{ "bcoid": "GLY_000134", "title": "Mouse Protein Function (NCBI Refseq)", "description": "The Mouse Protein Function (NCBI RefSeq) dataset contains biological function annotation of mouse [taxid:10090] ...", "filename": "mouse_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q61718-1...", "protein_xref..." ], [ "Q61718-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "Q61718-1", "protein_xref_refseq", "NP_996753.1", "21172865", "A distinct subset of plasmacytoid dendritic cells (pDC) is responsible for nearly all IFN-alpha production, while in bone marrow and spleen, cells that ultimately differentiate into pDC produce little or no IFN-alpha and instead promote immune tolerance." ], [ "Q61718-1", "protein_xref_refseq", "NP_996753.1", "16611902", "Results suggest that activation of the Ras/Raf/MEK pathway downregulates IFN-induced antiviral response" ], [ "Q7TRR7-1", "protein_xref_refseq", "NP_001011847.1", "", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]." ], [ "Q5QD04-1", "protein_xref_refseq", "NP_001010831.1", "16878137", "Previous studies reported TAAR expression in brain. This paper found TAAR expression only in olfactory epithelial cells and that each TAAR detects a unique set of amine ligands. TAARs seem to function as a family of chemosensory receptors for amines." ], [ "Q6PB66-1", "protein_xref_refseq", "NP_082509.2", "32203162", "LRPPRC sustains Yap-P27-mediated cell ploidy and P62-HDAC6-mediated autophagy maturation and suppresses genome instability and hepatocellular carcinomas." ], [ "Q6PB66-1", "protein_xref_refseq", "NP_082509.2", "29146908", "Study demonstrated that the LRPPRC-SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization, and polyadenylation. Publication Status: Online-Only" ], [ "Q6PB66-1", "protein_xref_refseq", "NP_082509.2", "19372376", "Includes the study of an upstream ORF in this gene, and shows that it functions to reduce protein levels by ~74%." ], [ "Q6PB66-1", "protein_xref_refseq", "NP_082509.2", "15081402", "Associates with mRNA/mRNP complexes at the outside of nuclear/endoplasmic reticulum, and plays a role in control of mRNA metabolisms" ], [ "Q6PB66-1", "protein_xref_refseq", "NP_082509.2", "12071956", "LRP130 may function in stabilizing minisatellite DNA sequences." ], [ "Q99JS0-1", "protein_xref_refseq", "NP_001161970.1", "18650334", "This study identified an evolutionarily conserved novel component of myelin called Mp11. The Mp11 genomic locus contains multiple conserved Egr binding sites, and Mp11 induction is regulated by the expression of Egr2 and expression in peripheral nerve." ], [ "Q91V13-1", "protein_xref_refseq", "NP_694709.1", "31424424", "Plasma LEAP2/acyl-ghrelin molar ratio may be a key determinant modulating acyl-ghrelin activity in response to body mass, feeding status, and blood glucose." ], [ "Q91V13-1", "protein_xref_refseq", "NP_694709.1", "29233536", "Liver-expressed antimicrobial peptide 2 (LEAP2) is an endogenous antagonist of GHSR." ], [ "A2AJB7-1", "protein_xref_refseq", "NP_001036095.1", "", "This gene encodes a small secreted protein that is expressed in the epididymis and binds retinoic acid. The precursor protein is processed into both a longer major form and a shorter minor form. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]." ], [ "A2AJB7-1", "protein_xref_refseq", "NP_001036095.1", "16740652", "Forkhead box A2 restricts androgen-regulated gene expression of lipocalin 5 in the mouse epididymis." ], [ "P25916-1", "protein_xref_refseq", "NP_031578.2", "31679686", "Bmi1 avoids hematopoietic stem cells (HSC) loss by aging without altering myeloid-biased differentiation. Bmi1 augments the multi-lineage repopulating capacity of single aged HSC. Bmi1 directly targets developmental genes marked with bivalent histone domains." ], [ "P25916-1", "protein_xref_refseq", "NP_031578.2", "31366257", "Co-delivery of UA and Bmi1 siRNA using folate-targeted liposomes." ], [ "P25916-1", "protein_xref_refseq", "NP_031578.2", "31408689", "Bmi1 deletion promoted the adipogenic differentiation of LepR(+) stromal cells and caused progressive fatty changes in the BM of limb bones with age, resulting in reductions in the numbers of HSCs and progenitors in BM and enhanced extramedullary hematopoiesis. Several adipogenic regulator genes appeared to be regulated by Bmi1." ], [ "Q9JM52-1", "protein_xref_refseq", "NP_057922.2", "28400474", "A critical regulator of Th17 cell differentiation" ], [ "Q9JM52-1", "protein_xref_refseq", "NP_057922.2", "27631493", "Using in vitro dephosphorylation assays, we demonstrate that Mastl promotes persistent MPS1 phosphorylation by inhibiting PP2A/B55-mediated MPS1 dephosphorylation rather than affecting Cdk1 kinase activity. Our findings establish a key regulatory function of the Greatwall kinase/Mastl - PP2A/B55 pathway in preventing premature SAC silencing Publication Status: Online-Only" ], [ "Q9JM52-1", "protein_xref_refseq", "NP_057922.2", "26598717", "MINK1 may be an important signaling molecule that mediates mitogen-activated protein kinase signaling and participates in platelet activation and thrombus formation." ], [ "Q8VH11-1", "protein_xref_refseq", "NP_667320.1", "", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]." ], [ "Q8BXR6-1", "protein_xref_refseq", "NP_766423.3", "26310831", "Pellino-3 is involved in endotoxin tolerance and functions as a negative regulator of Toll-like receptor 2/4 signaling." ], [ "Q8BXR6-1", "protein_xref_refseq", "NP_766423.3", "25483963", "Autophagy causes PELI3 degradation during TLR4-signaling, thereby impairing the hyperinflammatory phase during sepsis by inhibiting proinflammatory IL1B expression" ], [ "Q8BXR6-1", "protein_xref_refseq", "NP_766423.3", "23892723", "Our findings identify RIP2 as a substrate for Pellino3 and Pellino3 as an important mediator in the Nod2 pathway and regulator of intestinal inflammation." ], [ "Q8BXR6-1", "protein_xref_refseq", "NP_766423.3", "24113711", "Pellino3 targets RIP1 and regulates the pro-apoptotic effects of TNF-alpha." ], [ "Q8BXR6-1", "protein_xref_refseq", "NP_766423.3", "23042151", "Pellino3 targets the IRF7 pathway and facilitates autoregulation of TLR3- and viral-induced expression of type I interferons." ], [ "Q8BSN9-1", "protein_xref_refseq", "NP_001317352.1", "20869947", "These results introduce FASTKD3 as an essential component of mitochondrial respiration that may modulate energy balance in cells exposed to adverse conditions by functionally coupling mitochondrial protein synthesis to respiration." ], [ "Q9CQA3-1", "protein_xref_refseq", "NP_075863.2", "30159755", "The present study identified a potential role for the tumor microenvironment in influencing phenotypic features of SDHB-mutated Pheochromocytomas and paragangliomas." ], [ "Q3UFT3-1", "protein_xref_refseq", "NP_001028617.2", "24003223", "Data indicate that a subtype of GAREM, GAREM2, is specifically expressed in the mouse, rat, and human brain." ], [ "Q923J1-1", "protein_xref_refseq", "NP_001157797.1", "31392516", "Magnesium-Induced Cell Survival Is Dependent on TRPM7 Expression and Function." ], [ "Q923J1-1", "protein_xref_refseq", "NP_001157797.1", "31545149", "High levels of obesity hormone leptin induce hypertension by acting on Trpm7 channels in the carotid body." ], [ "Q923J1-1", "protein_xref_refseq", "NP_001157797.1", "31650715", "Functional expression of TRPM7 as a Ca(2+) influx pathway in adipocytes." ], [ "Q923J1-1", "protein_xref_refseq", "NP_001157797.1", "12508053", "The Trpm7 ion channel possesses the unique ability to efficiently conduct many essential trace metal ions such as Zn2+, Fe2+, Cu2+, Mn2+, and Co2+ into cells, along with several toxic metal ions such as Cd2+, Ba2+, and Sr2+ as well." ], [ "Q8CIT9-1", "protein_xref_refseq", "NP_001077372.1", "30919591", "SBSN expression was observed in human clinical specimens of colon and ovarian carcinomas, as well as in circulating tumour cells and metastases of the 4T1 mouse model. The association of SBSN expression with progressive stages of cancer development indicates its role in cancer evolution and therapy resistance." ], [ "Q8CIT9-1", "protein_xref_refseq", "NP_001077372.1", "25283635", "Findings suggest that SBSN is involved in the angiogenic potential of tumor endothelial cells (TEC) and may be a novel TEC marker." ], [ "Q8CIT9-1", "protein_xref_refseq", "NP_001077372.1", "17330888", "Sbsn, Dmkn and Krtdap are coordinately expressed during epidermal morphogenesis." ], [ "Q8CIT9-1", "protein_xref_refseq", "NP_001077372.1", "12228223", "These results indicate that the suprabasin protein potentially plays a role in the process of epidermal differentiation. GeneRIF: These results indicate that the suprabasin protein potentially plays a role in the process of epidermal differentiation" ], [ "Q8BFT9-1", "protein_xref_refseq", "NP_081081.1", "19013223", "These results indicate that