Persius/hicric huggingface dataset:
CHHIP

# Overview
CHHIP stands for Conventional or Hypofractionated High Dose Intensity Modulated Radiotherapy for Prostate Cancer, a treatment protocol currently undergoing clinical trials for the treatment of prostate cancer using external beam radiotherapy.

# Protocol Details
The main arm of the protocol prescribes 74 Gy to the prostate, with optional additional volumes around the prostate (such as the seminal vesicles and nodes prescribed to 71 Gy and 59 Gy. Each target with a prescribed dose must receive at least 95% of that dose to at least 99% of its volume and the dose to the 'hottest' 1% of the volume must be recorded.
There are various limits on doses delivered to healthy tissues:
Rectal dose constraints:
- No more than 68% dose (50 Gy) to 60% of the rectum
- No more than 81% (60 Gy) to 50%
- No more than 88% (65 Gy) to 30%
- No more than 95% (70 Gy) to 15%
- No more than 100% (74 Gy) to 5%
Femoral head constraints:
- No more than 50% of volume to receive more than 68% dose (50 Gy)
Bladder constraints:
- No more than 68% dose (50 Gy) to 50 % of the volume
- No more than 81% (60 Gy) to 25%
- No more than 100% (74 Gy) to 5%
Bowel constraints:
- No more than 68% dose (50 Gy) to 17 cc of the bowel
Additional targets:
- No more than 68% dose (50 Gy) to 50% of the urethral bulb
- No more than 81% (60 Gy) to 10% of the urethral bulb
- No more than 41% dose (30 Gy) to 80% of the rectum
- No more than 54% (40 Gy) to 70% of the rectum
The protocol has three arms, comparing conventional 2-Gray-per-fraction treatments against hypofractionated 3-Gray-per-fraction.  One arm of the trial is the control group, receiving the standard 74 Gy in 37 fractions.  The second arm prescribes 60 Gy in 20 fractions and the third prescribes 57 Gy in 19 fractions. The dose constraints for the hypofractionated arms of the trial are dose-scaled equivalents of those determined for the 74 Gy arm.

# Eligibility
Inclusion Criteria
a) Histologically confirmed, previously untreated locally confined adenocarcinoma of the prostate
b) All clinical T categories
Exclusion criteria
a) Patients with T3 cancers with Gleason Sum=8 cancers are ineligible
b) Prior pelvic radiotherapy or radical prostatectomy
c) Previous androgen deprivation
d) Life expectancy <10 years
e) Previous active malignancy within the last five years other than basal cell carcinoma
f) Co-morbid conditions likely to impact on the advisability of radical radiotherapy (e.g. previously inflammatory bowel disease, previous colorectal surgery, significant bladder instability or urinary incontinence)
g) Full anticoagulation with e.g. Warfarin or Heparin
h) Hip prosthesis or fixation which would interfere with standard radiation beam configuration

# Trial
The trial is being run and co-ordinated by Prof David Dearnaley at the Institute of cancer Research, Surrey.
The trial aims to recruit over 2162 patients.  As of May 2007, 671 patients had been recruited onto the trial, an accrual of 30%.  The trial will close in 2015.
CHODL
Chondrolectin is a protein that in humans is encoded by the CHODL gene. Mouse chondrolectin is encoded by Chodl.

# Structure
Chondrolectin is a type I membrane protein with a carbohydrate recognition domain characteristic of C-type lectins in its extracellular portion. In other proteins, this domain is involved in endocytosis of glycoproteins and exogenous sugar-bearing pathogens. This protein has been shown to localise to the perinucleus.

# Function
The exact function of chondrolectin is unknown but it has been show to be a marker of fast motor neurons in mice, and is involved in motor neuron development and growth in zebrafish (danio rerio). Furthermore, human chondrolectin has been shown to localise to motor neurons within the spinal cord.

