Persius/hicric huggingface dataset:
Shq1
Shq1p is a protein involved in the rRNA processing pathway.  It was discovered by Pok Yang in the Chanfreau labratory at UCLA.  Depletion of Shq1p has led to decreased level of various H/ACA box snoRNAs (H/ACA box snoRNAs are responsible for pseuduridylation of pre-rRNA) and certain pre-rRNA intermediates.

# Background
During the synthesis of eukaryotic ribosomes, four mature ribosomal RNAs (the 5S, 5.8S, 18S, and 25S) must be synthesized.  Three of these rRNAs (5.8S, 18S, and 25S) come from a single pre-rRNA known as the 35S.  Although many of the intermediates in this rRNA processing pathway have been identified in the last thirty years, there are still a number of proteins involved in this process whose specific function is unknown.
Shq1p, a protein thought to play a role in the stablization and/or production of box H/ACA snoRNA, is still uncharacterized.  It has been proposed that Shq1p, along with Naf1p, is involved in the initial steps of the biogenesis of H/ACA box snoRNPs (box H/ACA snoRNAs form complexes with proteins, thereby forming snoRNPs) because of its association with certain snoRNP proteins during the snoRNPs maturation, while showing very little association with the mature snoRNP.  Despite the known involvement of Shq1p with the H/ACA box snoRNP's production, the exact function of this protein in the overall rRNA processing pathway is still unknown.
Suet
Suet (/su.t/) is  raw beef or mutton fat, especially the hard fat found around the loins and kidneys.
Suet has a melting point of between 45 and 50C. (113 and 122F.), and congeals between 37 and 40C. (98.6 and 104F.).

# Uses
The primary use of suet is to make tallow, although it is also used as an ingredient in cooking. Suet is made into tallow in a process called rendering, which involves melting and extended simmering, followed by straining, cooling and usually a repetition of the entire process.
Unlike suet, tallow can be stored for extended periods without refrigeration. Tallow is used to make soap, for cooking (fried foods especially), as a bird food, and was once used for making candles.
Suet is essential to use in making the pastry for steamed steak and kidney pudding. The suet crust pastry lines a pudding bowl, the meat added and a lid of suet crust pastry tightly seals the meat. The pudding is then steamed for approximately four hours before serving in the bowl on the table. Suet pastry is soft in contrast to the crispness of shortcrust pastry. Its low melting point means that it is solid at room temperature but easily melts at moderate temperatures, such as in steaming.
Suet should not be confused with Beef Dripping, which is the collected fat and juices from the roasting pan when cooking roast beef and is not rendered.

# Availability
As it is the fat from around the kidneys, the connective tissue, blood and other non-fat items must be removed. It then needs to be coarsely grated to make it ready to use. It must be kept refrigerated prior to use and used within a few days of purchase like any meat.
Packaged suet sold in supermarkets is dehydrated suet. It is mixed with flour to make it stable at room temperature. Because of the addition of flour, some care is needed when using it for older recipes using fresh suet as the proportions of flour to fat can alter. Most modern recipes would stipulate packaged suet.
A vegetarian suet substitute is available in supermarkets in the United Kingdom that is made from fat such as palm oil combined with rice flour. It resembles shredded beef suet, and is used as a substitute in recipes, but with slightly different results from animal suet.
Woodpeckers, goldfinches, juncos, cardinals, thrushes, jays, kinglets, bluebirds, wrens, and starlings are all known to favour suet-based bird feeders.

# Suet recipes
- Haggis
- Windsor pudding
- Steak and kidney pudding
- Dumplings
- Suet Crust Pastry
- Christmas pudding
- Suet Cakes (for birdfeeding)
- Mincemeat
- Spotted dick
- Kishka/Kishke
- Chili con carne
- Rag Pudding
TAC1
Preprotachykinin-1, (abbreviated PPT-1, PPT-I, or PPT-A), is a precursor protein that in humans is encoded by the TAC1 gene.

# Isoforms and derivatives
The protein has four isoformsalpha-, beta-, gamma-, and delta-PPTwhich can variably undergo post-translational modification to produce neurokinin A (formerly known as substance K) and substance P. Alpha- and delta-PPT can only be modified to substance P, whereas beta- and gamma-PPT can produce both substance P and neurokinin A.
Neurokinin A can also be further modified to produce neuropeptide K (also known as neurokinin K) and neuropeptide gamma.
These hormones are thought to function as neurotransmitters which interact with nerve receptors and smooth muscle cells. They are known to induce behavioral responses and function as vasodilators and secretagogues.  Alternative splicing of exons 4 and/or 6 produces four known products of undetermined significance.

