Persius/hicric huggingface dataset:
TOMM40
Translocase of outer mitochondrial membrane 40 homolog (yeast), also known as TOMM40, is a protein which in humans is encoded by the TOMM40 gene.

# Function
TOMM40 codes for a protein that is embedded into outer membranes of mitochondria and is required for the movement of proteins into mitochondria. More precisely, TOMM40 is the channel-forming subunit of a translocase of the mitochondrial outer membrane (TOM) that is essential for protein transport into mitochondria.

# Clinical significance
In humans, certain alleles of this gene have been statistically associated with an increased risk of developing late-onset Alzheimer's Disease. One study has found that TOMM40 risk alleles appears twice as often in people with Alzheimer's disease than those without it.  Because  TOMM40 is located on chromosome 19, and is closely adjacent to APOE, another gene known to be associated with Alzheimer's, another study has suggested that the statistically significant correlation of TOMM40 with Alzheimer's is due to linkage disequilibrium.
TOPBP1
DNA topoisomerase 2-binding protein 1 is an enzyme that in humans is encoded by the TOPBP1 gene.

# Function
This gene encodes a binding protein which interacts with the C-terminal region of topoisomerase II beta. This interaction suggests a supportive role for this protein in the catalytic reactions of topoisomerase II beta through transient breakages of DNA strands.

# Meiotic silencing
In mammals, surveillance mechanisms remove meiotic cells in which chromosome synapsis is defective.  One such surveillance mechanism is meiotic silencing, the transcriptional silencing of genes on asynapsed chromosomes. TOPBP1, a DNA damage response protein, has a crucial role in meiotic sex chromosome silencing.

# Interactions
TOPBP1 has been shown to interact with:
- E2F1,
- Promyelocytic leukemia protein,
- RAD9A,
- UBR5, and
- ZBTB17

# Clinical relevance
This gene may be involved in the development of ovarian and breast cancer.
Mutations in TOPBP1 cause                 Idiopathic pulmonary arterial hypertension            .
TP53RK
TP53-regulating kinase, also known as PRPK is an enzyme that in humans is encoded by the TP53RK gene. This protein is a serine/threonine protein kinase that phosphorylates p53 at Ser15.
PRPK is part of the KEOPS/EKC complex, which participates in transcription control, telomere regulation  and tRNA modification.

# Model organisms
Model organisms have been used in the study of TP53RK function. A conditional knockout mouse line called Trp53rktm1a(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
TRAFD1
TRAF-type zinc finger domain-containing protein 1 is a protein that in humans is encoded by the TRAFD1 gene.

# Model organisms
Model organisms have been used in the study of TRAFD1 function. A conditional knockout mouse line, called Trafd1tm1a(EUCOMM)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 eight tests were carried out on homozygous mutant mice and two significant abnormalities were observed: abnormal spine curvature and atypical peripheral blood lymphocyte parameters.
TRDMT1
tRNA (cytosine-5-)-methyltransferase is an enzyme that in humans is encoded by the TRDMT1 gene.
CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a protein with similarity to DNA methyltransferases, but this protein does not display methyltransferase activity. The protein strongly binds DNA, suggesting that it may mark specific sequences in the genome. Alternative splicing results in multiple transcript variants encoding different isoforms.
It has been shown that human DNMT2 does not methylate DNA but instead methylates cytosine 38 in the anticodon loop of aspartic acid transfer RNA (tRNA(Asp)).
TRERF1
Transcriptional-regulating factor 1 is a protein that in humans is encoded by the TRERF1 gene.
This gene encodes a zinc-finger transcriptional regulating protein that interacts with CBP/p300 to regulate the human gene CYP11A1.

# Interactions
TRERF1 has been shown to interact with Steroidogenic factor 1, EP300 and CREB-binding protein.
TRIM21
Tripartite motif-containing protein 21 also known as E3 ubiquitin-protein ligase TRIM21 is a protein that in humans is encoded by the TRIM21 gene. Alternatively spliced transcript variants for this gene have been described but the full-length nature of only one has been determined. It is expressed in most human tissues.

# Structure
TRIM21 is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING finger domain, a B-box type 1 and a B-box type 2 zinc finger, and a coiled coil region.

# Function
TRIM21 is an intracellular antibody effector in the intracellular antibody-mediated proteolysis pathway. It recognizes Fc domain and binds to immunoglobulin G as well as immunoglobulin M on antibody marked non-enveloped virions which have infected the cell. Either by autoubiquitination or by ubiquitination of a cofactor, it is then responsible for directing the virions to the proteasome. TRIM21 itself is not degraded in the proteasome unlike both the viral capsid and the bound antibody.
TRIM21 is part of the RoSSA ribonucleoprotein, which includes a single polypeptide and one of four small RNA molecules. The RoSSA particle localizes to both the cytoplasm and the nucleus.

