Persius/hicric huggingface dataset:
CD45
In immunology, the CD45 antigen (CD stands for cluster of differentiation) is a protein which was originally called leukocyte common antigen.
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus belongs to receptor type PTP. This gene is specifically expressed in hematopoietic cells. This PTP has been shown to be an essential regulator of T- and B-cell antigen receptor signaling. It functions through either direct interaction with components of the antigen receptor complexes, or by activating various Src family kinases required for the antigen receptor signaling. This PTP also suppresses JAK kinases, and thus functions as a regulator of cytokine receptor signaling. Four alternatively spliced transcripts variants of this gene, which encode distinct isoforms, have been reported.
It is a type I transmembrane protein which is in various forms present on all differentiated hematopoietic cells except erythrocytes and plasma cells that assists in the activation of those cells (a form of co-stimulation).
It is expressed in lymphomas, B-cell chronic lymphocytic leukemia, hairy cell leukemia, and acute nonlymphocytic leukemia.
The CD45 family consists of multiple members that are all products of a single complex gene. This gene contains 34 exons and three exons of the primary transcripts are alternatively spliced to generate up to eight different mature mRNAs and after translation eight different protein products. This three exons generate the RA, RB and RC isoforms.
Various isoforms of CD45 exist:
CD45RA, CD45RB, CD45RC, CD45RAB, CD45RAC, CD45RBC, CD45RO, CD45R (ABC).
CD45 is also highly glycosylated. CD45R is the longest protein and migrates at 200 kDa when isolated from T cells. B cells also express CD45R with heavier glycosylation, bringing the molecular weight to 220 kDa, hence the name B220; B cell isoform of 220 kDa. B220 expression is not restricted to B cells and can also be expressed on activated T cells, on a subset of dendritic cells and other antigen presenting cells.
Naive T lymphocytes express large CD45 isoforms and are usually positive for CD45RA. Activated and memory T lymphocytes express the shortest CD45 isoform, CD45RO, which lacks RA, RB and RC exons. This shortest isoform facilitates T cell activation.
The cytoplasmic domain of CD45 is one of the largest known and it has an intrinsic phosphatase activity that removes an inhibitory phosphate group on a tyrosine kinase called Lck (in T cells) or Syk (in B cells) and activates it.
BAG1
BAG family molecular chaperone regulator 1 is a protein that in humans is encoded by the BAG1 gene.

# Function
The oncogene BCL2 is a membrane protein that blocks a step in a pathway leading to apoptosis or programmed cell death. The protein encoded by this gene binds to BCL2 and is referred to as BCL2-associated athanogene. It enhances the anti-apoptotic effects of BCL2 and represents a link between growth factor receptors and anti-apoptotic mechanisms. At least three protein isoforms are encoded by this mRNA through the use of alternative translation initiation sites, including a non-AUG site.

# Clinical significance
BAG gene has been implicated in age related neurodegenerative diseases as Alzheimer's.  It has been demonstrated that BAG1 and BAG 3 regulate the proteasomal and lysosomal protein elimination pathways, respectively.

# Interactions
BAG1 has been shown to interact with:
- Androgen receptor,
- C-Raf,
- Calcitriol receptor,
- Glucocorticoid receptor,
- HSPA8,
- HBEGF,
- PPP1R15A,
- NR1B1,  and
- SIAH1.
BAG3
BAG family molecular chaperone regulator 3 is a protein that in humans is encoded by the BAG3 gene. BAG3 is involved in chaperone-assisted selective autophagy.

# Function
BAG proteins compete with Hip-1 for binding to the Hsc70/Hsp70 ATPase domain and promote substrate release. All the BAG proteins have an approximately 45-amino acid BAG domain near the C terminus but differ markedly in their N-terminal regions. The protein encoded by this gene contains a WW domain in the N-terminal region and a BAG domain in the C-terminal region. The BAG domains of BAG1, BAG2, and BAG3 interact specifically with the Hsc70 ATPase domain in vitro and in mammalian cells. All 3 proteins bind with high affinity to the ATPase domain of Hsc70 and inhibit its chaperone activity in a Hip-repressible manner.

