 is an independent disorder with its own distinctive characteristics'.  At one time, mutations in the CDKL5 gene were said to cause a disorder called X-linked infantile spasm syndrome (ISSX) or West syndrome. but this research established CDKL5 disorder as a distinct clinical entity.

# Animal studies
GSK3 inhibitors in Cdkl5 knockout (Cdkl5 -/Y) mice rescues hippocampal development and learning.  Likewise,  IGF-1 treatment in CDKL5 null mice restores synaptic deficits.

# Therapeutics
There are currently no approved drugs to treat CDKL5 Deficiency, save for Anti-Epileptic Drugs (AEDs) to treat the epileptic seizures. These have limited efficacy, pointing to a strong need to develop new treatment strategies for patients.
A clinical trial of Ataluren for nonsense mutations in CDKL5 and Dravet Syndrome has been announced. This same drug was approved by the UK's National Institute for Health and Care Excellence (NICE) for use in treating nonsense mutations in Duchenne muscular dystrophy.  Finally a CDKL5 protein replacement therapy is in development.

# Location
The CDKL5 gene is located on the short (p) arm of the X chromosome at position 22. More precisely, the CDKL5 gene is located from base pair 18,443,724 to base pair 18,671,748 on the X chromosome.
CDKN3
Cyclin-dependent kinase inhibitor 3 is an enzyme that in humans is encoded by the CDKN3 gene.
The protein encoded by this gene belongs to the dual specificity protein phosphatase family. It was identified as a cyclin-dependent kinase inhibitor, and has been shown to interact with, and dephosphorylate CDK2 kinase, thus prevent the activation of CDK2 kinase. This gene was reported to be deleted, mutated, or overexpressed in several kinds of cancers.

# Interactions
CDKN3 has been shown to interact with Cyclin-dependent kinase 2, Cdk1 and MS4A3.
CEBPB
CCAAT/enhancer-binding protein beta is a protein that in humans is encoded by the CEBPB gene.

# Function
The protein encoded by this intronless gene is a bZIP transcription factor that can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related proteins CEBP-alpha, CEBP-delta, and CEBP-gamma. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses and has been shown to bind to the IL-1 response element in the IL-6 gene, as well as to regulatory regions of several acute-phase and cytokine genes. In addition, the encoded protein can bind the promoter and upstream element and stimulate the expression of the collagen type I gene.
CEBP-beta is critical for normal macrophage functioning, an important immune cell sub-type; mice unable to express CEBP-beta have macrophages that cannot differentiate (specialize) and thus are unable to perform all their biological functions - including macrophage-mediated muscle repair. Observational work has shown that expression of CEBP-beta in blood leukocytes is positively associated with muscle strength in humans, emphasizing the importance of the immune system, and particularly macrophages, in the maintenance of muscle function.
Function of CEBPB gene can be effectively examined by siRNA knockdown based on an independent validation.

# Target genes
CEBPB is capable of increasing the expression of several target genes.  Among them, some have specific role in the nervous system such as the preprotachykinin-1 gene, giving rise to substance P and neurokinin A and the choline acetyltransferase responsible for the biosynthesis of the important neurotransmitter acetylcholine.
Other targets include genes coding for cytokines such as IL-6, IL-4, IL-5, and TNF-alpha.
Genes coding for transporter proteins that confer multidrug resistance to the cells have also been found to be activated by CEBPB. Such genes include ABCC2 and ABCB1.

# Interactions
CEBPB has been shown to interact with:
- CREB1,
- CRSP3
- DNA damage-inducible transcript 3,
- EP300,
- Estrogen receptor alpha,
- Glucocorticoid receptor,
- HMGA1,
- HSF1,
- Nucleolar phosphoprotein p130,
- RELA,
- Serum response factor,
- SMARCA2,
- Sp1 transcription factor,
- TRIM28,  and
- Zif268.
CEBPD
CCAAT/enhancer-binding protein delta is a protein that in humans is encoded by the CEBPD gene.

# Function
The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages.

# Functions
CEBPD is involved in regulation of apoptosis and cell proliferation. It probably acts as tumor suppressor.
One study in mice showed that CEBPD prevents development of tubular injury and tubulointerstitial fibrogenesis during the progression of chronic obstructive nephropathy.
Function of CEBPD gene can be effectively examined by siRNA knockdown based on an independent validation.

# Interactions
CEBPD has been shown to interact with Mothers against decapentaplegic homolog 3.
CENPA
Centromere protein A, also known as CENPA, is a protein which in humans is encoded by the CENPA gene.

# Function
Centromeres are the chromosomal domains that specify the mitotic behavior of chromosomes. The CENPA gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. CENPA is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. Alternative splicing results in multiple transcript variants encoding distinct isoforms.
In higher eukaryotes, the recruitment of CENP-A nucleosomes to existing centromeres is an epigenetic process, independent of the underlying DNA sequence. In S. pombe, de novo recruitment of the CENP-A to the centromere is believed to be controlled by "centromeric" heterochromatin surrounding the centromere, and by an RNAi mechanism. The RNAi is cut to form siRNA; this complexes with the protein Chp1, which then binds the centromeric heterochromatin. This helps recruit other proteins, ultimately resulting in a protein complex that forms cohesin between two sister chromatids at the centromeric heterochromatin. This cohesin is believed to be essential in replacing the centromere H3 with CENP-A. CENP-A is one of the epigenetic changes that is believed to distinguish centromeric DNA from other DNA. Once the CENP-A has been added, the centromere becomes self-propagating, and the surrounding heterochromatin/RNAi mechanism is no longer necessary.
CENPH
Centromere protein H is a protein that in humans is encoded by the CENPH gene.

