Persius/hicric huggingface dataset:
TFCP2
Alpha-globin transcription factor CP2 is a protein that in humans is encoded by the TFCP2 gene.
TFCP2 is also called Late SV40 factor (LSF) and it is induced by well known oncogene AEG-1. Late SV40 factor (LSF) also acts as an oncogene in hepatocellular carcinoma. Late SV40 factor (LSF) enhances angiogenesis by transcriptionally up-regulating matrix metalloproteinase-9 (MMP9).
Along with its main oncogene function in hepatocellular carcinoma (HCC) it plays multifaceted role in chemoresistance, epithelial-mesenchymal transition (EMT), allergic response, inflammation and Alzheimer's disease. The small molecule FQI1 (factor quinolinone inhibitor 1) prevents LSF from binding to HCC DNA which results in HCC cell death.

# Interactions
TFCP2 has been shown to interact with APBB1 and RNF2.
TFIIA
Transcription Factor TFIIA
Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA.  TFIIA is one of several general (basal) transcription factors (GTFs) that are required for all transcription events that use RNA polymerase II.  Other GTFs include TFIID, a complex composed of the TATA binding protein TBP and TBP-associated factors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH.  Together, these factors are responsible for promoter recognition and the formation of a transcription preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA template.
Functions of TFIIA
TFIIA interacts with the TBP subunit of TFIID and aids in the binding of TBP to TATA-box containing promoter DNA.  Although TFIIA does not recognize DNA itself, its interactions with TBP allow it to stabilize and facilitate formation of the PIC.  Binding of TFIIA to TBP also results in the exclusion of negative (repressive) factors that might otherwise bind to TBP and interfere with PIC formation. TFIIA also acts as a coactivator for some transcriptional activators, assisting with their ability to increase, or activate, transcription. The requirement for TFIIA in in vitro (cell-free) transcription systems has been variable, and it can be considered either as a GTF and/or a loosely associated TAF-like coactivator.  Genetic analysis in yeast has shown that TFIIA is essential for viability.
TFIIA Genes
TFIIA is encoded by two separate genes, one of which encodes a large subunit (TFIIAalpha/beta, TFIIAL, TOA1;  gene name GTF2A1) and another which encodes a small subunit (TFIIAgamma, TFIIAS, TOA2;  gene name GTF2A2).  In humans, the sizes of the encoded proteins are approximately 55 kD and 12 kD.  Both genes are present in species ranging from humans to yeast, and their protein products interact to form a complex composed of a beta barrel domain and an alpha helical bundle domain.  It is the N-terminal and C-terminal regions of the large subunit that participate in interactions with the small subunit.  These regions are separated by another domain whose sequence is always present in large subunits from various species but whose size varies and whose sequence is poorly conserved.  The large subunit is often observed to be proteolytically processed into two smaller subunits (alpha and beta) of approximately 35 kD and 19 kD.  A second gene encoding a large TFIIA subunit has been found in some higher eukaryotes.  This gene, ALF/TFIIAtau (gene name GTF2A1LF) is expressed only in oocytes and spermatocytes, suggesting it has a TFIIA-like regulatory role for gene expression only in germ cells.
THAP1
THAP domain-containing protein 1 is a protein that in humans is encoded by the THAP1 gene. The synonyme is DYT6 (Dystonia 6).

# Function
The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed.

# Interactions
THAP1 has been shown to interact with PAWR.

# Clinical significance
Thanatos-associated  domain-containing apoptosis-associated protein 1 (THAP1) is a DNA-binding protein that has been associated with DYT6 dystonia, a hereditary movement disorder involving sustained, involuntary muscle contractions.
TIMP1
TIMP metallopeptidase inhibitor 1, also known as TIMP1, a tissue inhibitor of metalloproteinases, is a glycoprotein that is expressed from the several tissues of organisms.
This protein is a member of the TIMP family. The glycoprotein is a natural inhibitor of the matrix metalloproteinases (MMPs), a group of peptidases involved in degradation of the extracellular matrix. In addition to its inhibitory role against most of the known MMPs, the encoded protein is able to promote cell proliferation in a wide range of cell types, and may also have an anti-apoptotic function.

