Persius/hicric huggingface dataset:
DCTN1
Dynactin subunit 1 is a protein that in humans is encoded by the DCTN1 gene.

# Function
This gene encodes the largest subunit of dynactin, a macromolecular complex consisting of 23 subunits (11 individual proteins ranging in size from 22 to 150 kD). Dynactin binds to cytoplasmic dynein, dynein cargo adaptors, and microtubules. It is involved in a diverse array of cellular functions, including ER-to-Golgi transport, the centripetal movement of lysosomes and endosomes, spindle formation, chromosome movement, nuclear positioning, and axonogenesis.
This subunit is commonly referred to p150-glued.  It is present in two copies per dynactin complex and forms an ~75nm long flexible arm that extends from the main body of dynactin.  The p150-glued arm contains binding sites for microtubules, the microtubule plus tip binding protein EB1, and the N-terminus of the dynein intermediate chain.
Alternative splicing of this gene results in at least 2 functionally distinct isoforms: a ubiquitously expressed one and a brain-specific one. Based on its cytogenetic location, this gene is considered as a candidate gene for limb-girdle muscular dystrophy.

# Interactions
DCTN1 has been shown to interact with:
- BBS4,
- Dystonin,
- Grb2,  and
- RAB6A.
DCTN5
Dynactin 5 (p25) is a protein that in humans is encoded by the DCTN5 gene.
This gene encodes a subunit of dynactin, a component of the cytoplasmic dynein motor machinery involved in minus-end-directed transport. The encoded protein is a component of the pointed-end subcomplex and is thought to bind membranous cargo. A pseudogene of this gene is located on the long arm of chromosome 1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

# Model organisms
Model organisms have been used in the study of DCTN5 function. A conditional knockout mouse line, called Dctn5tm2a(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 tests were carried out on mutant mice and three significant abnormalities were observed. No homozygous mutant embryos were identified during gestation, and therefore none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice and abnormal lens morphology (including cataracts) was observed in female animals.
DDIT4
DNA-damage-inducible transcript 4 (DDIT4) protein also known as protein regulated in development and DNA damage response 1 (REDD1) is a protein that in humans is encoded by the DDIT4 gene.

# Function
DDIT4 acts as a negative regulator of mTOR, a serine/threonine kinase that regulates a variety of cellular functions such as growth, proliferation and autophagy. In particular, upregulation of HIF-1 in response to hypoxia upregulates DDIT4, leading to activation of Tsc1/2 via 1433 shuttling  and subsequent downregulation of mTOR via Rheb. In addition to hypoxia, DDIT4 expression has also been shown to be activated by DNA damage and energy stress.

# Clinical significance
Clinical interest in DDIT4 is based primarily on its effect on mTOR, which has been associated with aging and linked with diseases such as tuberous sclerosis, lymphangioleiomyomatosis, diabetes, and cancer. In particular, the overactivation of mTOR in many cancer types has led to the development of mTOR inhibitors for cancer treatment.  DDIT4 has begun to receive attention in this regard via the diabetes drug Metformin which has been shown to reduce cancer risk and increase DDIT4 expression.
DDX11
Probable ATP-dependent RNA helicase DDX11 is an enzyme that in humans is encoded by the DDX11 gene.
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. 
Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is an enzyme that possesses both ATPase and DNA helicase activities. This gene is a homolog of the yeast CHL1 gene, and may function to maintain chromosome transmission fidelity and genome stability. Alternative splicing results in multiple transcript variants encoding distinct isoforms.
DDX20
Probable ATP-dependent RNA helicase DDX20, also known as DEAD-box helicase 20 and gem-associated protein 3 (GEMIN3), is an enzyme that in humans is encoded by the DDX20 gene.

# Function
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which has an ATPase activity and is a component of the survival of motor neuron (SMN) complex. This DEAD box protein is one of the gem-associated proteins (GEMIN3) that interacts directly with SMN.
SMN is the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on RNPs.