# Clinical significance
BAG gene has been implicated in age related neurodegenerative diseases such as Alzheimer's. It has been demonstrated that BAG1 and BAG 3 regulate the proteasomal and lysosomal protein elimination pathways, respectively. It has also been shown to be a cause of familial dilated cardiomyopathy.
That BAG3 mutations are responsible for familial dilated cardiomyopathy is confirmed by another study describing 6 new molecular variants (2 missense and 4 premature Stops
). Moreover, the same publication reported that BAG3 polymorphisms are also associated with sporadic forms of the disease together with HSPB7 locus.
In muscle cells, BAG3 cooperates with the molecular chaperones Hsc70 and HspB8 to induce the degradation of mechanically damaged cytoskeleton components in lysosomes. This process is called chaperone-assisted selective autophagy and is essential for maintaining muscle activity in flies, mice and men.
BAG3 is able to stimulate the expression of cytoskeleton proteins in response to mechanical tension by activating the transcription regulators YAP1 and WWTR1. BAG3 balances protein synthesis and protein degradation under mechanical stress.

# Interactions
PLCG1 has been shown to interact with:
- FGFR1,
- CD117,
- CD31,
- Cbl gene
- CISH
- Epidermal growth factor receptor,
- Eukaryotic translation elongation factor 1 alpha 1,
- FLT1,
- GAB1,
- GIT1,
- Grb2,
- HER2/neu,
- IRS2,
- ITK,
- KHDRBS1,
- Linker of activated T cells,
- Lymphocyte cytosolic protein 2,
- PDGFRA,
- PLD2,
- RHOA,
- SOS1,
- TUB,
- TrkA,
- TrkB,
- VAV1,  and
- Wiskott-Aldrich syndrome protein.
BBS1
Bardet-Biedl syndrome 1 protein is a protein that in humans is encoded by the BBS1 gene.
BBS1 is part of the BBSome complex, which required for ciliogenesis. 
Mutations in this gene have been observed in patients with the major form (type 1) of Bardet-Biedl syndrome.

# History
As of  2008, research results indicated that the encoded protein may play a role in eye, limb, cardiac and reproductive system development.
BCL3
B-cell lymphoma 3-encoded protein is a protein that in humans is encoded by the BCL3 gene.
This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional coactivator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B.
Like BCL2, BCL5, BCL6, BCL7A, BCL9, and BCL10, it has clinical significance in lymphoma.

# Interactions
BCL3 has been shown to interact with:
- BARD1,
- C-Fos,
- C-jun,
- C22orf25,
- COPS5,
- EP300,
- HTATIP,
- NFKB1,
- NFKB2,
- PIR,  and
- NR2B1.
BCL6
B-cell lymphoma 6 protein is a protein that in humans is encoded by the BCL6 gene. Like BCL2, BCL3, BCL5, BCL7A, BCL9 and BCL10, it has clinical significance in lymphoma.

# Function
The protein encoded by this gene is an evolutionarily conserved zinc finger transcription factor and contains an N-terminal POZ/BTB domain. This protein acts as a sequence-specific repressor of transcription and has been shown to modulate the STAT-dependent Interleukin 4 (IL-4) responses of B cells. This protein can interact with several corepressor complexes to inhibit transcription. This gene is found to be frequently translocated and hypermutated in diffuse large B cell lymphoma (DLBCL) and contributes to the pathogenesis of DLBCL. An exon 7 skipping splice variant encodes a shorter form of the protein which lacks the first two zinc fingers of the DNA binding domain.
Physiologically, BCL6 is a master transcription factor which leads the differentiation of naive helper T cells in Follicular Helper T cells (TFH cells). Its action is negatively regulated by the gene PRDM1 encoding the transcription factor Blimp-1.

# Diagnostic utility
The presence of BCL6 can be demonstrated in tissue sections using immunohistochemistry. It is exclusively present in the B-cells of both healthy and neoplastic germinal centres. It therefore demonstrates both reactive hyperplasia in lymph nodes and a range of lymphomas derived from follicular B-cells, such as Burkitt's lymphoma, follicular lymphoma and the nodular lymphocyte predominant subtype of Hodgkin's disease. It is often used together with antibodies to Bcl-2 antigen to distinguish neoplastic follicles from those found in benign hyperplasia, for which Bcl-2 is negative.

