Persius/hicric huggingface dataset:
Pyemia
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Pyaemia (or pyemia) is a type of septicaemia that leads to widespread abscesses and is usually caused by the staphylococcus bacteria. Apart from the distinctive abscesses, pyaemia exhibits the same symptoms as other forms of septicaemia. It was almost universally fatal before the introduction of antibiotics.
Sir William Osler included a three-page discussion of pyaemia in his textbook The Principles and Practice of Medicine, published in 1892. He defined pyaemia as follows:
"A general disease, characterized by recurring chills and intermittent fever and the formation of abscesses in various parts, all of which result from the contamination of the blood by products arising from a focus contaminated by the bacteria of suppuration."
Earlier still, Ignaz Semmelweis included a section entitled "Childbed fever is a variety of pyaemia" in his treatise, The Etiology of Childbed Fever (1861). Jane Grey Swisshelm, in her autobiography entitled Half a Century, describes the treatment of pyaemia in 1862 during the American Civil War.
QRICH2
Glutamine-rich protein 2 is a protein that in humans is edcoded by the QRICH2 gene on human chromosome 17. The function of QRICH2 protein is mostly unknown, but it has been shown that QRICH2 gene contains a high molecular weight Glutenin domain and an ATPase involved domain. QRICH2 gene is highly expressed in testis, and the subcellular location of QRICH2 protein is in the nucleus.

# Gene
QRICH2 mRNA is 5411 bp long, and its chromosomal location in human is 17q25.1. QRICH2 mRNA has 19 exons and it contains two main function domains: a high molecular weight Glutenin domain (amino acid 446-979) and an ATPase involved domain (amino acid 1036-1413). QRICH2 locates between UBAL D2 gene and PRPSAP1 gene on chromosome 17. There is no predicted stem loop structure on QRICH2 mRNA because there isn't any complementary RNA sequences.

# Protein
QRICH2 protein is 1663 amino acids long, and 10.9% of the amino acids are Glutamine (Q). 38% of the QRICH2 protein secondary structure is alpha-helix, 39% is beta-sheet and 13% is turning. The human tissue type with the highest level of QRICH2 expression is testis, and this result is confirmed by the Gene Expression Profile for mouse and dog too. The subcellular location of QRICH2 protein is in the nucleus. QRICH2 is a soluble protein, its average hydrophobicity is -0.5995. QRICH2 protein interact with a number of other proteins including SSSCA1, TSSC1, GAPDH, NUP98 and SNAI1.

# Homology

## paralogs
FLJ25737 mRNA sequences perfectly match with two regions on the QRICH2 mRNA (bp 3157-4302 on QRICH2 match with bp 1-1146 on FLJ25737, bp 4998-5307 on QRICH2 match with bp 1140-1499 on FLJ25737). However, FLJ25737 locates on chromosome 7 and QRICH2 locates on chromosome 17.

## Orthologs
QRICH2 protein has well conserved orthologs in many species. The orthologous protein sequences match very well at the region where the high molecular weight Glutenin domain and ATPase involved domain is.

# Function
The function of QRICH2 protein is mostly unknown. QRICH2 has been shown to belong to the common expression groups on human chromosome 17. The following genes belonged to the common expression groups on chromosome 17: NCOR1, GFAP, QRICH2, ANAPC11 and PER1. QRICH2 may also be an up-regulated gene involved in cell adhesion and cellular morphogenesis. The high expression of QRICH2 gene in testis may suggest that QRICH2 protein has some functions related to hormone production in males. QRICH2 protein has some sequence similarities with the spermidine/spermine N(1)-acetyl-like protein 1 in several species.
RAB11A
Ras-related protein Rab-11A is a protein that in humans is encoded by the RAB11A gene.

# Function
The protein encoded by this gene belongs to the small GTPase superfamily, Rab family. It is associated with both constitutive and regulated secretory pathways, and may be involved in protein transport.
Rab-11a controls intracellular trafficking of the innate immune receptor TLR4, and thereby also receptor signalling

# Interactions
RAB11A has been shown to interact with:
- RAB11FIP1,
- RAB11FIP2,
- RAB11FIP3,
- RAB11FIP4,  and
- RAB11FIP5
RABEPK
Rab9 effector protein with Kelch motifs also known as p40 is a protein that in humans is encoded by the RABEPK gene.
Membrane-associated p40, in together with RAB9A, facilitates the transport of the mannose 6-phosphate receptor (MPR) from endosomes to the trans-Golgi network.