# Biological Implication
Previous research has revealed that DDX20 may act as a tumor suppressor in hepatocellular carcinoma and as a tumor promoter in breast cancer. DDX20 deficiency enhances NF-B activity by impairing the NF-B-suppressive action of microRNAs, and suggest that dysregulation of the microRNA machinery components may also be involved in pathogenesis in various human diseases. Such as miRNA-140 which acts as a liver tumor suppressor, and due to a deficiency of DDX20, miRNA-140 function gets impair, this subsequent functional impairment of miRNAs could lead to hepatocarcinogenesis.Similarly, DDX20 may promote the progression of Prostate cancer (PCa) through the NF-B pathway. In a clinical based study it has been observed that positive DP103/NF-B feedback loop promotes constitutive NF-B activation in invasive breast cancers and activation of this pathway is linked to cancer progression and the acquisition of chemotherapy resistance. It makes DP103 has potential as a therapeutic target for breast cancer treatment.

# Interactions
DDX20 has been shown to interact with:
- EIF2C2,
- GEMIN4,
- GEMIN5,
- LSM2,
- SMN1,
- SNRPB,
- SNRPD3 and
- SNRPG,
- SNRPD1,
- SNRPD2,
- SNRPE,
- SNRPF,  and
- SIP1.
DDX27
DEAD (Asp-Glu-Ala-Asp) box polypeptide 27, also known as DDX27, is a human gene.
The protein encoded by this gene belongs to the family of DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, the function of which has not been determined.

# Model organisms
Model organisms have been used in the study of DDX27 function. A conditional knockout mouse line, called Ddx27tm1a(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 seven tests were carried out and two phenotypes were reported. No homozygous mutant embryos were identified during gestation, and in a separate study only 1% survived until weaning (significantly less than the Mendelian ratio). The remaining tests were carried out on heterozygous mutant adult mice; no significant abnormalities were observed in these animals.
DDX3X
ATP-dependent RNA helicase DDX3X is an enzyme that in humans is encoded by the DDX3X gene.

# Function
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which interacts specifically with hepatitis C virus core protein resulting a change in intracellular location. This gene has a homolog located in the nonrecombining region of the Y chromosome. The protein sequence is 91% identical between this gene and the Y-linked homolog.

# Role in cancer
DDX3X is involved in many different types of cancer. For example, it is abnormally expressed in breast epithelial cancer cells in which its expression is activated by HIF1A during hypoxia. Increased expression of DDX3X by HIF1A in hypoxia is initiated by the direct binding of HIF1A to the HIF1A response element, as verified with chromatin immunoprecipitation and luciferase reporter assay. Since the expression of DDX3X is affected by the activity of HIF1A, the co-localization of these proteins has also been demonstrated in MDA-MB-231 xenograft tumor samples.
In HeLa cells DDX3X is reported to control cell cycle progression through Cyclin E1. More specifically, DDX3X was shown to directly bind to the 5  UTR of Cyclin E1 and thereby facilitating the translation of the protein. Increased protein levels of Cyclin E1 was demonstrated to mediate the transition of S phase entry.

# Clinical significance
Mutations of the DDX3X gene are also associated with medulloblastoma.
DDX42
ATP-dependent RNA helicase DDX42 is an enzyme that in humans is encoded by the DDX42 gene.

# Function
This gene encodes a member of the Asp-Glu-Ala-Asp (DEAD) box protein family. Members of this protein family are putative RNA helicases, and are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Two transcript variants encoding the same protein have been identified for this gene.

# Interactions
DDX42 has been shown to interact with SF3B1.

# Model organisms
Model organisms have been used in the study of DDX42 function. A conditional knockout mouse line called Ddx42tm1b(EUCOMM)Wtsi 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
DEFA1
Defensin, alpha 1 also known as human alpha defensin 1,   human neutrophil peptide 1 (HNP-1) or neutrophil defensin 1 is a human protein that is encoded by the DEFA1 gene. Human alpha defensin 1 belongs to the alpha defensin family of antimicrobial peptides.