# Human basal ganglia
The nature and distribution of PPT-1 has been studied in the human basal ganglia. The protein is expressed evenly throughout the caudate and putamen, and 80 to 85% of it exists in the beta-PPT isoform. 15-20% of the protein is in the gamma-PPT isoform, while no alpha-PPT was detected at all.

# Species comparison
In humans, beta-PPT is the dominant isoform in the brain, which contrasts with rats (predominantly gamma-PPT) and cows (alpha-PPT).
While both human and rat PPT-1 produce substance P and neurokinin A, humans produce more neuropeptide K, whereas rats produce more neuropeptide gamma. In cow brains, PPT-1 primarily encodes substance P, but not other neurokinin A-derived peptides.
TAF1
Transcription initiation factor TFIID subunit 1, also known as transcription initiation factor TFIID 250 kDa subunit (TAFII-250) or TBP-associated factor 250 kDa (p250), is a protein that in humans is encoded by the TAF1 gene.

# Function
Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is the basal transcription factor TFIID, which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes the largest subunit of TFIID. This subunit binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. This subunit contains two independent protein kinase domains at the N and C-terminals, but also possesses acetyltransferase activity and can act as a ubiquitin-activating/conjugating enzyme. Two transcripts encoding different isoforms have been identified for this gene.
Histones are often acetylated to open DNA for transcription. TAF1 contains two bromodomains, which each can bind one of two acetyllysine residues at position 5 and 12 in the H4 tail, to stabilize the TBP-TATA box complex.

# Clinical significance
A mutation in TAF1 was identified that contributes to a phenotype with severe intellectual disability (ID), a characteristic intergluteal crease, and distinctive facial features, including a broad, upturned nose, sagging cheeks, downward sloping palpebral fissures, prominent periorbital ridges, deep-set eyes, relative hypertelorism, thin upper lip, a high-arched palate, prominent ears with thickened helices, and a pointed chin This is a non-synonymous change in TAF1 that results in an isoleucine (hydrophobic) to threonine (polar) change on the 1337th amino acid residue in the protein (NP_001273003.1). Two other mutations were reported in TAF1 in two families with intellectual disability, although further clinical details were not reported.

# Interactions
TAF1 has been shown to interact with:
- CSNK2A1,
- CCND1,
- GTF2F1,
- RB1,
- TAF7,
- TBP,  and
- UBTF.
TAF4
Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.

# Function
Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the larger subunits of TFIID that has been shown to potentiate transcriptional activation by retinoic acid, thyroid hormone and vitamin D3 receptors. In addition, this subunit interacts with the transcription factor CREB, which has a glutamine-rich activation domain, and binds to other proteins containing glutamine-rich regions. Aberrant binding to this subunit by proteins with expanded polyglutamine regions has been suggested as one of the pathogenetic mechanisms underlying a group of neurodegenerative disorders referred to as polyglutamine diseases.

# Interactions
TAF4 has been shown to interact with:
- CBX5m
- TATA binding protein,  and
- Transcription initiation protein SPT3 homolog.

# Protein domain
Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4.
TAF7
Transcription initiation factor TFIID subunit 7 also known as TAFII55 is a protein that in humans is encoded by the TAF7 gene.

# Function
The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II.
The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown but studies have shown that it interacts with the C-jun pathway. The conserved region is situated towards the N-terminal of the protein. This entry talks about the N-terminal domain.
Crystallographic studies have revealed a very significant hydrophobic pocket between TAF7 and TAF1, its main binding partner. Due to the incredible hydrophobicity of this interaction, its unlikely that TAF1 would be able to fold properly without the presence of TAF7. Thus, it is possible that TAF7 is required for proper production of TAF1

# Interactions
TAF7 has been shown to interact with:
- TAF15,
- TAF1,  and
- TATA binding protein.
TAF9
TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, also known as TAF9, is a protein that in humans is encoded by the TAF9 gene.

# Function
Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein complex that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the smaller subunits of TFIID that binds to the basal transcription factor GTF2B as well as to several transcriptional activators such as p53 and VP16. A similar but distinct gene (TAF9B) has been found on the X chromosome and a pseudogene has been identified on chromosome 19. Alternative splicing results in multiple transcript variants encoding different isoforms.