# Function
TIMP1 is an inhibitory molecule that regulates matrix metalloproteinases (MMPs), and disintegrin-metalloproteinases (ADAMs and ADAMTSs). In regulating MMPs, TIMP1 plays a crucial role in extracellular matrix (ECM) composition, wound healing, and pregnancy.
The dysregulated activity of TIMP1 has been implicated in cancer. In pregnancy, TIMP1 plays a regulatory role in the process of implantation, particularly the cytotrophoblast invasion of the uterine endometrium. Additionally, it plays a role in regulating the transcriptional profile of fetal and placental tissues associated with the early stages of pregnancy. Studies attribute this role to a mechanism involving the chromatin structure at the TIMP1 promoter region, implicating new pharmaceutical possibilities for the therapeutic regulation of TIMP1. Accordingly, TIMP1 can be manipulated in vitro using techniques, like the TIMP1 knock-out.

# Other names
- Erythroid potentiating activity (EPA)
- Human collagenase inhibitor (HCI)

# Regulation of TIMP expression
Transcription of this gene is highly inducible in response to many cytokines and hormones. In addition, the expression from some but not all inactive X chromosomes suggests that this gene inactivation is polymorphic in human females. This gene is located within intron 6 of the synapsin I gene and is transcribed in the opposite direction.
In adrenocortical cells the trophic hormone ACTH induces expression of TIMP-1 and the increase in TIMP expression is also associated with decreased collagenase activity.
Increased expression of TIMP1 has been found to be associated with worse prognosis of various tumors, such as laryngeal carcinoma  or melanoma.
TIMP2
Tissue inhibitor of metalloproteinases 2 (TIMP2) is a gene and a corresponding protein. The gene is a member of the TIMP gene family. The protein is thought to be a metastasis suppressor.

# Function
The proteins encoded by this gene family are natural inhibitors of the matrix metalloproteinases (MMP), a group of peptidases involved in degradation of the extracellular matrix. In addition to an inhibitory role against metalloproteinases, the encoded protein has a unique role among TIMP family members in its ability to directly suppress the proliferation of endothelial cells. As a result, the encoded protein may be critical to the maintenance of tissue homeostasis by suppressing the proliferation of quiescent tissues in response to angiogenic factors, and by inhibiting protease activity in tissues undergoing remodelling of the extracellular matrix. TIMP2 functions as both an MMP inhibitor and an activator. TIMPs inhibit active MMPs, but different TIMPs inhibit different MMPs better than others. For example, TIMP-1 inhibits MMP-7, MMP-9, MMP-1 and MMP-3 better than TIMP-2, and TIMP-2 inhibits MMP-2 more effectively than other TIMPs.
In melanocytic cells TIMP2 gene expression may be regulated by MITF.
A more recent discovery is that TIMP2 plays an important role in hippocampal function and cognitive function. It plays a critical role in the benefit conferred to old mice when given human umbilical cord blood.

# Interactions
TIMP2 has been shown to interact with:
- MMP14  and
- MMP2.
TIP39
Tuberoinfundibular peptide of 39 residues is a protein that in humans is encoded by the PTH2 gene.
TIP39 is related to parathyroid hormone (PTH; MIM 168450) and PTH-related protein (PTHRP; MIM 168470) and is a ligand for PTH receptor-2 (PTHR2; MIM 601469) (John et al., 2002).
The molecular interaction of TIP39 with the PTH2 receptor has been characterized in full 3D molecular detail, identifying among other residues, Tyr-318 in transmembrane helix 5 as a key residue for high affinity binding
TLR10
Toll-like receptor 10 is a protein that in humans is encoded by the TLR10 gene. TLR10 has also been designated as CD290 (cluster of differentiation 290).
TLR10 has not been extensively studied because it is a pseudogene in mice, though all other mammalian species contain an intact copy of the TLR10 gene. Unlike other TLRs, TLR10 does not activate the immune system and has instead been shown to suppress inflammatory signaling on primary human cells. This makes TLR10 unique among the TLR family. No ligand is currently known for TLR10.