# Clinical significance
RoSSA interacts with autoantigens in patients with Sjogren's syndrome and systemic lupus erythematosus. In addition, the inability for lupus-prone macrophages to degrade immune complexes in the lysosome results in the leakage of autoantibodies into the cytosol that can bind to TRIM21 and enhance NF-B signaling.
TRIM21 can be used to knockout specific proteins with their corresponding antibodies, a method known as Trim-Away. In this assay, TRIM21 and  antibodies are delivered into cells through electroporation, and the targeted protein is degraded within a few minutes.
TRIM22
Tripartite motif-containing 22, also known as TRIM22, is a protein which in humans is encoded by the TRIM22 gene.

# Function
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein localizes to the cytoplasm and its expression is induced by interferon. TRIM22 is also a target gene of the  tumor suppressor protein p53.
TRIM22 possesses E3 ubiquitin ligase activity and is able to ubiquitinate itself with the assistance of the E2 enzyme UbcH5B.  Furthermore, TRIM22 is located in the nucleus and therefore may function as a nuclear E3 ubiquitin ligase.

# Clinical significance
The protein down-regulates transcription from the HIV-1 long terminal repeat promoter region, suggesting that function of this protein may be to mediate interferon's antiviral effects. Other proteins that function to restrict HIV replication include TRIM5alpha and APOBEC3G.
It has been demonstrated that treatment of cells with interferon type I inhibits HIV replication and TRIM22 is strongly up-regulated by interferon treatment.  Furthermore, HIV particle release from cells depleted of TRIM22 with RNA interference is enhanced. TRIM22 appears to prevent the movement of the HIV Gag protein to the plasma membrane and hence TRIM22 can block HIV replication in cell cultures by preventing the assembly of the virus.
TRIM23
GTP-binding protein ARD-1 is a protein that in humans is encoded by the TRIM23 gene.

# Function
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein is also a member of the ADP ribosylation factor family of guanine nucleotide-binding family of proteins. Its carboxy terminus contains an ADP-ribosylation factor domain and a guanine nucleotide binding site, while the amino terminus contains a GTPase activating protein domain which acts on the guanine nucleotide binding site. The protein localizes to lysosomes and the Golgi apparatus. It plays a role in the formation of intracellular transport vesicles, their movement from one compartment to another, and phospholipase D activation. Three alternatively spliced transcript variants for this gene have been described.

# Interactions
TRIM23 has been shown to interact with TRIM31, TRIM29 and PSCD1.
TRIM24
Tripartite motif-containing 24 (TRIM24) also known as transcriptional intermediary factor 1 (TIF1) is a protein that, in humans, is encoded by the TRIM24 gene.

# Function
The protein encoded by this gene mediates transcriptional control by interaction with the activation function 2 (AF2) region of several nuclear receptors, including the estrogen, retinoic acid, and vitamin D3 receptors. The protein localizes to nuclear bodies and is thought to associate with chromatin and heterochromatin-associated factors. The protein is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains  a RING, a B-box type 1 and a B-box type 2  and a coiled-coil region. Two alternatively spliced transcript variants encoding different isoforms have been described for this gene.

# Interactions
TRIM24 has been shown to interact with Mineralocorticoid receptor, TRIM33, Estrogen receptor alpha and Retinoid X receptor alpha.
TRIM25
Tripartite motif-containing protein 25 is a protein that in humans is encoded by the TRIM25 gene.

# Function
The protein encoded by this gene is a member of the tripartite motif (TRIM) family grouping more than 70 TRIMs. TRIM proteins primarily function as ubiquitin ligases that regulate the innate response to infection. TRIM25 localizes to the cytoplasm. The presence of potential DNA-binding and dimerization-transactivation domains suggests that this protein may act as a transcription factor, similar to several other members of the TRIM family. Expression of the gene is upregulated in response to estrogen, and it is thought to mediate estrogen actions in breast cancer as a primary response gene.

# Domain Architecture
TRIM25 has an N-terminal RING domain, followed by a B-box type 1 domain, a B-box type 2 domain, a coiled-coil domain (CCD) and a C-terminal SPRY domain.  The RING domain coordinates two zinc atoms and is essential for recruiting ubiquitin-conjugating enzymes. The function of the B-box domains is unknown. The CCD domain has been implicated in multimerization and other protein-protein interactions. The SPRY domain is required for substrate recruitment.  The NMR chemical shifts for backbone of the PRYSPRY domain of TRIM25 is assigned based on triple-resonance experiments using uniformly isotopic labeled protein and  the secondary structure of the domain PRYSPRY domain of TRIM25 predicted based on the NMR assignments.