# Interactions
RABEPK has been shown to interact with RAB9A and FYVE finger-containing phosphoinositide kinase.
RAD23B
UV excision repair protein RAD23 homolog B is a protein that in humans is encoded by the RAD23B gene.

# Function
The protein encoded by this gene is one of two human homologs of Saccharomyces cerevisiae Rad23, a protein involved in nucleotide excision repair (NER). This protein was found to be a component of the protein complex that specifically complements the NER defect of xeroderma pigmentosum group C (XP-c) cell extracts in vitro. This protein was also shown to interact with, and elevate the nucleotide excision activity of 3-methyladenine-DNA glycosylase (MPG), which suggested a role in DNA damage recognition in base excision repair. This protein contains an N-terminal ubiquitin-like domain, which was reported to interact with 26S proteasome, and thus this protein may be involved in the ubiquitin mediated proteolytic pathway in cells.

# Role in DNA repair
The complex of XPC-RAD23B is the initial damage recognition factor in global genomic nucleotide excision repair (GG-NER).  XPC-RAD23B recognizes a wide variety of lesions that thermodynamically destabilize DNA duplexes, including UV-induced photoproducts (cyclopyrimidine dimers and 6-4 photoproducts ), adducts formed by environmental mutagens such as benzopyrene or various aromatic amines, certain oxidative endogenous lesions such as cyclopurines and adducts formed by cancer chemotherapeutic drugs such as cisplatin. The presence of XPC-RAD23B is required for assembly of the other core NER factors and progression through the NER pathway both in vitro and in vivo. Although most studies have been performed with XPC-RAD23B, it is part of a trimeric complex with centrin-2, a calcium-binding protein of the calmodulin family.

# Epigenetic repression
The protein expression level of RAD23B can be epigenetically repressed, either by promoter methylation of the RAD23B gene or by either of two microRNAs (miR-744-3p or miR-373).

# Deficiency of RAD23B in cancer
A deficiency in expression of a DNA repair gene increases the risk for cancer (see Deficient DNA repair in carcinogenesis).  The expression of RAD23B is reduced in tumor tissue of women with breast cancer.  A low percentage of RAD23B positive nuclei in high grade breast cancer was also observed.
RAD23B was substantially reduced by promoter methylation in a cell line derived from multiple myeloma. and reduced by promoter methylation in a small proportion of non-small cell lung cancer (NSCLC) tumours.
RAD23B appears to be one of 26 DNA repair genes that are epigenetically repressed in various cancers (see Cancer epigenetics).

# Interactions
RAD23B has been shown to interact with PSMD4 and Ataxin 3.
RAD54B
DNA repair and recombination protein RAD54B is a protein that in humans is encoded by the RAD54B gene.
The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer.

# Interactions
RAD54B has been shown to interact with RAD51.

# Cancer
The RAD54B gene is somatically mutated or deleted in numerous types of cancer including colorectal cancer (~3.3%), breast cancer (~3.4%), and lung cancer (~2.6%).   In North America, these three cancers alone account for about 20,500 individuals diagnosed annually with RAD54B defective cancer.  In a pre-clinical study, colon cancer cells defective in RAD54B were determined to be selectively killed by inhibitors of the DNA repair protein PARP1.   Inhibitors of PARP1 likely impede alternative DNA repair responses that might otherwise compensate for loss of the RAD54B pathway in cancer cells.  Thus RAD54B-deficient cancer cells treated with a PARP1 inhibitor are apparently more vulnerable to killing by naturally occurring DNA damages than non-cancerous cells without a RAD54 defect (see article Synthetic lethality).
RANBP1
Ran-specific binding protein 1 is an enzyme that in humans is encoded by the RANBP1 gene.
Ran/TC4-binding protein, RanBP1, interacts specifically with GTP-charged RAN. RANBP1 encodes a 23-kD protein that binds to RAN complexed with GTP but not GDP. RANBP1 does not activate GTPase activity of RAN but does markedly increase GTP hydrolysis by the RanGTPase-activating protein (RanGAP1). The RANBP1 cDNA encodes a 201-amino acid protein that is 92% similar to its mouse homolog. In both mammalian cells and in yeast, RANBP1 acts as a negative regulator of RCC1 by inhibiting RCC1-stimulated guanine nucleotide release from RAN.

# Interactions
RANBP1 has been shown to interact with XPO1, KPNB1 and Ran.
RANBP2
RAN binding protein 2 (RANBP2) is protein which in humans is encoded by the RANBP2 gene. It is also known as nucleoporin 358 (Nup358) since it is a member nucleoporin family that makes up the nuclear pore complex. RanBP2 has a mass of 358 kDa.