# Interactions
BCL6 has been shown to interact with
- BCOR,
- C-jun,
- HDAC1,
- HDAC4,
- HDAC7A,
- HDAC5,
- IRF4,
- NCOR2,
- SMRT,
- ZBTB7A
- T-bet,
- ZBTB16
BCL9
B-cell CLL/lymphoma 9 protein is a protein that in humans is encoded by the BCL9 gene.

# Function
BCL9, together with its paralogue gene BCL9L (BCL9 like or BCL9.2), have been extensively studied for their role as transcriptional beta-catenin cofactors, fundamental for the transcription of Wnt target genes.
Recent work, using the mouse (Mus musculus) and Zebrafish (Danio rerio) as model organisms, identified an ancient role of BCL9 and BCL9L as key factors required for cardiac development . This work emphasises the tissue-specific nature of the Wnt/-catenin mechanism of action, and implicates alterations in BCL9 and BCL9L in human congenital heart defects.
BCL9 and BCL9L have been shown to take part in other tissue-specific molecular mechanisms, showing that their role in the Wnt signaling cascade is only one aspect of their mode of action.

# Clinical significance
BCL9 is associated with B-cell acute lymphoblastic leukemia. It may be a target of translocation in B-cell malignancies with abnormalities of 1q21. The overexpression of BCL9 may be of pathogenic significance in B-cell malignancies.
BCL9 and BCL9L are potential clinical targets for human cancers; for instance, the gene expression changes that they promote is associated with a poor outcome in colorectal cancer.
Like BCL2, BCL3, BCL5, BCL6, BCL7A, and BCL10, it has clinical significance in lymphoma.
Common variations in the BCL9 gene, which is in the distal area, confer risk of schizophrenia and may also be associated with bipolar disorder and major depressive disorder.
BCL9, together with the paralogue protein BCL9l and PYGO2 also have cytoplasmic functions during tooth development and is particularly important for the formation of enamel. Mice lacking both Pygo1 and Pygo2 or both Bcl9 and Bcl9l develop teeth, a process that requires Wnt/-catenin transcriptional regulation, but the enamel is structurally disorganized and contains less iron than teeth from control mice. Bcl9, Bcl9l, and Pygo2 are present in the cytoplasm of ameloblasts, the cells that secrete enamel proteins, and colocalize in these cells with amelogenin, the main component of enamel, encoded by the AMELX gene, which has been already implicated as a causative factor of Amelogenesis Imperfecta in humans. Bcl9 interacts with amelogenin and proteins involved in exocytosis and vesicular trafficking, suggesting that these proteins function in the trafficking or secretion of enamel proteins. Therefore, Bcl9, Bcl9l, and Pygo2 have cytoplasmic functions distinct from their roles as transcriptional cofactors downstream of Wnt signaling. This new discovery might improve our understanding for the treatment of human caries.

# Related gene problems
- 1q21.1 deletion syndrome
- 1q21.1 duplication syndrome
BIN1
Myc box-dependent-interacting protein 1, also known as Bridging Integrator-1 and Amphiphysin-2 is a protein that in humans is encoded by the BIN1 gene.
This gene encodes several isoforms of a nucleocytoplasmic adaptor protein, one of which was initially identified as a MYC-interacting protein with features of a tumor suppressor.
Isoforms that are expressed in the central nervous system may be involved in synaptic vesicle endocytosis and may interact with dynanim, synaptojanin, endophilin, and clathrin.
Isoforms that are expressed in muscle and ubiquitously expressed isoforms localize to the cytoplasm and nucleus and activate a caspase-independent apoptotic process.
Studies in mouse suggest that this gene plays an important role in cardiac muscle development. Alternate splicing of the gene results in ten transcript variants encoding different isoforms. Aberrant splice variants expressed in tumor cell lines have also been described.