# TRIM25 functions
TRIM25 plays a key role in the RIG-I signaling pathway. RIG-I is a cytosolic pattern recognition receptor that senses viral RNA. Following RNA recognition, the caspase recruitment domain (CARD) of RIG-I undergoes K(63)-linked ubiquitination by TRIM25. The RING and SPRY domains of TRIM25 mediate its interaction with RIG-I. IFN production then follows by an intracellular signaling pathway involving IRF3.

# Viral escape
To avoid IFN production, the non structural protein (NS1) of influenza will interact with CCD domain of TRIM25 to block RIG-I ubiquitination. Some studies have shown that a deletion of the CCD domain of TRIM25 prevents the binding of NS1. Without this ubiquitination, there wont be IFN production.
TRIM33
Tripartite motif-containing 33 (TRIM33) also known as transcriptional intermediary factor 1 gamma (TIF1-), is a human gene.
The protein encoded by this gene is thought to be a transcriptional corepressor. However unlike the related TIF1- and TIF1- proteins, few transcription factors such as Smad4 that interact with TIF1- have been identified.

# Structure
The protein is a member of the tripartite motif family. This motif includes three zinc-binding domains:
- RING
- B-box type 1 zinc finger
- B-box type 2 zinc finger
and a coiled-coil region.
Three alternatively spliced transcript variants for this gene have been described, however, the full-length nature of one variant has not been determined.

# Interactions
TRIM33 has been shown to interact with TRIM24.

# Role in cancer
TRIM33 acts as a tumor suppressor gene preventing the development chronic myelomonocytic leukemia.
TRIM33 regulates also the TGF-1 receptor and promotes physiological aging of hematopoietic stem cells.
TRIM33 acts as an oncogene by preventing apoptosis in B-cell leukemias.
TRIM45
tripartite motif containing 45, also known as TRIM45, is a human gene.
This gene encodes a member of the tripartite motif family. The encoded protein may function as a 

# Model organisms
Model organisms have been used in the study of TRIM45 function. A conditional knockout mouse line, called Trim45tm1a(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 six 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; males had increased circulating magnesium levels while animals of both sex displayed increased bone strength.
TRIM63
E3 ubiquitin-protein ligase TRIM63 is an enzyme that in humans is encoded by the TRIM63 gene.
This gene encodes a member of the RING zinc finger protein family found in striated muscle and iris. The product of this gene is localized to the Z-line and M-line lattices of myofibrils, where titin's N-terminal and C-terminal regions respectively bind to the sarcomere. In vitro binding studies have shown that this protein also binds directly to titin near the region of titin containing kinase activity. Another member of this protein family binds to microtubules. Since these family members can form heterodimers, this suggests that these proteins may serve as a link between titin kinase and microtubule-dependent signal pathways in muscle.
The protein encoded by the Trim63 gene is also called MuRF1.  MuRF1 is the name most commonly used in the literature, and it stands for "Muscle RING Finger 1."  Structurally, there are two closely related MuRFs, MuRF2 and MuRF3.  These also have TRIM codes:  MuRF2 is TRIM55; MuRF3 is TRIM54.

# Interactions
Trim63/MuRF1 has been shown to be an E3 ubiquitin ligase.  It's major substrate is Myosin Heavy Chain. MuRF1 is upregulated during skeletal muscle atrophy - and thus the degradation of myosin heavy chain, which is a major component of the sarcomere, is an important mechanism in the breakdown of skeletal muscle under atrophy conditions.  MuRF1 has been shown to be upregulated during denervation, administration of glucocorticods, immobilization, and casting.  All of these treatments cause skeletal muscle atrophy.
TRIM63 has been shown to interact with Titin, GMEB1 and SUMO2.
TRIP11
Thyroid receptor-interacting protein 11 is a protein that in humans is encoded by the TRIP11 gene.

# Function
TRIP11 was first identified through its ability to interact functionally with thyroid hormone receptor-beta (THRB; MIM 190160). It has also been found in association with the Golgi apparatus and microtubules.

# Interactions
TRIP11 has been shown to interact with Retinoblastoma protein and Thyroid hormone receptor alpha.
TSG101
Tumor susceptibility gene 101, also known as TSG101, is a human gene that encodes for a cellular protein of the same name.

# Function
The protein encoded by this gene belongs to a group of apparently inactive homologs of ubiquitin-conjugating enzymes. The gene product contains a coiled-coil domain that interacts with stathmin, a cytosolic phosphoprotein implicated in tumorigenesis. The protein may play a role in cell growth and differentiation and act as a negative growth regulator. In vitro steady-state expression of this tumor susceptibility gene appears to be important for maintenance of genomic stability and cell cycle regulation. Mutations and alternative splicing in this gene occur in high frequency in breast cancer and suggest that defects occur during breast cancer tumorigenesis and/or progression.
The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV protein domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions.