# Function
RAN is a small GTP-binding protein of the RAS superfamily. Ran GTPase is a master regulatory switch, which among other functions, controls the shuttling of proteins between the nuclear and cytoplasm compartments of the cell. Ran GTPase controls a variety of cellular functions through its interactions with other proteins. The RanBP2 gene encodes a very large RAN-binding protein that localizes to cytoplasmic filaments emanating from the nuclear pore complex. RanBP2/Nup358 is a giant scaffold and mosaic cyclophilin-related nucleoporin implicated in controlling selective processes of the Ran-GTPase cycle. RanBP2 is composed of multiple domains. Each domain of RanBP2 selectively and directly interacts with distinct proteins such as Ran GTPase, importin-beta, exportin-1/CRM1, red opsin, subunits of the proteasome, cox11 and the kinesin-1 isoforms, KIF5B and KIF5C. Another partner of RanBP2 is  the E2 enzyme UBC9. RanBP2 strongly enhances SUMO1 transfer from UBC9 to the SUMO1 target SP100. Another target for SUMOylation is RanGAP which is the GTPase activating protein for Ran. SUMO-RanGAP interacts with a domain near the carboxyl terminus of RanBP2. These findings place sumoylation at the cytoplasmic filaments of the nuclear pore complex and suggest that, for some substrates, modification and nuclear import are linked events. The pleiotropic (multifunctional) role of RanBP2 reflects its interaction with multiple partners, each presenting distinct cellular or molecular functions. This gene is partially duplicated in a gene cluster that lies in a hot spot for recombination on human chromosome 2q.

# Clinical significance
Insufficiency of RanBP2 is directly linked to carcinogenesis, aneuploidy, and neuroprotection of photoreceptor neurons to light-elicited stress and aging. Human missense mutations in RanBP2 were identified in its leucine-rich domain and they cause autosomal dominant necrotizing encephalopathy (ADNE).

# Interactions
RANBP2 has been shown to interact with KPNB1 and UBE2I.
RASSF1
Ras association domain-containing protein 1 is a protein that in humans is encoded by the RASSF1 gene.

# Function
This gene encodes a protein similar to the RAS effector proteins. Loss or altered expression of this gene has been associated with the pathogenesis of a variety of cancers, which suggests the tumor suppressor function of this gene. The inactivation of this gene was found to be correlated with the hypermethylation of its CpG-island promoter region. The encoded protein was found to interact with DNA repair protein XPA. The protein was also shown to inhibit the accumulation of cyclin D1, and thus induce cell cycle arrest. Seven alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported.

# Interactions
RASSF1 has been shown to interact with:
- CNKSR1,
- Death associated protein 6
- HRAS,
- MAP1B,
- MAP1S, and
- RASSF5.

# Pathology
Cervical cancer is known to be one of the most severe forms of cancer and is frequently associated with human papilloma virus (HPV). A few studies have been done to investigate the relationship between cervical cancers and RASSF1A, an isoform of RASSF1 that has been shown to suppress the proliferation in tumor cells. Through these studies, it was found that RASSF1A is commonly inactivated in adenocarcinomas (ACs) due to hypermethylation of the promotor region. However, this is not observed in squamous cell carcinomas (SCC) of the cervix, though they can be associated with HPV as well. It was found that RASSF1A was silenced in cancer cells when the promotor region was hypermethylated. It is speculated that cancer subtypes may develop due to the inverse relationship of RASSF1A and HPV. RASSF1A promoter hypermethylation and oncogenic HPV were detected in ACs, but SCCs displayed a high level of HPV DNA and no RASSF1A promoter methylation. Another study used Hela cells to study the potential therapeutic effects of RASSF1A. Hela cells are a line of cells that are derived from cervical cancer cells and are used in scientific research. When Hela cells were generated with RASSF1A expression, the growth of these cells decreased when compared to cells without RASSF1A expression. The rate of apoptosis in those cells had also increased with RASSF1A expression. Through these studies, it was indicated that RASSF1A expression could induce apoptosis and regulate proliferation to suppress tumors, making it a potential therapeutic mechanism for cervical cancers.
RASSF5
Ras association domain-containing protein 5 is a protein that in humans is encoded by the RASSF5 or F5 gene.