# Structure
The 17-amino-acid-long trans-activating domains (TAD) of several transcription factors were reported to bind directly to TAF9: p53, VP16, HSF1, NF-IL6, NFAT1, NF-B, and ALL1/MLL1. Inside of these 17 amino acids, a unique Nine-amino-acid transactivation domain (9aaTAD) was identified for each reported transcription factor. 9aaTAD is a novel domain common to a large superfamily of eukaryotic transcription factors represented by Gal4, Oaf1, Leu3, Rtg3, Pho4, Gln4, Gcn4 in yeast and by p53, NFAT, NF-B and VP16 in mammals. TAF9 is supposed to be a universal transactivation cofactor for 9aaTAD transcription factors.

# Interactions
TAF9 has been shown to interact with:
- GCN5L2,
- Myc,
- SF3B3,
- SUPT7L,
- TADA3L,
- TAF5,
- TAF6L,
- TAF10,
- TAF12,
- TAF5L,
- TATA binding protein,
- Transcription initiation protein SPT3 homolog,  and
- Transformation/transcription domain-associated protein.
TAL2
T-cell acute lymphocytic leukemia 2, also known as TAL2, is a protein which in humans is encoded by the TAL2 gene.

# Function
TAL2 is a member of the basic helix-loop-helix family of transcription factors.

# Clinical significance
Tumor-specific alterations of the TAL2 gene occurs in some patients with T-cell acute lymphoblastic leukemia (T-ALL).
TBCE
Tubulin-specific chaperone E is a protein that in humans is encoded by the TBCE gene.
Cofactor E is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. Two transcript variants encoding the same protein have been found for this gene.
The TBCE gene is either deleted or mutated in Sanjad-Sakati Syndrome
TBX1
T-box transcription factor TBX1 also known as T-box protein 1 and testis-specific T-box protein is a protein that in humans is encoded by the TBX1 gene. Genes in the T-box family are transcription factors that play important roles in the formation of tissues and organs during embryonic development. To carry out these roles, proteins made by this gene family bind to specific areas of DNA called T-box binding element (TBE) to control the expression of target genes.

# Gene
The TBX1 gene is located on the long (q) arm of chromosome 22 at position 11.21, from base pair 18,118,779 to base pair 18,145,669.

# Function
The T-box 1 protein appears to be necessary for the normal development of large arteries that carry blood out of the heart, muscles and bones of the face and neck, and glands such as the thymus and parathyroid. Although the T-box 1 protein acts as a transcription factor, it is not yet known which genes are regulated by the protein.

# Clinical significance
Most cases of 22q11.2 deletion syndrome are caused by the deletion of a small piece of chromosome 22. This region of the chromosome contains about 30 genes, including the TBX1 gene. In a small number of affected individuals without a chromosome 22 deletion, mutations in the TBX1 gene are thought to be responsible for the characteristic signs and symptoms of the syndrome. Of the three known mutations, two mutations change one amino acid (a building block of proteins) in the T-box 1 protein. The third mutation deletes a single amino acid from the protein. These mutations likely disrupt the ability of the T-box 1 protein to bind to DNA and regulate the activity of other genes.
Loss of the TBX1 gene, due to either a mutation in the gene or a deletion of part of chromosome 22, is responsible for many of the features of 22q11.2 deletion syndrome. Specifically, a loss of the TBX1 gene is associated with heart defects, an opening in the roof of the mouth (a cleft palate), distinctive facial features, and low calcium levels, but does not appear to cause learning disabilities.
TBX6
T-box 6 is a protein that in humans is encoded by the TBX6 gene.

# Function
This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures.
Tbx6 is also required for the segmentation of the paraxial mesoderm into somites, and for the normal development of the dermomyotome in zebrafish. In the absence of Tbx6, the central dermomyotome of zebrafish fails to develop.
Tbx6 functions in a gene regulatory network with mesp-b and ripply1.
TCF3
Transcription factor 3 (E2A immunoglobulin enhancer-binding factors E12/E47), also known as TCF3, is a protein that in humans is encoded by the TCF3 gene. TCF3 has been shown to directly enhance Hes1 (a well-known target of Notch signaling) expression.

# Function
This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. The 9aaTAD transactivation domains of E proteins and MLL are very similar and both bind to the KIX domain of general transcriptional mediator CBP.  E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development.
9aaTADs in the E protein family
E2A and MLL binding to the KIX domain of CBP
This gene regulates many developmental patterning processes such as lymphocyte and central nervous system (CNS) development. E proteins are involved in the development of lymphocytes. They initiate transcription by binding to regulatory E-box sequences on target genes.