# Clinical significance
In humans, mutations in BIN1 have been associated with skeletal myopathies including centronuclear myopathy causing muscle weakness and myotonic dystrophy causing progressive muscle wasting, myotonia, cataracts, and heart conduction defects.  An association has also been found between BIN1 mutations and Alzheimer's disease.  Knockdown of BIN1 in produces a cardiomyopathy phenotype in zebrafish, and in sheep BIN1 may be responsible for the loss of T-tubules seen in heart failure.

# Interactions
BIN1 has been shown to interact with Phospholipase D1, SNX4 and PLD2.
BL22
BL22, also called CAT-3888 or GCR-3888, is an immunotoxin which attaches to and, upon internalization, kills B cells.  It has completed a Phase I clinical (human) trial and is currently in a Phase II clinical trial for the treatment of hairy cell leukemia at a Phase I clinical trial for pediatric acute lymphoblastic leukemia and non-Hodgkin's lymphoma at the NIH in the U.S.  It may be useful against any B cell leukemia or lymphoma.
Technically, BL22 is an anti-CD22 immunotoxin fusion protein between a murine anti-CD22 disulphide-linked Fv (dsFv) antibody fragment and an edited copy of bacterial Pseudomonas exotoxin PE38.  The toxin is activated intracellularly, by the low pH of the lysosome into which the entire protein was internalized via the CD22 receptor.  The toxin kills the targeted cell through ribosome inactivation.
BL22 is very similar to the newer HA22, which changes one amino acid in the antibody fragment to increase the binding affinity for the target molecule.  Both of these proteins are designed to bind to the CD22 receptor on the surface of B cells.

# Business History
BL22 was initially designed and produced at the U.S. National Cancer Institute, one of the agencies which make up the NIH.  Early development of BL22 was funded by California biotech Genencor.  The future drug was acquired by Cambridge Antibody Technology at the end of 2005; less than a year later, CAT was purchased by British pharmaceutical company AstraZeneca.
BNC1
Zinc finger protein basonuclin-1 is a protein that in humans is encoded by the BNC1 gene.
The protein encoded by this gene is a zinc finger protein present in the basal cell layer of the epidermis and in hair follicles. It is also found in abundance in the germ cells of testis and ovary. This protein is thought to play a regulatory role in keratinocyte proliferation and it may also be a regulator for rRNA transcription. This gene seems to have multiple alternatively spliced transcript variants, but their full-length nature is not known yet. There seems to be evidence of multiple polyadenylation sites for this gene.
BNC1 or Basonuclin 1 does not interact with PICK1. This suggestion that is does is based on the article that proved that PICK1 interacts with the non-voltage gated sodium channels BNC1 (brain Na+ channel 1). Both Basonuclin 1 and brain Na+ channel 1 have the same abbreviation BNC1, but they are not similar proteins and PICK1 interacts with the second protein, not the first one.
BOLL
Protein boule-like is a protein that in humans is encoded by the BOLL gene.

# Function
This gene belongs to the DAZ gene family required for germ cell development. It encodes an RNA-binding protein which is more similar to Drosophila Boule than to human proteins encoded by genes DAZ (deleted in azoospermia) or DAZL (deleted in azoospermia-like). Loss of this gene function results in the absence of sperm in semen (azoospermia). Histological studies demonstrated that the primary defect is at the meiotic G2 / M transition in fruitfly but in mice the primary defect is postmeiotic at round spermatid stage. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
The boule-like protein appears to be ubiquitously expressed in males of all animal species, except in the most primitive trichoplax.
BOP1
Ribosome biogenesis protein BOP1 is a protein that in humans is encoded by the BOP1 gene.

# Function
It is a WD40 repeat-containing nucleolar protein involved in rRNA processing, thereby controlling the cell cycle. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels.
Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1.

# Structure
BOP1 contains a conserved N-terminal domain, BOP1NT.
BPY2
Testis-specific basic protein Y 2 also known as basic charge, Y-linked 2 is a protein that in humans is encoded by the BPY2 gene which resides on the Y chromosome.

