Persius/hicric huggingface dataset:
LRRC7
Leucine rich repeat containing 7 also known as LRRC7,  Densin-180, or LAP1 is a protein which in humans is encoded by the LRRC7 gene.

# Structure
Found to be densely associated to the postsynaptic density (PSD), it has been characterised as a 188 kDa (originally thought to be 180 kDa, hence nomenclature), 1495 residues long, brain-specific protein containing 16 leucine-rich repeats (LRRs) within the 500 N-terminal residues, and one Psd95/Discs large/Zona occludens (PDZ) domain within the 200 C-terminal residues. Originally postulated to have an apparent transmembrane domain, it has now been shown that the protein has numerous phosphorylation sites both N- and C-term of this domain, and that protein is therefore cytoplasmic; palmitoylation is thought to occur near the N-terminus of the protein which would account for localisation of the protein at the PSD.

# Interactions
LRRC7 has been shown to interact with CDH2.
The currently exposed interactions of Densin-180 portray the protein as a promiscuous player amongst key synaptic players, fitting with the original observation of the proteins dense presence among core PSD proteins by Mary B. Kennedy's Laboratory. Identified interaction partners include: CaMKII-alpha, alpha-Actinin and NR2B (via CaMKII-alpha), Cav1.3 (L-type Ca2+) channels, MAGUIN-1, Shank, PSD-95 (via Shank and MAGUIN-1), beta-Catenin, delta-Catenins and NCadherin (via the Catenins). The nature and function of these interactions, detailed in tables 1-1 and 1-2, portray Densin-180 as a key interactor in the midst of receptor proteins, scaffolding proteins and structural proteins. 
It is also quite possible that Densin-180 dimerises or multimerises through interactions between its PDZ domain and its own terminal amino acid residues. [Subcellular localisation of recombinant Densin-180 clones expressed in HEK293 TSA cells
Ranatunga, J.M. (2011) Subcellular localisation of recombinant Densin-180 clones expressed in HEK293 TSA cells. Masters thesis, UCL (University College London). /]
LYNX1
Ly6/neurotoxin 1 is a protein in humans that is encoded by the LYNX1 gene. Alternatively spliced variants encoding different isoforms have been identified.

# Function
This gene encodes a member of the Ly-6/neurotoxin gene family, a group of lymphocyte antigens that attach to the cell surface by a glycosylphosphatidylinositol anchor and have a unique structure showing conserved 8-10 cysteine residues with a characteristic spacing pattern. Functional analysis indicates that this protein is not a ligand or neurotransmitter but has the capacity to enhance nicotinic acetylcholine receptor function in the presence of acetylcholine. This gene may also play a role in the pathogenesis of psoriasis vulgaris.
The LYNX1 gene codes for a protein (Lynx1) that binds to acetylcholine receptors in the brain. Lynx1 a member of the Ly6 superfamily of proteins that are capable of modulating neurotransmitter receptors.

## Lynx1 and Visual Plasticity
Transgenic mice without Lynx1 expression do not have a normal critical period of neuroplasticity in the visual cortex for  development of ocular dominance columns. These mice show unusually rapid recovery from amblyopia in adulthood indicating a role in reduction of synaptic plasticity during the normal expression of Lynx1 in adult brain.
Lynx1 reduces adult visual cortex plasticity by binding to nicotinic acetylcholine receptors (NAchR) and diminishing acetylcholine signaling. After the developmental critical period and into adulthood, both Lynx1 mRNA and protein levels increase in the adult V1 and the lateral geniculate nucleus (LGN). Lynx1 and nAChR mRNAs are co-expressed in the LGN, as well as in parvalbumin-positive GABAergic interneurons. After monocular deprivation during the critical period to induce amblyopia, Lynx1 knock-out rat models spontaneously recovered normal visual acuity by reopening the closed eye. Similarly, an infusion of physostigmine to increase acetylcholine signaling prompted recovery from amblyopia in wild type mice Inhibition of Lynx1 may be a possible therapeutic mechanism to prolong synaptic plasticity of the visual cortex and improve binocular function of some amblyopes.
LYRM7
LYR motif containing 7, also known as Complex III assembly factor LYRM7 or LYR motif-containing protein 7 is a protein that in humans is encoded by the LYRM7 gene. The protein encoded by this gene is a nuclear-encoded mitochondrial matrix protein that stabilizes UQCRFS1 and chaperones it to the CIII complex. Defects in this gene are a cause of mitochondrial complex III deficiency, nuclear type 8. Three transcript variants encoding two different isoforms have been found for this gene.