# HIV
TSG101 seems to play an important role in the pathogenesis of HIV.  In uninfected cells, TSG101 functions in the biogenesis of the multivesicular body (MVB), which suggests that HIV may bind TSG101 in order to gain access to the downstream machinery that catalyzes MVB vesicle budding.

# Interactions
TSG101 has been shown to interact with:
- EP300,
- HGS,
- LRSAM1,
- P21,
- P53,  and
- VPS28.

# Orthologue, Vps23
In humans, the orthologue of vps23 which has a component of ESCRT-1 is called Tsg101. Mutations in Tsg-101 have been linked to cervical, breast, prostate and gastrointestinal cancers. In molecular biology, vps23 (vacuolar protein sorting) is a protein domain. Vps proteins are components of the ESCRTs (endosomal sorting complexes required for transport) which are required for protein sorting at the early endosome. More specifically, vps23 is a component of ESCRT-I. The ESCRT complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis and  budding of HIV.

# Structure
Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues.
TSPAN4
Tetraspanin-4 is a protein that in humans is encoded by the TSPAN4 gene.
The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein and is similar in sequence to its family member CD53 antigen. It is known to complex with integrins and other transmembrane 4 superfamily proteins. Alternatively spliced transcript variants encoding different isoforms have been identified.

# Interactions
TSPAN4 has been shown to interact with CD9, ITGA6, CD29, CD49c and CD81.
TSPAN8
Tetraspanin-8 is a protein that in humans is encoded by the TSPAN8 gene.

# Function
The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. This gene is expressed in different carcinomas. The use of alternate polyadenylation sites has been found for this gene.

# Clinical significance
Overall survival of breast cancer patients was effectively predicted by TSPAN8.
TUC338
TUC338 (transcribed ultra-conserved region 338) is an ultra-conserved element which is transcribed to give a non-coding RNA. The TUC338 gene was first identified as uc.338, along with 480 other ultra-conserved elements in the human genome. Expression of this RNA gene has been found to dramatically increase in hepatocellular carcinoma (HCC) cells.
The TUC338 RNA gene is 590 base-pairs long, and partially overlaps the gene encoding Poly(rC)-binding protein 2 (PCBP2), a protein involved in mRNA processing. Despite this overlap, PCBP2 and TUC388 were found to be independently expressed.
TUC338 is predicted to function in cell growth, possibly at the interface between G1 phase and S phase, and could potentially present a therapeutic target to treat HCC cells. Experimental evidence shows knocking out TUC338 using siRNA reduced the growth rate of both mouse and human HCC cells.
Tai Ji
Taiji () is a state of being from Tao and Wuji. It is a state of absolute, and of infinite potentiality.  In Tao Te Ching, Tao manifested as One, which is Taiji.  In a Taoist guidance book, the same verse was amplified as out of Tao came Taiji, which then split into yin and yang or Two Aspects, yin and yang slitting into the Four Realms, Wu xing the Five Elements, and from there the world was created.
Taiji was a state in which the world became intelligible before creation. Taiji may be equated to the One, Oneness, Unity, as in attaining One or Unity ()  and as stated in the Tao Te Ching.

# Core concept
Translated as "the great ultimate," the Taiji is understood to be the ideal of existence. Yin and yang represent the contrasting qualities within reality and experience. For example, light contrasts with darkness, providing them both with context and therefore meaning. Taiji is not perceived as a simple list of all things and potential things, but rather a complex interconnection of all things in all possible contexts. This concept is often used to illustrate the doctrine of cosmological unity. It is also used to explain the creation of the "myriad things" (i.e., everything in existence) through the dialectical process of alternating polarity between yin and yang. Western proponents of Taoism sometimes conflate Taiji and the "myriad things," but Taiji is not only representative of what exists, but also that which has existed, will exist, and could potentially exist.

# Taiji in historical China
The concept of Taiji was introduced in the Zhuang Zi, showing its early place in Taoism. It also appears in the Xi Ci (Great Appendix) of the I Ching, a fundamental Taoist classic.
When Confucianism came to the fore again during the Song Dynasty as Neo-Confucianism, it synthesized aspects of Chinese Buddhism and Taoism, and drew them together using threads that traced back to the metaphysical discussions in the Book of Changes.

# See Also
- Taegeuk
- Tomoe
- Wuji
- Xiuzhen

# Notes
-  Tao te Ching Chapter 42 : 
-  Tiantang Yiuchi Chapter 4 :  (Wuji)  (Taiji), (two aspects)  (yin and yang), (Four Realms) (Wu xing)......
-  Robinet (1981), p. 16.
-  Tao Te Ching Chapter 39 : 
-  Chen, Ellen M. (1989). The Tao Te Ching: A New Translation and Commentary. St. Paul Minnesota: Paragon House.

# Reference
- Robinet, Isabelle. Taoism: Growth of a Religion (Stanford: Stanford University Press, 1997 ) page 103. ISBN 0-8047-2839-9.