# Clinical significance
Chondrolectin is alternatively spliced in the spinal cord of mouse models of the neuromuscular disease, spinal muscular atrophy (SMA), which predominantly affects lower motor neurons. Increased levels of chondrolectin in a zebrafish model of SMA results in significant improvements in disease-related motor neuron defects.
CHRND
Acetylcholine receptor subunit delta is a protein that in humans is encoded by the CHRND gene.

# Function
The acetylcholine receptor of muscle has 5 subunits of 4 different types: 2 alpha and 1 each of beta, gamma and delta subunits.  After acetylcholine binding, the receptor undergoes an extensive conformation change that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane.

# Interactions
CHRND has been shown to interact with Cholinergic receptor, nicotinic, alpha 1.
CHRNE
Acetylcholine receptor subunit epsilon is a protein that in humans is encoded by the CHRNE gene.
Acetylcholine receptors at mature mammalian neuromuscular junctions are pentameric protein complexes composed of four subunits in the ratio of two alpha subunits to one beta, one epsilon, and one delta subunit. The achetylcholine receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the epsilon subunit are associated with congenital myasthenic syndrome.

# Role in health and disease
Congenital myasthenic syndrome (CMS) is associated with genetic defects that affect proteins of the neuromuscular junction. Postsynaptic defects are the most frequent cause of CMS and often result in abnormalities in the acetylcholine receptor (AChR). The majority of mutations causing CMS are found in the AChR subunits genes.
Out of all mutations associated with CMS, more than half are mutations in one of the four genes encoding the adult AChR subunits. Mutations of the AChR often result in endplate deficiency. The most common AChR gene mutation that underlies CMS is the mutation of the CHRNE gene. The CHRNE gene codes for the epsilon subunit of the AChR. Most mutations are autosomal recessive loss-of-function mutations and as a result there is endplate AChR deficiency. CHRNE is associated with changing the kinetic properties of the AChR. One type of mutation of the epsilon subunit of the AChR introduces an arginine (Arg) into the binding site at the / subunit interface of the receptor. The addition of a cationic Arg into the anionic environment of the AChR binding site greatly reduces the kinetic properties of the receptor. The result of the newly introduced ARG is a 30-fold reduction of agonist affinity, 75-fold reduction of gating efficiency, and an extremely weakened channel opening probability. This type of mutation results in an extremely fatal form of CMS.
CIITA
CIITA is a human gene which encodes a protein called the class II, major histocompatibility complex, transactivator.  Mutations in this gene are responsible for the bare lymphocyte syndrome in which the immune system is severely compromised and cannot effectively fight infection. Chromosomal rearrangement of CIITA is involved in the pathogenesis of Hodgkin lymphoma and primary mediastinal B cell lymphoma.

# Function
CIITA mRNA can only be detected in human leukocyte antigen (HLA) system class II-positive cell lines and tissues. This highly restricted tissue distribution suggests that expression of HLA class II genes is to a large extent under the control of CIITA.  However CIITA does not appear to directly bind to DNA. Instead CIITA functions through activation of the transcription factor RFX5. Hence CIITA is classified as a transcriptional coactivator.
The CIITA protein contains an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus, the protein acts as a positive regulator of class II major histocompatibility complex gene transcription, and is often referred to as the "master control factor" for the expression of these genes.