# Function
The protein encoded by this gene is a member of the toll-like receptor (TLR) family which play a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity.
TLR10 is unique among the TLR family in having an anti-inflammatory function, rather than a pro-inflammatory function similar to the other TLR family members. This was discovered by over-expressing TLR10 in human cell lines and using antibody-mediated engagement of the receptor on primary human cells. When TLR10 is activated in this manner, it suppresses the amount of cytokines produced, as compared to control cells. TLR10 engagement also has long-term effects on monocyte and B cell activation/differentiation by suppressing the transcription of activation markers. TLR10's mechanism of action is not yet known but activation of the receptor has been shown to suppress NF-B, MAP kinase and Akt signaling events stimulated by TLR and CD40 ligands. Currently, no ligand has been identified for this receptor.

# Expression
TLR10 has been transcriptionally shown to be expressed in secondary lymphoid tissues such as the spleen, lymph nodes, and tonsils. More specifically, protein level expression of TLR10 has been shown on the surface of B cells, monocytes and neutrophils; but not on T cells. Monocytes have the highest expression of TLR10 among these cell types but the overall expression of TLR10 is low compared to other TLRs. TLR10 has also been shown to be produced intracellularly in neutrophils and B cells differentiating into plasma cells.
Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene.
TLR 1
TLR 1 is a member of the toll-like receptor family (TLR) of pattern recognition receptors of the innate immune system. TLR1 recognizes pathogen-associated molecular pattern with a specificity for gram-positive bacteria. TLR1 has also been designated as CD281 (cluster of differentiation 281).
TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. This gene is ubiquitously expressed, and at higher levels than other TLR genes. Different length transcripts presumably resulting from use of alternative polyadenylation site, and/or from alternative splicing, have been noted for this gene.
TLR1 recognises peptidoglycan and (triacyl) lipoproteins in concert with TLR2 (as a heterodimer). Toll-like receptors, including TLR-1, found on the epithelial cell layer that lines the small and large intestine are important players in the management of the gut microbiota and detection of pathogens. It is also found on the surface of macrophages and neutrophils.

# Interactions
TLR 1 has been shown to interact with TLR 2.
TLR 3
TLR 3 is a member of the Toll-like receptor family of pattern recognition receptors of the innate immune system. Discovered in 2001, TLR3 recognizes double-stranded RNA, a form of genetic information carried by some viruses such as influenza. Upon recognition, TLR 3 induces the activation of NF-kB to increase production of type I interferons which signal other cells to increase their antiviral defenses. Double-stranded RNA is also recognised by the cytoplasmic receptors RIG-I and MDA-5.

# Structure
The structure of TLR3 was reported in June 2005 by researchers at The Scripps Research Institute. TLR3 forms a large horseshoe shape that contacts with a neighboring horseshoe, forming a "dimer" of two horseshoes. Much of the TLR3 protein surface is covered with sugar molecules, making it a glycoprotein, but on one face (including the interface between the two horseshoes), there is a large sugar-free surface. This surface also contains two distinct patches rich in positively-charged amino acids, which may be a binding site for negatively-charged double-stranded RNA.
Despite being a glycoprotein, TLR3 crystallises readily - a prerequisite for structural analysis by x-ray crystallography.
TMLHE
Trimethyllysine dioxygenase, mitochondrial is an enzyme that in humans is encoded by the TMLHE gene in chromosome X. Mutations in the TMLHE gene resulting in carnitine biosynthesis disruption have been associated with autism symptoms.

# Structure
The TMHLE gene is located at the extreme end of the Xq28 region with high genomic instability, and encodes a protein trimethyllysine dioxygenase, a, Fe2+ and 2-oxoglytarate dependent non-heme-ferrous iron hydrolase localized to the mitochondrial matrix.

# Function
The trimethyllysine dioxygenase enzyme catalyzes the first step in the carnitine biosynthesis pathway, which is part of amine biosynthesis. Carnitine is a molecule that play an essential role in the transport of activated fatty acids across the inner mitochondrial membrane where they are metabolized. The encoded protein converts trimethyllysine into hydroxytrimethyllysine with the reaction (EC 1.14.11.8):
N6,N6,N(6)-trimethyl-L-lysine + 2-oxoglutarate + O2 = 3-hydroxy-N6,N6,N(6)-trimethyl-L-lysine + succinate + CO2.
and requires iron and L-ascorbate as co-factors.