# Function
This gene is a member of the Ras association domain family. It functions as a tumor suppressor, and is inactivated in a variety of cancers. The encoded protein localizes to centrosomes and microtubules, and associates with the GTP-activated forms of Ras, Rap1, and several other Ras-like small GTPases. The protein regulates lymphocyte adhesion and suppresses cell growth in response to activated Rap1 or Ras. Multiple transcript variants encoding different isoforms have been found for this gene.

# Interactions
RASSF5 has been shown to interact with RRAS, RAP2A, MRAS and RASSF1.
RASSF9
Ras association domain-containing protein 9 (RASSF9), also known as PAM COOH-terminal interactor protein 1 (PCIP1) or peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor (PAMCI) is a protein that in humans is encoded by the RASSF9 gene.

# Function
RASSF9 the N-terminal RASSF family member Ras association (RalGDS/AF-6) domain family (N-terminal) member 9 12q21.31, is one of two new wild type RASSF9 and RASSF10 proteins. Three proteins that interact with a fragment of the PAM cytosolic domain containing signaling switch I and II the RA1 and RA2ras complex. RASSF7, the first member of the N-terminal RASSF family is required for mitosis. RASSF9 is recently found to be involved in regulation of epidermal homeostasis.

# Regulation
The mutant  proregion encoding PAM COOH-terminal interactor protein-1 (P-CIP1) is comparable to that of human band 4.1-like TF (blood plasma protein) as a recycling endosomal pathway in microtubule locations, does NOT bind RasGTP. Specificity of interaction may all be related to microtubule locations of the endosomal-lysosomal system localized within the centrosome with Transferrin and different Ras proteins or with that one (N-Ras), but on the other hand, it interacts with three (Ha-Ras, Ki-Ras, and Rap)  residues function, blocked by a mutation that affects Ras effector function is the critical product of the t (6:11) abnormality associated with some human leukemias. Phosphatidylinositol-3-kinase make contacts with both (6:11) switch I and II regions of ras and yeast adenylyl cyclase molecules carrying these mutations are rendered unactivatable by Ras in vitro.  Ras-interacting residues, are appreciably different from that of RalGDS-RBD through their C-terminal Ras-binding domains (RBD). Such outliers as afadin/AF-6 and Rin1  were found to inhibit the binding of Raf to Ras. Adenylyl cyclase molecules carrying these mutations are rendered unactivatable by Ras in vitro with the Ras-associating domain-RA,   not all RA domains bind RasGTP it is a primary Ras-binding site.

# Interactions
- PAM Peptidyl-glycine alpha-amidating monooxygenase precursor (PAM)
- RASSF7 Ras association domain-containing protein 7 (HRAS1-related cluster protein 1)
- BLOC1S2 Biogenesis of lysosome-related organelles complex-1 subunit 2 (BLOC subunit 2)
- TF Serotransferrin precursor (Transferrin) (Beta-1-metal- binding globulin)
- RAB11A Ras-related protein Rab-11A
RBFOX1
Fox-1 homolog A, also known as ataxin 2-binding protein 1 (A2BP1) or hexaribonucleotide-binding protein 1 (HRNBP1) or RNA binding protein, fox-1 homolog (Rbfox1), is a protein that in humans is encoded by the RBFOX1  gene.

# Function
Rbfox1 has an RNA recognition motif that is highly conserved among RNA-binding proteins. Rbfox1, and the related protein Rbfox2, bind the consensus RNA sequence motif (U)GCAUG within introns to exert their functions as alternative splicing factors.
Additionally, the Rbfox1/A2BP1 protein binds to the C-terminus of ataxin-2, and may contribute to the restricted pathology of spinocerebellar ataxia type 2 (SCA2). Ataxin-2 is the gene product of the SCA2 gene which causes familial neurodegenerative diseases. Several alternatively spliced transcript variants have been found for this gene. Some of these variants localize to the nucleus and some other to the cytoplasm. Nuclear variants have a well-established role in tissue specific alternative splicing. Rbfox1 cytoplasmic variants modulate mRNA stability and translation. In stressed cells, Rbfox1 has been demonstrated to localize to cytoplasmic stress granules.
RECQL4
ATP-dependent DNA helicase Q4 is an enzyme that in humans is encoded by the RECQL4 gene.
Mutations in RECQL4 are associated with the autosomal recessive disease Rothmund-Thomson Syndrome, a disorder that has features of premature aging.  In addition to the Rothmund-Thomson syndrome, RECQL4 mutations are also associated with RAPADILINO and Baller-Gerold syndromes.  There are two types of Rothmund Thomson syndrome and it is Type 2 that occurs in patients carrying deleterious mutations in both copies of the RECQL4 gene.  This condition is associated with a high risk of developing osteosarcoma (malignant tumor of the bone).
RECQL4 gets its name from being homologous (sharing sequence) with other members of the RecQ helicase family.  Two other genetic diseases are due to mutations in other RECQ helicases. Bloom syndrome is associated with mutations in the BLM gene and Werner syndrome is associated with mutations in the WRN gene.