# Function
Defensins are a family of microbicidal and cytotoxic peptides thought to be involved in host defense. They are abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the intestine, respiratory tract, urinary tract, and vagina. Members of the defensin family are highly similar in protein sequence and distinguished by a conserved cysteine motif. Several alpha defensin genes are clustered on chromosome 8. The protein encoded by this gene, defensin, alpha 1, is found in the microbicidal granules of neutrophils and likely plays a role in phagocyte-mediated host defense. It differs from the defensins, alpha 2 and alpha 3 by only one amino acid.

# Biosynthesis
HNPs are generated as 94 amino acids preproHNPs, which are co-translationally cleaved to 75 amino acids pro-peptides with a N-terminal prosegment having a negative charge that neutralizes the highly positively charged C terminal peptide. Processing of proHNPs occurs mainly in late promyelocytes, where the 75 amino acids proHNPs are cleaved to a 56 amino acids intermediate form and onward to 29-30 amino acids mature peptides designated HNPs. Cationic 29-30 amino acids HNPs associate with the negatively charged proteoglycan serglycin and translocate to azurophil granules. At later stages of granulocytic differentiation in which HNP expression peaks (i.e. myelocytes and metamyelocytes), proHNPs are not cleaved, rendering the peptides overall neutral. This prevents binding to serglycin and most proHNP is accordingly secreted into the bone marrow plasma although some is retained in specific granules.
DEFA6
Defensin, alpha 6 (DEFA6) also known as human alpha defensin 6  (HD6) is a human protein that is encoded by the DEFA6 gene.  DEFA6 is expressed in the Paneth cells of the ileum.

# Function
The alpha defensins are a family of microbicidal and cytotoxic peptides that defend the host against bacteria and viruses.  HD6 has poor antibacterial potency.  However, HD6 affords protection against invasion by enteric bacterial pathogens by self-assembly to form fibrils and nanonets that surround and entangle bacteria.
Several alpha defensin genes, including DEFA6, are clustered on chromosome 8.
DFNA5
Non-syndromic hearing impairment protein 5 is a protein that in humans is encoded by the DFNA5 gene.

# Function
Hearing impairment is a heterogeneous condition with over 40 loci described. The protein encoded by this gene is expressed in fetal cochlea, however, its function is not known. Nonsyndromic hearing impairment is associated with a mutation in this gene.
The observation that DFNA5 is epigenetically inactivated in a large number of cancers of frequent types (gastric, colorectal, and breast) is another important finding and is in line with its apoptosis-inducing properties. Indeed, if apoptosis is an intrinsic feature of DFNA5, shutting the gene down in tumor cells makes them more susceptible to uncontrolled cellular growth. Moreover, the fact that DFNA5 is regulated by P53 strongly suggests that DFNA5 is a tumor suppressor gene.
DGCR8
The DGCR8 microprocessor complex subunit (DiGeorge syndrome chromosomal  region 8) is a protein that in humans is encoded by the DGCR8 gene. In other animals, particularly the common model organisms Drosophila melanogaster and Caenorhabditis elegans, the protein is known as Pasha (partner of Drosha). It is a required component of the RNA interference pathway.