# Clinical significance
Mutations in the THLHE gene causes Epsilon-trimethyllysine hydroxylase deficiency (TMLHED), an inborn error of metabolism in carnitine biosynthesis, which may increase the risks of developing neurodevelopmental disorders, autism-related behaviors, and Autism spectrum disorders.

# Interactions
THLHE has been shown to have 14 binary protein-protein interactions including 12 co-complex interactions. THLHE appears to interact with SUGCT.
TOP2A
DNA topoisomerase 2-alpha is an enzyme that in humans is encoded by the TOP2A gene.
This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This nuclear enzyme is involved in processes such as chromosome condensation, chromatid separation, and the relief of torsional stress that occurs during DNA transcription and replication. It catalyzes the transient breaking and rejoining of two strands of duplex DNA which allows the strands to pass through one another, thus altering the topology of DNA. Two forms of this enzyme exist as likely products of a gene duplication event. The gene encoding this form, alpha, is localized to chromosome 17 and the beta gene is localized to chromosome 3. The gene encoding this enzyme functions as the target for several anticancer agents and a variety of mutations in this gene have been associated with the development of drug resistance. Reduced activity of this enzyme may also play a role in ataxia-telangiectasia.

# Interactions
TOP2A has been shown to interact with HDAC1, CDC5L, Small ubiquitin-related modifier 1 and P53.
TOP3A
DNA topoisomerase 3-alpha is an enzyme that in humans is encoded by the TOP3A gene.

# Function
This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one another, thus reducing the number of supercoils and altering the topology of DNA. This enzyme forms a complex with BLM which functions in the regulation of recombination in somatic cells.

# Meiosis
Recombination during meiosis is often initiated by a DNA double-strand break (DSB). During recombination, sections of DNA at the 5' ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule then "invades" the DNA of an homologous chromosome that is not broken forming a displacement loop (D-loop). After strand invasion, the further sequence of events may follow either of two main pathways leading to a crossover (CO) or a non-crossover (NCO) recombinant (see Genetic recombination and see Figure).  The pathway leading to a NCO is referred to as Synthesis-dependent strand annealing (SDSA).
In the plant Arabidopsis thaliana, multiple mechanisms limit meiotic COs.  During meiosis TOP3A and RECQ4A/B helicase antagonize formation of COs in parallel to FANCM helicase.  Sequela-Arnaud et al.  suggested that CO numbers are restricted because of the long-term costs of CO recombination, that is, the breaking up of favorable genetic combinations of alleles built up by past natural selection.
In the budding yeast Saccharomyces cerevisiae, the topoisomerase III (TOP3)-RMI1 heterodimer (that catalyzes DNA single-strand passage) forms a conserved complex with Sgs1 helicase (an ortholog of the human Bloom syndrome helicase). This complex promotes early formation of NCO recombinants during meiosis  The TOP3-RMI1 strand passage activity appears to have two important functions during meiosis.  First, strand passage activity is employed early in coordination with Sgs1 helicase to promote proper recombination pathway choice.  Second, strand passage activity is used later, independently of Sgs1 helicase, to prevent the persistence of unresolvable strand entanglements in recombination intermediates.

# Interactions
TOP3A has been shown to interact with Bloom syndrome protein.
TPCN1
Two pore segment channel 1 (TPC1) is a human protein encoded by the TPCN1 gene.  The protein encoded by this gene is an ion channel.  In contrast to other calcium and sodium channels which have four homologous domains, each containing 6 transmembrane segments (S1 to S6), TPCN1 only contains two domains (each containing segments S1 to S6).

# Structure
The structure of a TPC1 ortholog from Arabidopsis thaliana has been solved by two laboratories. The structures were solved using X-ray crystallography and contained the fold of a voltage-gated ion channel and EF hands. Only a single voltage sensor domain appears to responsible for voltage sensing.