# Structure
The LYRM7 gene is located on the q arm of chromosome 5 at position 23.3 to 31.1, spans 34,512 base pairs, and has 5 exons. The LYRM7 gene produces a 6.2 kDa protein composed of 53 amino acids, which is a soluble matrix protein with an N-terminal LYR motif. LYRM7 is an assembly factor of the enzyme Ubiquinol Cytochrome c Reductase (UQCR, Complex III or Cytochrome bc1 complex) of the mitochondrial respiratory chain.

# Function
The LYRM7 gene encodes for an assembly factor necessary for the incorporation of the iron-sulfur cluster in the Rieske (Fe-S) protein (UQCRFS1), which is an essential subunit of the Ubiquinol Cytochrome c Reductase (complex III) of the mitochondrial respiratory chain. LYRM7 acts by binding to the co-chaperone HSC20 of the Fe-S biogenesis machinery, which brings a cluster assembled on the main scaffold protein ISCU. Direct binding of HSC20 to the LYR motif of LYRM7 in a pre-assembled UQCRFS1-LYRM7 intermediate in the mitochondrial matrix facilitates transfer of the Fe-S cluster from holo-ISCU to UQCRFS1.
UQCRFS1, or Rieske (Fe-S) protein (UQCRFS1) is the last catalytic subunit added to the complex. Complex III is required for the catalysis of electron transfer from coenzyme Q to cytochrome c as well as the pumping of protons into the inner membrane from the matrix for the generation of an ATP-coupled electrochemical potential.

# Clinical significance
Variants of LYRM7 have been associated with mitochondrial complex III deficiency, nuclear 8 (MC3DN8). Mitochondrial complex III deficiency, nuclear 8 is a form of mitochondrial complex III deficiency, a disorder of Complex III of the mitochondrial respiratory chain. The deficiency is known to be highly variable in phenotype depending on which tissues are affected. Clinical features include mitochondrial encephalopathy, psychomotor retardation, ataxia, severe failure to thrive, liver dysfunction, renal tubulopathy, muscle weakness and exercise intolerance. Pathogenic Mutations of the LYRM7 gene have included (c.73G>A), (c.214C>T), (c.37delA), and others.
LZTR1
Leucine-zipper-like transcriptional regulator 1 is a protein that in humans is encoded by the LZTR1 gene.
This gene encodes a member of the BTB-kelch superfamily. Initially described as a putative transcriptional regulator based on weak homology to members of the basic leucine zipper-like family, the encoded protein subsequently has been shown to localize exclusively to the Golgi network where it may help stabilize the Golgi complex.

# Clinical significance
Deletion of this gene may be associated with DiGeorge syndrome.
This gene has also been implicated in an autosomal dominant form of schwannomatosis.
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MAGI2
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 also known as membrane-associated guanylate kinase inverted 2 (MAGI-2) and atrophin-1-interacting protein 1 (AIP-1) is an enzyme that in humans is encoded by the MAGI2 gene.

# Function
The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral-pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family.

# Interactions
MAGI2 has been shown to interact with ATN1 and PTEN (gene).
MAGOH
Protein mago nashi homolog is a protein that in humans is encoded by the MAGOH gene.
Drosophila that have mutations in their mago nashi (grandchildless) gene produce progeny with defects in germplasm assembly and germline development. This gene encodes the mammalian mago nashi homolog. In mammals, mRNA expression is not limited to the germ plasm, but is expressed ubiquitously in adult tissues and can be induced by serum stimulation of quiescent fibroblasts.