# Function
Centromere and kinetochore proteins play a critical role in centromere structure, kinetochore formation, and sister chromatid separation. The protein encoded by this gene colocalizes with inner kinetochore plate proteins CENP-A and CENP-C in both interphase and metaphase. CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex. CENP-H localizes outside of centromeric heterochromatin, where CENP-B is localized, and inside the kinetochore corona, where CENP-E is localized during prometaphase. It is thought that this protein can bind to itself, as well as to CENP-A, CENP-B or CENP-C. Multimers of the protein localize constitutively to the inner kinetochore plate and play an important role in the organization and function of the active centromere-kinetochore complex. CENP-H contains a coiled-coil structure and a nuclear localisation signal.
Studies show that CENP-H may be associated with certain human cancers.
CENP-H shows sequence similarity to the Schizosaccharomyces pombe kinetochore protein Fta3 which is a subunit of the Sim4 complex. This complex is required for loading the DASH complex onto the kinetochore via interaction with dad1. Fta2, Fta3 and Fta4 associate with the central core and inner repeat region of the centromere.

# Other Protein Interactions
CENPH has also been shown to interact with KIAA0090.  The significance of this interaction is unclear.
CENPJ
Centromere protein J is a protein that in humans is encoded by the CENPJ gene. It is also known as centrosomal P4.1-associated protein (CPAP).
During cell division, this protein plays a structural role in the maintenance of centrosome integrity and normal spindle morphology, and it is involved in microtubule disassembly at the centrosome. This protein can function as a transcriptional coactivator in the Stat5 signaling pathway, and also as a coactivator of NF-kappaB-mediated transcription, likely via its interaction with the coactivator p300/CREB-binding protein. Mutations in this gene are associated with Seckel syndrome and primary autosomal recessive microcephaly, a disorder characterized by severely reduced brain size and mental retardation.
The Drosophila ortholog, sas-4, has been shown to be a scaffold for a cytoplasmic complex of Cnn, Asl, CP-190, tubulin and D-PLP (similar to the human proteins PCNT and AKAP9). These complexes are then anchored at the centriole to begin formation of the centrosome.

# Model organisms
Model organisms have been used in the study of CENPJ function. A conditional knockout mouse line, called Cenpjtm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium programa 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 tests were carried out on mutant mice and thirteen significant abnormalities were observed. Homozygous mutants were subviable, had a decreased body weight, abnormal open field, body composition, X-ray imaging, peripheral blood lymphocytes and indirect calorimetry parameters, abnormal head, genitalia and tail morphology, an impaired glucose tolerance, hypoalbuminemia, a 1.5 fold increase in micronuclei, a reduction in dentate gyrus length and abnormal corneal epithelium and endothelium.
A more detailed analysis revealed this mutant to model a number of aspects of Seckel syndrome (type 4). The authors concluded that, "increased cell death due to mitotic failure during embryonic development is likely to contribute to the proportionate dwarfism" that is characteristic of the disorder.

# Interactions
CENPJ has been shown to interact with EPB41.
CEP63
Centrosomal protein of 63 kDa is a protein that in humans is encoded by the CEP63 gene.   Several alternatively spliced transcript variants have been found, but their biological validity has not been determined.

# Function
This gene encodes a protein with six coiled-coil domains. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. Recent computational analysis revealed pathogenic property of L61P point mutation in CEP63 protein that affected its native structural conformation.

# Interactions
CEP63 has been shown to interact with DISC1, CEP152 and CDK1.
CHD1L
Chromodomain-helicase-DNA-binding protein 1-like (ALC1) is an enzyme that in humans is encoded by the CHD1L gene. It has been implicated in chromatin remodeling and DNA relaxation process required for DNA replication, repair and transcription. The ALC1 comprises ATPase domain and macro domain. On the basis of homology within the ATPase domain, ALC1 belongs to Snf2 family.

# Function

## In development
CHD1L, a DNA helicase, possesses chromatin remodeling activity and interacts with PARP1/PARylation in regulating pluripotency during developmental reprogramming.  The CHD1L macro-domain interacts with the PAR moiety of PARylated-PARP1 to facilitate early-stage reprogramming and pluripotency in stem cells.  It appears that CHD1L expression is vital for early events in embryonic development. 

## In DNA repair
To allow the critical cellular process of DNA repair, the chromatin must be remodeled at sites of damage.  CHD1L (ALC1) a chromatin remodeling protein, acts very early in DNA repair.  Chromatin relaxation occurs rapidly at the site of a DNA damage.  This process is initiated by PARP1 protein that starts to appear at DNA damage in less than a second, with half maximum accumulation within 1.6 seconds after the damage occurs.  Next the chromatin remodeler CHD1L (ALC1) quickly attaches to the product of PARP1, and completes arrival at the DNA damage within 10 seconds of the damage.  About half of the maximum chromatin relaxation, due to action of  CHD1L (ALC1), occurs by 10 seconds. This then allows recruitment of the DNA repair enzyme MRE11, to initiate DNA repair, within 13 seconds.  MRE11 is involved in homologous recombinational repair.  CHD1L (ALC1) is also required for repair of UV-damaged chromatin through nucleotide excision repair.

# Related gene problems
- 1q21.1 deletion syndrome
- 1q21.1 duplication syndrome
With 1q21.1 deletion syndrome a disturbance occurs, which leads to increased DNA breaks. The role of CHD1L is similar to that of helicase with the Werner syndrome