# Clinical significance
Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1 and t(17;19), with HLF), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384).

# Interactions
TCF3 has been shown to interact with:
- CBFA2T3,
- CREBBP,
- ELK3,
- EP300,
- ID3,
- LDB1,
- LMX1A,
- LYL1,
- MAPKAPK3,
- MyoD,
- Myogenin,
- PCAF,
- TAL1
- TWIST1,  and
- UBE2I.
TCF4
Transcription factor 4 (TCF-4) also known as immunoglobulin transcription factor 2  (ITF-2) is a protein that in humans is encoded by the TCF4 gene located on chromosome 18q21.2.

# Function
TCF4 proteins act as transcription factors which will bind to the immunoglobulin enhancer mu-E5/kappa-E2 motif. TCF4 activates transcription by binding to the E-box (5-CANNTG-3) found usually on SSTR2-INR, or somatostatin receptor 2 initiator element. TCF4 is primarily involved in neurological development of the fetus during pregnancy by initiating neural differentiation by binding to DNA. It is found in the central nervous system, somites, and gonadal ridge during early development. Later in development it will be found in the thyroid, thymus, and kidneys while in adulthood TCF4 it is found in lymphocytes, muscles, and gastrointestinal system.

# Clinical significance
Mutations in TCF4 cause Pitt-Hopkins Syndrome (PTHS). These mutations cause TCF4 proteins to not bind to DNA properly and control the differentiation of the nervous system. In most cases that have been studied, the mutations were de novo, meaning it was a new mutation not found in other family members of the patient. Common symptoms of Pitt-Hopkins Syndrome include a wide mouth, gastrointestinal problems, developmental delay of fine motor skills, speech and breathing problems, epilepsy, and other brain defects.
TDP1
Tyrosyl-DNA phosphodiesterase 1 is an enzyme that in humans is encoded by the TDP1 gene.
The protein encoded by this gene is involved in repairing stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of the phosphodiester bond between the tyrosine residue of Type I topoisomerase and the 3-prime phosphate of DNA. This protein may also remove glycolate from single-stranded DNA containing 3-prime phosphoglycolate, suggesting a role in repair of free-radical mediated DNA double-strand breaks.
This gene is a member of the phospholipase D family and contains two PLD phosphodiesterase domains. Mutations in this gene are associated with the disease spinocerebellar ataxia with axonal neuropathy (SCAN1). While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same isoform.
TECR
Trans-2,3-enoyl-CoA reductase is an enzyme that in humans is encoded by the TECR gene.
This gene encodes a multi-pass membrane protein that resides in the endoplasmic reticulum, and belongs to the steroid 5-alpha reductase family. The elongation of microsomal long and very long chain fatty acid consists of 4 sequential reactions. This protein catalyzes the final step, reducing trans-2,3-enoyl-CoA to saturated acyl-CoA. Alternatively spliced transcript variants have been found for this gene.

# Clinical relevance
Mutations in this gene have been shown to cause non-syndromic mental retardation.
TFAM
Mitochondrial transcription factor A, abbreviated as TFAM or mtTFA, is a protein that in humans is encoded by the TFAM gene.

# Function
This gene encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM binds mitochondrial promoter DNA to aid transcription of the mitochondrial genome. Studies in mice have demonstrated that this gene product is required to regulate the mitochondrial genome copy number and is essential for embryonic development. A mouse model for Kearns-Sayre syndrome was produced when expression of this gene was eliminated by targeted disruption in heart and muscle cells.
TFAM is a double box High-mobility group DNA-binding and bending protein.

# Interactions
TFAM has been shown to interact with TFB1M.
TFE3
Transcription factor E3 is a protein that in humans is encoded by the TFE3 gene.

# Function
TFE3, a member of the helix-loop-helix family of transcription factors, binds to the mu-E3 motif of the immunoglobulin heavy-chain enhancer and is expressed in many cell types (Henthorn et al., 1991).

# Interactions
TFE3 has been shown to interact with:
- E2F3,
- Microphthalmia-associated transcription factor, and
- Mothers against decapentaplegic homolog 3

# Translocations
A proportion of renal carcinomas  (RCC) that occur in young patients are associated with translocations involving the TFE3 gene at chromosome Xp11.2 PRCC