# Interactions
MAGOH has been shown to interact with RBM8A and NXF1. In Drosophila melanogaster, Mago Nashi and Tsunagi/Y14 (core components of the exon junction complex) form a complex with a novel zinc finger protein, Ranshi, that has a role in oocyte differentiation.
MALT1
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 is a protein that in humans is encoded by the MALT1 gene. It's the human paracaspase.

# Function
Genetic ablation of the paracaspase gene in mice and biochemical studies have shown that paracaspase is a crucial protein for T and B lymphocytes activation. It has an important role in the activation of the transcription factor NF-B, in the production of interleukin-2 (IL-2) and in T and B lymphocytes proliferation Two alternatively spliced transcript variants encoding different isoforms have been described for this gene.
In addition, a role for paracaspase has been shown in the innate immune response mediated by the zymosan receptor Dectin-1 in macrophages and dendritic cells, and in response to the stimulation of certain G protein-coupled receptors.
Sequence analysis proposes that paracaspase has an N-terminal death domain, two central immunoglobulin-like domains involved in the binding to the B-cell lymphoma 10 (Bcl10) protein and a caspase-like domain.
Paracaspase has been shown to have proteolytic activity through its caspase-like domain in T lymphocytes. Cysteine 464 and histidine 414 are crucial for this activity. Like metacaspases, the paracaspase cleaves substrates after an arginine residue. To date, several paracaspase substrates have been described (see below). Bcl10 is cut after arginine 228. This removes the last five amino acids at the C-terminus and is crucial for T cell adhesion to fibronectin, but not for NF-B activation and IL-2 production. However, using a peptide-based inhibitor (z-VRPR-fmk) of the paracaspase proteolytic activity, it has been shown that this activity is required for a sustain NF-B activation and IL-2 production, suggesting that paracaspase may have others substrates involved in T cell-mediated NF-B activation. A20, a deubiquitinase, has been shown to be cut by paracaspase in Human and in mouse. Cells expressing an uncleavable A20 mutant is however still capable to activate NF-B, but cells expressing the C-terminal or the N-terminal A20 cleavage products activates more NF-B than cells expressing wild-type A20, indicating that cleavage of A20 leads to its inactivation. Since A20 has been described has an inhibitor of NF-B, this suggests that paracaspase-mediated A20 cleavage in T lymphocytes is necessary for a proper NF-B activation.
By targeting paracaspase proteolytic activity, it might be possible to develop new drugs that might be useful for the treatment of certain lymphomas or autoimmune disorders.

# Interactions
MALT1 has been shown to interact with BCL10, TRAF6 and SQSTM1/p62.

# Protease substrates
MALT1 (PCASP1) is part of the paracaspase family and shows proteolytic activity. Since many of the substrates are involved in regulation of inflammatory responses, the protease activity of MALT1 has emerged as an interesting therapeutic target. Currently known protease substrates are:
- TNFAIP3 (A20) 
- BCL10 
- CYLD 
- RELB 
- regnase-1 (MCPIP1) 
- Roquin-1 and -2 
- MALT1 auto-proteolysis 
- HOIL1 
Specifically by the oncogenic IAP2-MALT1 fusion:
- NIK 
- LIMA1
MAML1
Mastermind-like protein 1 is a protein that in humans is encoded by the MAML1 gene.

# Function
This protein is the human homolog of mastermind, a Drosophila protein that plays a role in the Notch signaling pathway involved in cell-fate determination. There is in vitro evidence that the human homolog forms a complex with the intracellular portion of human Notch receptors and can increase expression of a Notch-induced gene. This evidence supports its proposed function as a transcriptional co-activator in the Notch signaling pathway.
Details on the activity of the N-terminal domain of Mastermind-like protein 1
may be found under MamL-1.