# Function
DGCR8 is localized to the cell nucleus and is required for microRNA (miRNA) processing. It binds to Drosha, an RNase III enzyme, to form the Microprocessor complex that cleaves a primary transcript known as pri-miRNA to a characteristic stem-loop structure known as a pre-miRNA, which is then further processed to miRNA fragments by the enzyme Dicer. DGCR8 contains an RNA-binding domain and is thought to bind pri-miRNA to stabilize it for processing by Drosha.
DGCR8 is also required for some types of DNA repair.  Removal of UV-induced DNA photoproducts, during transcription coupled nucleotide excision repair (TC-NER), depends on JNK phosphorylation of DGCR8 on serine 153.  While DGCR8 is known to function in microRNA biogenesis, this activity is not required for DGCR8-dependent removal of UV-induced photoproducts.  Nucleotide excision repair is also needed for repair of oxidative DNA damage due to hydrogen peroxide (H2O2), and DGCR8 depleted cells are sensitive to H2O2.
DHRS1
Dehydrogenase/reductase SDR family member 1, also known as Short chain dehydrogenase/reductase family 19C member 1 is an enzyme that in humans is encoded by the DHRS1 gene located on chromosome 14.

# Structure
The DHRS1 gene is located on the chromosome 14q21.3 region and contains 9 exons. It encodes a 314-amino-acid, 33-kDa protein that is thought to be located to the endoplasmic reticulum and the mitochondrial inner membrane inside the cell.

# Function
The DHRS1 protein is thought to have oxidoreductase activity based on sequence similarity and conserved catalytic sites with other short-chain oxidoreductase enzymes. The enzyme is found to be expressed in the fetal brain.

# Interactions
The DHRS1 protein is thought to interact with the protein phospholipid scrambase 1 (PLSCR1).
DHX29
DExH-box helicase 29 (DHX29) is a 155 kDa protein that in humans is encoded by the DHX29 gene.

# Function
This gene encodes a member of the DEAH (Asp-Glu-Ala-His) subfamily of proteins, part of the DEAD (Asp-Glu-Ala-Asp) box family of RNA helicases. The encoded protein functions in translation initiation, and is specifically required for ribosomal scanning across stable mRNA secondary structures during initiation codon selection. This protein may also play a role in sensing virally derived cytosolic nucleic acids. Knockdown of this gene results in reduced protein translation and impaired proliferation of cancer cells.

# Interactions
DHX29 has been shown to interact with the eukaryotic small ribosomal subunit (40S) and eIF3.
DHX36
Probable ATP-dependent RNA helicase DHX36 also known as DEAH box protein 36 (DHX36) or MLE-like protein 1 (MLEL1) or G4 resolvase 1 (G4R1) or RNA helicase associated with AU-rich elements (RHAU) is an enzyme that in humans is encoded by the DHX36 gene.

# Structure
Structurally, DHX36 is a 1008 amino acid-long modular protein that has been crystallized in a complex with a DNA G-quadruplex. It consists of a ~440-amino acid helicase core comprising all signature motifs of the DEAH/RHA family of helicases with N- and C-terminal flanking regions of ~180 and ~380 amino acids, respectively. Part of the N-terminal flanking region forms an alpha-helix called the DHX36-specific motif, which recognizes the 5'-most G-quadruplex quartet.  The OB-fold domain binds to the 3'-most G-tract sugar-phosphate backbone.  Like all the DEAH/RHA helicases, the helicase associated domain is located adjacent to the helicase core region and occupies 75% of the C-terminal region.

# Function
DEAH/RHA proteins are RNA and DNA helicases typically characterized by low processivity translocation on substrates and the capability to bind/unwind non-canonical nucleic acid secondary structures. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAH/RHA protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division.
DHX36 exhibits a unique ATP-dependent guanine-quadruplex (G4) resolvase activity and specificity for its substrate in vitro.  DHX36 displays repetitive unwinding activity as a function of the thermal stability of the G-quadruplex substrate, characteristic of a number of other G-quadruplex resolvases such as the BLM/WRN helicases.  DHX36 binds G4-nucleic acid with sub-nanomolar affinity and unwinds G4 structures much more efficiently than double-stranded nucleic acid. Consistent with these biochemical observations, DHX36 was also identified as the major source of tetramolecular RNA-resolving activity in HeLa cell lysates.
Previous work showed that DHX36 associates with mRNAs and re-localises to stress granules (SGs) upon translational arrest induced by various environmental stresses. A region of the first 105 amino acid was shown to be critical for RNA binding and re-localisation to SGs.
PARK7
Protein deglycase DJ-1, also known as Parkinson disease protein 7, is a protein which in humans is encoded by the PARK7 gene.