# DNA repair
Double-strand breaks in DNA are potentially lethal to a cell and need to be repaired.  Repair of double-strand breaks by homologous recombination (HR) is an important cellular mechanism for avoiding this lethality.  RECQL4 has a crucial role in the first step of HR, referred to as end resection.  When RECQL4 is deficient, end resection, and thus HR, is reduced.  Evidence suggests that other forms of DNA repair including non-homologous end joining, nucleotide excision repair and base excision repair also depend on RECQL4 function.  In the Rothmund-Thomson syndrome, the association of deficient RECQL4-mediated DNA repair and premature aging is consistent with the DNA damage theory of aging.
RHBDF2
Rhomboid family member 2 is a protein that in humans is encoded by the RHBDF2 gene. The alternative name iRhom2 has been proposed, in order to clarify that it is a catalytically inactive member of the rhomboid family of intramembrane serine proteases.
The RHBDF2 gene is located on the long arm of chromosome 17 (17q25.1) on the Crick (minus) strand. It is 30.534 kilobases in length and encodes a protein of 856 amino acids with a predicted molecular weight of 96.686 kiloDaltons.
The RHBDF2 protein plays an important role in the secretion of tumor necrosis factor alpha, and has also been implicated in familial esophageal cancer.
It is involved in the regulation of the secretion of several ligands of the epidermal growth factor receptor.
RIPOR2
RHO family interacting cell polarization regulator 2 is a protein that in humans is encoded by the RIPOR2 gene.

# Function
The protein encoded by this gene stimulates the formation of a non-mitotic multinucleate syncytium from proliferative cytotrophoblasts during trophoblast differentiation. Alternative splicing of this gene results in multiple transcript variants. .

# Clinical significance
Mutations in RIPOR2 are associated to                 hearing loss            .
RMND5B
Required for meiotic nuclear division 5 homolog B (S. cerevisiae), also known as RMND5B, is a protein which in humans is encoded by the RMND5B gene. It has a zinc finger domain and  is highly conserved throughout many eukaryotic organisms.

# Protein sequence
This protein is rich in leucine (14.0%) and might belong to the protein family of leucine-rich repeats

# Homology
CAD28476 is highly conserved in many eukaryotic organism. Its high conservation suggests that it plays a primary role in meiosis.

# Orthologs

# Zinc finger domain
Two domains  were predicted by the program BLIMPS to exist in the protein of which one of the domains contains a zinc finger domain.
Zinc finger domains assist the binding of the protein to nucleic acids. This points to a direct interaction of CAD28476 with DNA during meiosis.  By comparing CAD28476 with a related zinc finger protein in a local sequence alignment using LALIGN, the amino acids His359, Cys381 and Cys384 could be attributed to the zinc finger domain.  This zinc finger structure is uncommon in the way that it involves one histidine instead of two.

# Expression
Microarray data show that CAD28476 is highly expressed in tissue where meiosis occurs like in testis and ovaries. Moreover it is also highly expressed in the brain around the hypothalamus.

# Transcriptional regulation
The analysis of the promoter region (tools on the page rVista . were used) shows that there are several transcription factor binding sites localized in conserved regions . 
It is very likely that the transcription factor Ets-1 which belongs to the ETS transcription factor family and its core binding factor CBF are involved in regulation of transcription since they both have independent binding sites.

# Interacting proteins
There were two proteins predicted which interact with CAD28476.
RNF111
E3 ubiquitin-protein ligase Arkadia is an enzyme that in humans is encoded by the RNF111 gene.

# Function
The protein encoded by this gene contains a RING finger domain, a motif known to be involved in protein-protein and protein-DNA interactions. The mouse counterpart of this gene (Rnf111/arkadia) has been shown to genetically interact with the transforming growth factor (TGF) beta-like factor Nodal, and act as a modulator of the nodal signaling cascade, which is essential for the induction of mesoderm during embryonic development.

# Interactions
RNF111 has been shown to interact with Mothers against decapentaplegic homolog 7 and Mothers against decapentaplegic homolog 3.