# Interactions
MAML1 has been shown to interact with EP300 and NOTCH1.
MAP1B
Microtubule-associated protein 1B is a protein that in humans is encoded by the MAP1B gene.

# Function
This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1B heavy chain and LC1 light chain. Gene knockout studies of the mouse microtubule-associated protein 1B gene suggested an important role in development and function of the nervous system. Two alternatively spliced transcript variants have been described.

# Interactions
MAP1B has been shown to interact with Acidic leucine-rich nuclear phosphoprotein 32 family member A and RASSF1.
MAPK1
Mitogen-activated protein kinase 1, also known as MAPK1, p42MAPK, and ERK2, is an enzyme that in humans is encoded by the MAPK1 gene.

# Function
The protein encoded by this gene is a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. The activation of this kinase requires its phosphorylation by upstream kinases. Upon activation, this kinase translocates to the nucleus of the stimulated cells, where it phosphorylates nuclear targets. Two alternatively spliced transcript variants encoding the same protein, but differing in the UTRs, have been reported for this gene.

# Model organisms
Model organisms have been used in the study of MAPK1 function. A conditional knockout mouse line, called Mapk1tm1a(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 seven 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 males had decreased circulating amylase levels.

# Interactions
MAPK1 has been shown to interact with:
- ADAM17,
- CIITA,
- DUSP1,
- DUSP22,
- DUSP3,
- ELK1,
- FHL2,
- HDAC4,
- MAP2K1,
- MAP3K1
- MAPK14,
- MKNK1,
- MKNK2,
- Myc,
- NEK2,
- PEA15,
- PTPN7,
- Phosphatidylethanolamine binding protein 1,
- RPS6KA1,
- RPS6KA2,
- RPS6KA3,
- SORBS3,
- STAT5A,
- TNIP1,
- TOB1,
- TSC2,
- UBR5, and
- VAV1.

# Clinical significance
Mutations in MAPK1 are implicated in many types of cancer.
MAPK3
Mitogen-activated protein kinase 3, also known as p44MAPK and ERK1, is an enzyme that in humans is encoded by the MAPK3 gene.

# Function
The protein encoded by this gene is a member of the mitogen-activated protein kinase (MAP kinase) family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act in a signaling cascade that regulates various cellular processes such as proliferation, differentiation, and cell cycle progression in response to a variety of extracellular signals. This kinase is activated by upstream kinases, resulting in its translocation to the nucleus where it phosphorylates nuclear targets. Alternatively spliced transcript variants encoding different protein isoforms have been described.

# Clinical significance
It has been suggested that MAPK3, along with the gene IRAK1, is turned off by two microRNAs that were activated after the influenza A virus had been made to infect human lung cells.

# Signaling pathways
Pharmacological inhibition of ERK1/2 restores GSK3 activity and protein synthesis levels in a model of tuberous sclerosis.

# Interactions
MAPK3 has been shown to interact with:
- DUSP3,
- DUSP6
- GTF2I,
- HDAC4,
- MAP2K1,
- MAP2K2,
- PTPN7,
- RPS6KA2,  and
- SPIB.
MAPK6
Mitogen-activated protein kinase 6 is an enzyme that in humans is encoded by the MAPK6 gene.
The protein encoded by this gene is a member of the Ser/Thr protein kinase family, and is most closely related to mitogen-activated protein kinases (MAP kinases). MAP kinases, also known as extracellular signal-regulated kinases (ERKs), are activated through protein phosphorylation cascades and act as integration points for multiple biochemical signals. This kinase is localized in the nucleus, and has been reported to be activated in fibroblasts upon treatment with serum or phorbol esters.

# Discovery
ERK3/MAPK6 was initially cloned from the rat brain cDNA library by homology screening with probes ERK1 derived probe.