# Structure

## Gene
The gene PARK7, also known as DJ-1, encodes a protein of the peptidase C56 family. The human gene PARK7 has 8 Exons and locates at chromosome band 1p36.23.

## Protein
The human protein deglycase DJ-1 is 20 kDa in size and composed of 189 amino acids with seven -strands and nine -helices in total and is present as a dimer.  It belongs to the peptidase C56 family of proteins.
The protein structures of human protein DJ-1, Escherichia coli chaperone Hsp31, YhbO and YajL and an Archaea protease are evolutionarily conserved.

# Function
Under an oxidative condition, protein deglycase DJ-1 inhibits the aggregation of -synuclein via its chaperone activity, thus functions as a redox-sensitive chaperone and as a sensor for oxidative stress. Accordingly, DJ-1 apparently protects neurons against oxidative stress and cell death. In parallel, Protein DJ-1 acts as a positive regulator of androgen receptor-dependent transcription.
Pyrroloquinoline quinone (PQQ) has been shown to reduce the self-oxidation of the DJ-1 protein, an early step in the onset of some forms of Parkinson's disease.
Functional DJ-1 protein has been shown to bind metals and protect against metal-induced cytotoxicity from copper and mercury.

# Clinical significance
Defects in this gene are the cause of autosomal recessive early-onset Parkinson's disease 7.

# Interactions
PARK7 has been shown to interact with:
- CASK,
- EFCAB6,  and
- PIAS2.
DMBT1
Deleted in malignant brain tumors 1 protein is a protein that in humans is encoded by the DMBT1 gene.

# Function
Loss of sequences from human chromosome 10q has been associated with the progression of human cancers.  The gene DMBT1 was originally isolated based on its deletion in a medulloblastoma cell line.  DMBT1 is expressed with transcripts of 6.0, 7.5, and 8.0 kb in fetal lung and with one transcript of 8.0 kb in adult lung, although the 7.5 kb transcript has not been characterized.  The DMBT1 protein is a glycoprotein containing multiple scavenger receptor cysteine-rich (SRCR) domains separated by SRCR-interspersed domains (SID).  Transcript variant 2 (8.0 kb) has been shown to bind surfactant protein D independently of carbohydrate recognition.  This indicates that DMBT1 may not be a classical tumor suppressor gene, but rather play a role in the interaction of tumor cells and the immune system.

# Pattern recognition and potential use of DMBT1 in nanomedicine
At epithelial barriers molecular pattern recognition mechanisms act as minesweepers against harmful environmental factors and thereby play a crucial role in the defense against invading bacterial and viral pathogens. However, it became evident that some of the proteins participating in these host defense processes may simultaneously function as regulators of tissue regeneration when in the extracellular matrix, thus coupling defense functions with regulation of stem cells. Although molecular pattern recognition has complex physiological roles and we just begin to understand its various functions, the simplicity of the underlying principles for recognition of specific classes of molecules may generate novel starting points for nanomedical approaches in drug delivery across epithelial barriers. The protein DMBT1, showed pattern recognition activity for poly-sulfated and poly-phosphorylated ligands, including nucleic acids, and the ability to aggregate ligands. This raises the interesting question in how far these properties can be utilized to assemble nucleic acidpeptide nano-complexes and whether this can be exploited to modulate the pharmacological properties of nucleic acids and/or for nucleic acid delivery to target cells  Recently, DMBT1-derived peptides have been successfully harnessed for siRNA intracellular delivery. 

# Interactions
DMBT1 has been shown to interact with Surfactant protein D. DMBT1-derived peptides also interacts with nucleic acids.