# Function
This gene is located in the nonrecombining portion of the Y chromosome, and expressed specifically in testis. The encoded protein interacts with ubiquitin protein ligase 
E3A and may be involved in male germ cell development and male infertility. Three nearly identical copies of this gene exist on chromosome Y; two copies are part of a palindromic region. This record represents the copy outside of the palindromic region.
BRD2
Bromodomain-containing protein 2 is a protein that in humans is encoded by the BRD2 gene. BRD2 is part of the Bromodomain and Extra-Terminal motif (BET) protein family that also contains BRD3, BRD4, and BRDT in mammals 
Early descriptions demonstrated that BRD2 gene product is a mitogen-activated kinase which localizes to the nucleus. The gene maps to the major histocompatibility complex (MHC) class II region on chromosome 6p21.3 but sequence comparison suggests that the protein is not involved in the immune response. Homology to the Drosophila gene female sterile homeotic suggests that this human gene may be part of a signal transduction pathway involved in growth control.

# Functions
- BRD2 has been implicated in cancer.
- BRD2 loss in mice causes obesity without diabetes for unknown reasons.
- BRD2 may have functional overlap with close homolog BRD3.
- BRD2 function is blocked by BET inhibitors.

# Interactions
BRD2 has been shown to interact with E2F2, and many transcription factors including GATA1.
BRD4
Bromodomain-containing protein 4 is a protein that in humans is encoded by the BRD4 gene.
BRD4 is a member of the BET (bromodomain and extra terminal domain) family, which also includes BRD2, BRD3, and BRDT. BRD4, similar to other BET family members, contains two bromodomains that recognize acetylated lysine residues. BRD4 also has an extended C-terminal domain with little sequence homology to other BET family members.

# Structure
The two bromodomains in BRD4, termed BD1 and BD2, consist of 4 alpha-helices linked by 2 loops. The ET domain structure  is made up of 3 alpha-helices and a loop. The C-terminal domain of BRD4 has been implicated in promoting gene transcription through interaction with the transcription elongation factor P-TEFb and RNA polymerase II.

# Function
The protein encoded by this gene is homologous to the murine protein MCAP, which associates with chromosomes during mitosis, and to the human RING3 protein, a serine/threonine kinase. Each of these proteins contains two bromodomains, a conserved sequence motif which may be involved in chromatin targeting. This gene has been implicated as the chromosome 19 target of translocation t(15;19)(q13;p13.1), which defines the NUT midline carcinoma. Two alternatively spliced transcript variants have been described.

# Role in cancer
Most cases of NUT midline carcinoma involve translocation of the BRD4 with NUT genes. BRD4 is often required for expression of Myc and other "tumor driving" oncogenes in hematologic cancers including multiple myeloma, acute myelogenous leukemia and acute lymphoblastic leukaemia.
BRD4 is a major target of BET inhibitors, a class of pharmaceutical drugs currently being evaluated in clinical trials.

# Interactions
Notably, BRD4 interacts with P-TEFb via its P-TEFb interaction domain (PID), thereby stimulating its kinase activity and stimulating its phosphorylation of the carboxy-terminal domain (CTD) of RNA polymerase II. Recent review.
BRD4 has been shown to interact with GATA1, JMJD6, RFC2, RFC3, RFC1, RFC4 and RFC5.
BRD4 has also been implicated in binding with the diacetylated Twist protein, and the disruption of this interaction has been shown to suppress tumorigenesis in basal-like breast cancer.
BRD4 has also been shown to interact with a variety of inhibitors, such as MS417; inhibition of BRD4 with MS417 has been shown to down-regulate NF-B activity seen in  HIV-associated kidney disease. BRD4 also interacts with RVX-208, which is being evaluated for treatment of atherosclerosis and cardiovascular disease.
BRD8
Bromodomain-containing protein 8 is a protein that in humans is encoded by the BRD8 gene.
The protein encoded by this gene interacts with thyroid hormone receptor in a ligand-dependent manner and enhances thyroid hormone-dependent activation from thyroid response elements. This protein contains a bromodomain and is thought to be a nuclear receptor coactivator. Three alternatively spliced transcript variants that encode distinct isoforms have been identified.

# Interactions
BRD8 has been shown to interact with Thyroid hormone receptor beta and Retinoid X receptor alpha.