# Interactions
CIITA has been shown to interact with:
- MAPK1,
- Nuclear receptor coactivator 1,
- RFX5,
- RFXANK,
- XPO1,  and
- ZXDC.
CKAP2
Cytoskeleton-associated protein 2 is a protein that in humans is encoded by the CKAP2 gene.
Human CKAP2 gene, the cDNA of which is known as LB1, is a cytoskeleton-associated protein involved in mitotic progression. Its high transcriptional activity has been observed in the testes, thymus, and diffuse B-cell lymphomas. The gene codes for a protein of 683 residues, which lacks a homology to known amino acid sequences. On evidence of immunofluorescence analysis, the CKAP2 product is a cytoplasmic protein associated with cytoskeletal fibrils.
The CKAP2 gene is in chromosome 13q14. Rearrangements of this region result in various tumors. Thus deletions have been detected in multiple myeloma, prostate cancer, head-and-neck squamous-cell carcinoma, B-cell prolymphocytic leukemia, non-Hodgkin lymphoma, and in more than half cases of B-cell chronic lymphocytic leukemia.
CKAP4
Cytoskeleton-associated protein 4 is a protein that in humans is encoded by the CKAP4 gene.
CKAP4 also historically known as CLIMP-63 (cytoskeleton-linking membrane protein 63), or just p63 (during the 90s) is an abundant type II transmembrane protein residing predominantly in the endoplasmic reticulum (ER) of eukaryotic cells and encoded in higher vertebrates by the gene CKAP4.

# Discovery
CLIMP-63 was discovered in the early 90s as the most S-palmitoylated protein during mitosis , Nevertheless, the effect of this modification to date remains unclear. CLIMP-63 was extensively studied during the 90s by the group of Hans-Peter Hauri (University of Basel, CH) which has characterized CLIMP-63s life in the ER. More recently, different groups have also reported CLIMP-63s presence at the plasma membrane acting as a ligand-activated receptor. CLIMP-63 has also now been described as a marker in different cancers.

# Localization, molecular functions and regulation
CLIMP-63s cellular distribution has been assessed (and re-assessed) several times in the last two decades. The protein includes a cytosolic segment composed of positively charged amino acid (223) which might act as a preponderant motif for folding and ER localization. Furthermore, CLIMP-63 was one of the first discovered ER-shaping proteins. and is mostly known for participating in the generation and maintenance of the ER sheets  This is thought to occur after dimerization of CLIMP-63s luminal COILED-COIL domains in cis (two CLIMP-63 proteins of the same ER membrane layer) and/or trans (between two different ER membrane layers, across the ER lumen). Multimerization might in addition limit CLIMP-63s diffusion out of ER-sheets.
CLIMP-63 was also shown to bind microtubules through its cytoplasmic disordered tail which might help anchoring the ER-sheets to the cytoskeleton. This is regulated by phosphorylation of at least three serine residues of CLIMP-63s cytosolic tail (S3, S17 and S19) as phosphorylation interferes with CLIMP-63s microtubule binding capacity.
In addition, CLIMP-63 can undergo another post-translational modification, S-palmitoylation, on cysteine 100 of its cytoplasmic domain. So far only the palmitoyl-acyltransferase ZDHHC2 has been identified as a potential regulator of CLIMP-63s palmitoylation but as ZDHHC2 resides mostly at the plasma membrane, supplementary investigations are needed. The consequence of S-palmitoylation remain to be investigated but could play a role in the cell cycle as CLIMP-63s palmitoylation was reported to strongly increase during mitosis.
Finally, CLIMP-63 has been shown by different groups to serve as a cell surface receptor for various extracellular ligands, in particular for surfactant protein A (SP-A) in lungs alveoli , tissue plasminogen activator (tPA) in vascular smooth muscle cells  and for anti-proliferative factor (APF) in bladder epithelial cells of patients with interstitial cystitis disorder.