# Gene location
In humans, MAPK 6 gene  is located on the distal arm of chromosome 15 (15q21.2). It is 47.01kb long and is transcribed in the centromere to telomere orientation. It consist of 6 exons with the translation initiation codon which is located in exon2.

# Structure
It is an atypical member of the mitogen activated kinases family. The molecular mass of the translated protein is approximately 100kDa, and is made up of 721 amino acid residues. It contains a typical kinase domain at the N- terminal and an extended C- terminal. The first 150 residues at c- terminal are 50% similar to ERK4 protein. At the kinase domain it exhibits about 70% similarity with the ERK4 protein. The activation loop of the phosphorylation motif contains only one phospho acceptor site (Ser-Glu-Gly).
The structure is predicted by homology modelling using the crystal structure of phoshphorylated ERK2. According to the model, the structure of ERK3/MAPK6 kinase domain resembles other MAP kinases.  The modelled ERK3/MAPK6 kinase domain is predicted to fold with a topology similar to other MAP kinases.

# Expression
ERK3/MAPK6 is widely expressed protein however it is expressed in significantly higher amounts in skeletal muscles and brain. It is localized in cytoplasm and the nucleus of cells. ERK3/MAPK6 is a highly unstable protein and has a very little half life of less than an hour. It is degraded by ubiquitin mediated proteasomal pathway.

# Function
It is very important for neonatal growth and survival. ERK3/MAPK6 forms a complex with microtubule associated protein2 (MAP2) and MAPKAPK5 which mediates the phosphorylation of MAPKAPK5 which in turn phosphorylates ERK3/MAPK6 at serine 189 residue mediating the entry into cell cycle. It also acts as a regulator for T- cell development. The  catalytic  activity of ERK3/MAPK6 plays an important for the proper differentiation of T-cells in the thymus. The long c- terminal is responsible for thymic differentiation.

# Role in cancer
ERK3/MAPK6  interacts with and phosphorylated steroid receptor coactivator 3 (SRC-3) This coreceptor   is an oncogenic protein which when overexpressed at serine 857 leads to cancer. After the phosphorylation of  SRC-3 results in the upregulation of  MMP activity ERK3-mediated phosphorylation at S857 was essential for interaction of SRC-3 with the ETS transcription factor PEA3, which promotes upregulation of MMP gene expression and proinvasive activity.
MAPK7
Mitogen-activated protein kinase 7 also known as MAP kinase 7 is an enzyme that in humans is encoded by the MAPK7 gene.

# Function
MAPK7 is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is specifically activated by mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5). It is involved in the downstream signaling processes of various receptor molecules including receptor tyrosine kinases, and G protein-coupled receptors. In response to extracellular signals, this kinase translocates to the cell nucleus, where it regulates gene expression by phosphorylating, and activating different transcription factors. Four alternatively spliced transcript variants of this gene encoding two distinct isoforms have been reported.
MAPK7 is also critical for cardiovascular development  and is essential for endothelial cell function.

# Interactions
MAPK7 has been shown to interact with:
- C-Raf,
- Gap junction protein, alpha 1
- MAP2K5,
- MEF2C,
- MEF2D,
- PTPRR,
- SGK,  and
- YWHAB.
MARK4
MAP/microtubule affinity-regulating kinase 4 is an enzyme that in humans is encoded by the MARK4 gene. MARK4 belongs to the family of serine/threonine kinases that phosphorylate microtubule-associated proteins (MAP) causing their detachment from microtubules. Detachment thereby increases microtubule dynamics and facilitates a number of cell activities including cell division, cell cycle control, cell polarity determination, and cell shape alterations.
There are four members of the MARK protein family, MARK1-4, which are highly conserved. MARK4 kinase has been shown to be involved in microtubule organization in neuronal cells. Levels of MARK4 are elevated in Alzheimer's disease and may contribute to the pathological phosphorylation of tau in this disease.

# Interactions
MARK4 has been shown to interact with USP9X and Ubiquitin C.