# Filoviral Infections
Genetic knockout and pharmacological inhibition experiments demonstrate that Two-pore Channels, TPC1 and TPC2, are required for infection by Filoviruses Ebola and Marburg in mice.
TPCN2
Two pore segment channel 2 (TPC2) is a human protein encoded by the TPCN2 is a protein which in humans is encoded by the TPCN2 gene.  TPC2 is an ion channel, however, in contrast to other calcium and sodium channels which have four homologous domains, each containing 6 transmembrane segments (S1 to S6), TPCN1 only contains two domain (each containing segments S1 to S6).

# Structure
TPC2 is homologous to TPC1, the best characterized member of the TPC family. The structure of a TPC1 ortholog from Arabidopsis thaliana has been solved by two laboratories. The structures were solved using X-ray crystallography and contained the fold of a voltage-gated ion channel and EF hands.

# Filoviral Infections
Genetic knockout and pharmacological inhibition experiments demonstrate that Two-pore Channels, TPC1 and TPC2, are required for infection by Filoviruses Ebola and Marburg in mice.
TRAF2
TNF receptor-associated factor 2 is a protein that in humans is encoded by the TRAF2 gene.

# Function
The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from members of the TNF receptor superfamily. This protein directly interacts with TNF receptors, and forms complexes with other TRAF proteins. TRAF2 is required for TNF-alpha-mediated activation of MAPK8/JNK and NF-B. The protein complex formed by TRAF2 and TRAF1 interacts with the IAP family members cIAP1 and cIAP2, and functions as a mediator of the anti-apoptotic signals from TNF receptors. The interaction of this protein with TRADD, a TNF receptor associated apoptotic signal transducer, ensures the recruitment of IAPs for the direct inhibition of caspase activation. cIAP1 can ubiquitinate and induce the degradation of this protein, and thus potentiate TNF-induced apoptosis. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of only one transcript has been determined.

# Interactions
TRAF2 has been shown to interact with:
- ASK1,
- BCL10,
- BIRC2,
- Baculoviral IAP repeat-containing protein 3,
- CASP8AP2,
- CD134,
- CD137,
- CD27,
- CD40,
- CFLAR,
- CHUK,
- Caveolin 1,
- EDARADD,
- HIVEP3,
- IKK2,
- Low affinity nerve growth factor receptor,
- MAP3K14,
- MAP3K1
- MAP3K7IP2,
- MAP4K2,
- MAP4K5,
- RANK,
- RIPK1,
- SPHK1,
- TANK,
- TANK-binding kinase 1,
- TNFAIP3,
- TNFRSF13B,
- TNFRSF14,
- TNFRSF1A,
- TNFRSF1B,
- TNFSF14,
- TRADD,
- TRAF interacting protein,
- TRAF1,  and
- UBE2N.

# Model organisms
Model organisms have been used in the study of TRAF2 function. A conditional knockout mouse line called Traf2tm1a(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
TRAF4
TNF receptor-associated factor 4 (TRAF4) also known as RING finger protein 83 (RNF83) is a protein that in humans is encoded by the TRAF4 gene.
TRAF4 is a member of the TNF receptor associated factor (TRAF) family, a family of scaffold proteins. TRAF proteins connect IL-1R/Toll and TNF receptors with signaling factors that lead to the activation of NF-B and mitogen-activated protein kinases. However, TRAF4 is not known to interact with TNF receptors and its cellular functions are not well understood.

# Protein interactions
TRAF4 has been shown to interact with neurotrophin receptor, p75 (NTR/NTSR1), and negatively regulate NTR induced cell death and NF-kappa B activation. This protein has been found to bind to p47phox, a cytosolic regulatory factor included in a multi-protein complex known as NAD(P)H oxidase. This protein thus, is thought to be involved in the oxidative activation of MAPK8/JNK. Alternatively spliced transcript variants have been observed but the full-length nature of only one has been determined.
A recent report indicates that TRAF4 binds to NOD-Like Receptors NOD1 and NOD2, and specifically inhibits activation of NF-B by the activated NOD2-RIP2 complex