# Diseases
More recently, CLIMP-63 has been related to different types of cancer prognosis. Upregulation of CLIMP-63 is observed in cholangio-cellular and hepatocellular carcinoma and it correlates with lymph node metastasis appearance.
CKMT2
Creatine kinase S-type, mitochondrial is an enzyme that in humans is encoded by the CKMT2 gene.
Mitochondrial creatine kinase (MtCK) is responsible for the transfer of high energy phosphate from mitochondria to the cytosolic carrier, creatine. The "energy-rich" gamma-phosphate group of ATP that is generated by oxidative phosphorylation inside mitochondria is trans-phosphorylated to creatine (Cr) to give phospho-creatine (PCr), which then is exported from the mitochondria into the cytosol, where it is made available to cytosolic creatine kinases (CK) for in situ regeneration of the ATP that has been used for cellular work. Cr then is returning to the mitochondria where it stimulates mitochondrial respiration and again is charged-up by mitochondrial ATP via MtCK. This process is termed the PCr/Cr-shuttle or circuit. 
MtCK belongs to the creatine kinase (CK) isoenzyme family. It exists as two isoenzymes, sarcomeric MtCK and ubiquitous MtCK, encoded by separate genes. Mitochondrial creatine kinase occurs in two different oligomeric forms: dimers and octamers, in contrast to the exclusively dimeric cytosolic creatine kinase isoenzymes. Sarcomeric mitochondrial creatine kinase has 80% homology with the coding exons of ubiquitous mitochondrial creatine kinase. This gene contains sequences homologous to several motifs that are shared among some nuclear genes encoding mitochondrial proteins and thus may be essential for the coordinated activation of these genes during mitochondrial biogenesis.
CKS1B
Cyclin-dependent kinases regulatory subunit 1 is a protein that in humans is encoded by the CKS1B gene.

# Function
The CKS1B protein binds to the catalytic subunit of the cyclin-dependent kinases and is essential for their biological function. The CKS1B mRNA is found to be expressed in different patterns through the cell cycle in HeLa cells, which reflects a specialized role for the encoded protein.
CKS1B and CKS2 proteins have demonstrated principal roles in cell cycle regulation. Defined originally as suppressors of mutations in both fission and budding yeast Cdk1 genes, Cks molecules interact with Cdk1, Cdk2 and Cdk3. These Cdk-dependent enzyme complexes in cell cycle regulation frequently consist of Cdk molecules bound to a catalytic Cdk subunit, i.e. Cks and a regulatory cyclin subunit, such as a G1 cyclin, controlling Cdk function by directing cyclin-cdk complex activity toward specific and significant substrates. Malfunctions of cdk-dependent associations lead to defects into the entry of mitosis for cells.
Cks1 in the Cdk-independent pathway involves the recognition of substrates p27Kip1 and p21cip1 by directly associating with E3 SCFSkp2 when stimulated by certainmitogenic signals, such as TGF-.

# Clinical significance
Cks1-depleted breast cancer cells not only exhibit slowed G(1) progression, but also accumulate in G(2)-M due to blocked mitotic entry. Cdk1 expression, which is crucial for M phase entry, is drastically diminished by Cks1 depletion, and that restoration of cdk1 reduces G(2)-M accumulation in Cks1-depleted cells.

# Interactions
CKS1B has been shown to interact with SKP2 and CDKN1B.
CLCF1
Cardiotrophin-like cytokine factor 1 (CLCF1), also known as Novel Neurotrophin-1 (NNT-1) or B cell-stimulating factor-3 (BSF-3), is a protein that in humans is encoded by the CLCF1 gene.

# Function
CLCF1 induces tyrosine phosphorylation of the IL-6 receptor common subunit glycoprotein 130 (gp130), leukemia inhibitory factor receptor beta, and the transcription factor STAT3. It has been implicated in the induction of IL-1 (via induction of corticosterone and IL-6) and serum amyloid A, and in B cell hyperplasia. This cytokine is capable of B cell activation via gp130 receptor stimulation.

# Structure
CLCF1 is a cytokine belonging to the interleukin-6 (IL6) family. It is a secreted protein, found predominantly in lymph nodes and spleen, and contains 225 amino acids with a molecular mass of 22 kDa in its mature form. IL6 family members share similarity in gene structure and have a 4-helix bundle in their protein structure. CLCF1 is closely related to other proteins called cardiotrophin-1 and ciliary neurotrophic factor.
CLCN1
The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. The protein encoded by this gene regulates the electric excitability of the skeletal muscle membrane. Mutations in this gene cause two forms of inherited human muscle disorders: recessive generalized myotonia congenita (Becker) and dominant myotonia (Thomsen).
Chloride channel protein, skeletal muscle (CLCN1) is a protein that in humans is encoded by the CLCN1 gene.  Mutations in this protein cause congenital myotonia.
CLCN1 is critical for the normal function of skeletal muscle cells. For the body to move normally, skeletal muscles must tense (contract) and relax in a coordinated way. Muscle contraction and relaxation are controlled by the flow of ions into and out of muscle cells. CLCN1 forms an ion channel that controls the flow of negatively charged chloride ions into these cells. The main function of this channel is to stabilize the cells' electrical charge, enabling muscles to contract normally.
In people with congenital myotonia due to a mutation in CLCN1, the ion channel admits too few chloride ions into the cell.  This shortage of chloride ions causes prolonged muscle contractions, which are the hallmark of myotonia.
CLCN4
H(+)/Cl(-) exchange transporter 4 is a protein that in humans is encoded by the CLCN4 gene.

# Function
The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders.

# Clinical significance
Mutations in this gene have been linked to cases of early onset epilepsy
CLDN2
Claudin-2 is a protein that in humans is encoded by the CLDN2 gene. It belongs to the group of claudins.
Members of the claudin protein family, such as CLDN2, are expressed in an organ-specific manner and regulate the tissue-specific physiologic properties of tight junctions (Sakaguchi et al., 2002).

# Function
Claudin-2 is expressed in cation-leaky epithelia such as that of the kidney proximal tubule. Mice that are deficient in claudin-2 have reduced reabsorption of Na+ in the proximal tubule, consistent with a role in paracellular transport.
Similar results have been obtained with cultured cells, as overexpression in claudin-2 lacking cells leads to increase of permeability for small cations.
Furthermore, claudin-2 has been shown to form paracellular channels for water.
CLIC4
Chloride intracellular channel 4, also known as CLIC4, is a eukaryotic gene.
Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 4 (CLIC4) protein, encoded by the CLIC4 gene, is a member of the p64 family; the gene is expressed in many tissues and exhibits an intracellular vesicular pattern in PANC-1 cells (pancreatic cancer cells).

# Binding partners
CLIC4 binds to dynamin I, -tubulin, -actin, creatine kinase and two 14-3-3 isoforms.
CLIC5
Chloride intracellular channel protein 5 is a protein that in humans is encoded by the CLIC5 gene.

# Expression and localization
CLIC5 exists in two alternative splice variants, a smaller CLIC5A and larger CLIC5B protein.
CLIC5A is expressed chiefly in the renal glomerulus, specifically in podocytes. Within the cell, CLIC5A is localized to the plasma membrane and the cytosol, and associates and is regulated by the actin cytoskeleton. CLIC5A can form ion channels in vitro and its channel activity is regulated by actin, though measurement of its chloride conductance in vitro suggests that CLIC5A is equally selective for cations and anions.

# Function
Although chloride intracellular channel (CLIC) proteins were thought to be involved in ion transport in subcellular compartments, their actual functions suggest their role in diverse cellular and physiological functions including apoptosis and angiogenesis in CLIC1.
CLIC5A, through its interactions with the small GTPase Rac1, induces the phosphorylation of ezrin-moeisin-radixin (ERM) proteins and localized production of the phosphoinositide phosphatidylinositol-4,5-bisphosphate. These two events activate ezrin, enabling it to couple transmembrane proteins to the actin cytoskeleton, which could represent a mechanism by which podocyte foot processes form to enable renal filtration.

# Clinical relevance
CLIC5A deficiency in mouse models potentiates glomerular injury in hypertension. In these mice, podocyte foot processes were also more sparse and disperse than in wild-type mice.
CNDP1
Beta-Ala-His dipeptidase is an enzyme that in humans is encoded by the CNDP1 gene.
This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region.
The metabolic disorder Carnosinemia may be caused by mutations in this gene.