msvop is a central nervous system-specific gene and could be utilized for elucidating gene regulation in neuronal cells." ], [ "Q61702-1", "protein_xref_refseq", "NP_001293007.1", "", "This gene encodes a heavy chain of inter-alpha trypsin inhibitor (IaI) family of plasma serine protease inhibitors. IaI proteins are protein-glycosaminoglycan-protein complexes comprised of two heavy chains and a light chain. The encoded protein covalently associates with the light chain via a chondroitin sulfate moiety. Intravenous administration of the encoded protein improved survival of mice after infection with Escherichia coli. This gene is located adjacent to two other IaI heavy chain genes. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing to generate mature protein. [provided by RefSeq, Oct 2015]." ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "31408613", "Study demonstrates that CD82 is a specific regulator of TLR9 signaling, which may be critical in cancer immunotherapy approaches and coordinating the innate immune response to pathogens." ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "31010852", "These data demonstrate that CD82 organizes the proper assembly of Dectin-1 signaling machinery in response to Candida albicans" ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "30133344", "Data provide evidence that CD82 is an important regulator of HSPC bone marrow maintenance, homing, and engraftment." ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "29782939", "Loss of CD82 resulted in defects in osteoclast, osteoblast, and adipocyte lineages." ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "29760437", "CD82-RUNX1-Rab5/22 axis may be a previously unrecognized virulence mechanism of Mycobacterium tuberculosis pathogenesis. Publication Status: Online-Only" ], [ "P40237-1", "protein_xref_refseq", "NP_001129527.1", "16372335", "An antibody to this protein that can specifically detect murine Kai1/CD82, should be useful in addressing the mechanism of action of Kai1 in metastatic suppression." ], [ "Q9ERS5-1", "protein_xref_refseq", "NP_112547.1", "27859053", "This study shows that TAPP1/2 double knock-out mice develop chronic germinal centers with age and show abnormal expression of B-cell activation and develop lupus-like characteristics including anti-DNA antibodies and deposition of immune complexes in kidneys" ], [ "Q9ERS5-1", "protein_xref_refseq", "NP_112547.1", "22777911", "Interacts with phosphatidylinositol (3,4)-bisphosphate thus regulating B-cell activation and autoantibody production" ], [ "Q9QXW2-1", "protein_xref_refseq", "NP_038936.1", "30703849", "FBXW5 facilitated the addition of Lys63-linked ubiquitin to ASK1 and thus exacerbated ASK1-c-Jun N-terminal kinase/p38 MAPK signaling, inflammation, and lipid accumulation." ], [ "P23298-1", "protein_xref_refseq", "NP_001300906.1", "", "Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and the second messenger diacylglycerol. PKC family members phosphorylate a wide variety of protein targets and are known to be involved in diverse cellular signaling pathways. PKC family members also serve as major receptors for phorbol esters, a class of tumor promoters. Each member of the PKC family has a specific expression profile and is believed to play a distinct role in cells. The protein encoded by this gene is one of the PKC family members. It is a calcium-independent and phospholipids-dependent protein kinase. It is predominantly expressed in epithelial tissues and has been shown to reside specifically in the cell nucleus. This protein kinase can regulate keratinocyte differentiation by activating the MAP kinase MAPK13 (p38delta)-activated protein kinase cascade that targets CCAAT/enhancer-binding protein alpha (CEBPA). It is also found to mediate the transcription activation of the transglutaminase 1 (TGM1) gene. Mutations in the human gene are associated with susceptibility to cerebral infarction. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]." ], [ "P23298-1", "protein_xref_refseq", "NP_001300906.1", "30154443", "These findings reveal a novel Rictor-Prkch-Klf4 pathway that plays an important role in the regulation of Embryonic stem cells differentiation" ], [ "P23298-1", "protein_xref_refseq", "NP_001300906.1", "24705298", "Genetic deficiency results in defective suppressive activity of T reg cells" ], [ "Q8VD00-1", "protein_xref_refseq", "NP_598467.1", "28644012", "Study generated a series of sigma1R and sigma2R/Tmem97 agonists and antagonists and tested them for efficacy in the mouse spared nerve injury model. Results show robust antineuropathic pain effects of sigma1R and sigma2R/Tmem97 ligands, demonstrate that sigma2R/Tmem97 is a novel neuropathic pain target, and identify sigma2R/Tmem97 agonist UKH-1114 as a lead molecule for further development." ], [ "Q8CHS7-1", "protein_xref_refseq", "NP_001013031.2", "29330505", "Study demonstrates that the skeletal muscle protein SRP-35, a retinol dehydrogenase, is directly involved in skeletal muscle metabolism, since its over-expression results in higher glucose uptake and increased glycogen storage. In addition, SRP-35 over-expression improves muscle performance in vivo. Publication Status: Online-Only" ], [ "Q8CHS7-1", "protein_xref_refseq", "NP_001013031.2", "27806939", "Taken together, our findings suggested that DHRS7C maintains intracellular Ca(2+) homeostasis involving the ER/SR and that functional loss of DHRS7C leads to Ca(2+) overload in the cytosol and ER/SR, resulting in enlarged cellular morphology via calpain activation" ], [ "Q8CHS7-1", "protein_xref_refseq", "NP_001013031.2", "21995425", "Skeletal muscle SRP-35 is involved in the generation of all-trans-retinaldehyde and may play an important role in the generation of intracellular signals linking Ca2+ release (i.e. muscle activity) to metabolism." ], [ "G3X972-1", "protein_xref_refseq", "NP_001161745.1", "29939162", "These data suggest that SEC24C is a major cargo adapter for COPII-dependent transport in postmitotic neurons in developing and adult brains and that its functions overlap at least partially with those of SEC24D in mammals." ], [ "G3X972-1", "protein_xref_refseq", "NP_001161745.1", "24876386", "Thus, SEC24C is required in early mammalian development but is dispensable in a number of tissues, likely as a result of compensation by other Sec24 paralogs." ], [ "G3X972-1", "protein_xref_refseq", "NP_001161745.1", "21454670", "The serotonin transporter is an exclusive client of the coat protein complex II (COPII) component SEC24C" ], [ "Q8K409-1", "protein_xref_refseq", "NP_035260.1", "30763888", "DNA polymerases beta and lambda in single-nucleotide and multinucleotide pathways of mammalian base excision DNA repair" ], [ "Q8K409-1", "protein_xref_refseq", "NP_035260.1", "30274781", "The Polb/p53 double knockout animals exclusively developed medulloblastoma and no other type of brain tumor." ], [ "Q8K409-1", "protein_xref_refseq", "NP_035260.1", "29968395", "To evaluate whether Polb might be causative in senescence induction, the study evaluated the impact of murine Polb nullizygosity on senescence. Unexposed DNA polymerase beta-null primary fibroblasts exhibit a robust increase in the number of senescent cells compared to wild-type (11-fold, P < 0.001), demonstrating that loss DNA polymerase betais sufficient to induce senescence." ], [ "Q8K019-1", "protein_xref_refseq", "NP_001020564.1", "31644907", "RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex." ], [ "Q8K019-1", "protein_xref_refseq", "NP_001020564.1", "29466738", "Myogenic differentiation is achieved through the specific interaction between Cry2 and Bclaf1, which stabilizes mRNAs encoding cyclin D1, a G1/S phase transition regulator, and Tmem176b, a transmembrane regulator for myogenic cell fusion." ], [ "Q8K019-1", "protein_xref_refseq", "NP_001020564.1", "28120329", "Constitutive expression of the anti-apoptotic molecule Bfl1 (A1) in murine vascular Endothelial Cells leads to prolonged allograft survival due to modifying inflammation." ], [ "Q925J9-1", "protein_xref_refseq", "NP_001073587.1", "31894315", "MiR146a improves hepatic lipid and glucose metabolism by targeting MED1." ], [ "Q925J9-1", "protein_xref_refseq", "NP_001073587.1", "31798643", "MicroRNA-146a exerts a protective effect against myocardial ischemia reperfusion injury, which might be partially mediated by the target gene Med1 and related to the apoptosis signaling pathway. Publication Status: Online-Only" ], [ "Q925J9-1", "protein_xref_refseq", "NP_001073587.1", "30461303", "DEletion of cardiac Med1 inhibits RNA polymerase II promoter occupancy and promotes chromatin remodeling." ], [ "Q925J9-1", "protein_xref_refseq", "NP_001073587.1", "29293266", "B-cell conditional deficient mice for the Med1 subunit display robust somatic hypermutation." ], [ "P98086-1", "protein_xref_refseq", "NP_031598.2", "32719333", "Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model. Publication Status: Online-Only" ], [ "P98086-1", "protein_xref_refseq", "NP_031598.2", "31801811", "These findings illustrate that the development and experience-dependent plasticity of V1b is mostly normal in the absence of C1q, even though C1q has previously been shown to be required for developmental synapse elimination in the mouse visual thalamus as well as sensorimotor cortex." ], [ "Q9DA37-1", "protein_xref_refseq", "NP_080559.1", "25605874", "Study reveals that all mouse SMS family members (SMSr, SMS1, and SMS2) have CPE synthase activity" ], [ "Q9R087-1", "protein_xref_refseq", "NP_035951.1", "28869591", "Adult female Gpc6-/- mice were compared with wild-type control mice of identical C57BL/6 background. Consistent with the phenotype of omodysplasia 1, Gpc6-/-mice had femurs and vertebrae that were shorter than those of wild-type mice. They also had increased femoral bone mineral content and increased cortical thickness." ], [ "J3QNX5-1", "protein_xref_refseq", "NP_001193950.1", "26623514", "This study indicates that AMPAR function is very precisely controlled by the cell-type specific expression of the CKAMP family members 39, 52 and 59. Erratum:[Elife. 2018 Oct 11;7:. PMID: 30306889] Publication Status: Online-Only" ], [ "Q6PAV2-1", "protein_xref_refseq", "NP_080377.2", "26825710", "HERC4 plays an important role in Multiple myeloma progression." ], [ "Q6PAV2-1", "protein_xref_refseq", "NP_080377.2", "17967448", "The E3 ubiquitin ligase Herc4, though ubiquitously expressed in all tissues, is most highly expressed in the testis, specifically during spermiogenesis" ], [ "Q61789-1", "protein_xref_refseq", "NP_001334390.1", "27729280", "The gradual disappearance of alpha3 chain-containing laminins along the dermal-epidermal junction and formation of subepidermal blisters like in congenital junctional epidermis bullosa." ], [ "Q8R149-1", "protein_xref_refseq", "NP_666112.1", "30639243", "BUD13 is a protein that has the ability to increase splicing of the Irf7 intron. BUD13 depletion compromises type I interferon response by countering intron retention in Irf7." ], [ "Q8VG16-1", "protein_xref_refseq", "NP_666957.1", "", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]." ], [ "O88196-1", "protein_xref_refseq", "NP_033467.2", "27586445", "USP16 and TTC3 were dysregulated in all affected human cells and two mouse models of Down syndrome. Publication Status: Online-Only" ], [ "O88196-1", "protein_xref_refseq", "NP_033467.2", "17488780", "These results suggest that the TTC3-RhoA-CIT-K pathway could be a crucial determinant of in vivo neuronal development, whose hyperactivity may result in detrimental effects on the normal differentiation program." ], [ "O88708-1", "protein_xref_refseq", "NP_001170784.1", "28230328", "Together, these data demonstrate that ORC4 oligomerization is required to form the ORC4 cage and that it is required for polar body extrusion." ], [ "O88708-1", "protein_xref_refseq", "NP_001170784.1", "25502171", "ORC4 surrounds the chromatin that will be extruded in the polar body in both female meiotic divisions, then makes a transition from the cytoplasm to the chromosomes at zygotic anaphase, suggesting multiple roles for this replication licensing protein." ], [ "Q8K3W0-2", "protein_xref_refseq", "NP_653124.1", "28436570", "Bre enhances osteoblastic differentiation by promoting the Mdm2-mediated degradation of p53." ], [ "Q8K3W0-2", "protein_xref_refseq", "NP_653124.1", "27001068", "Results demonstrate a role for BRE in both replicative senescence and DNA damage-induced premature senescence. This can be attributed to BRE being required for BRCA1-A complex-driven HR DNA repair Publication Status: Online-Only" ] ] }, "readme": "Name\n - Mouse Protein Function (NCBI Refseq)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-03-16T15:38:06.344586\n\nModified on\n - 2022-01-19T11:17:18.850708\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Protein Function (NCBI RefSeq) dataset contains biological function annotation of mouse [taxid:10090] genes from GeneRIF section in the NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen. \n\nDescription Domain\n Keywords\n - protein function\n - NCBI RefSeq\n - geneRIF\n - PMID\n\n Pipeline Steps\n - Step-1: The script extract-from-gp.py extracts protein function information from NCBI RefSeq gpff format files and maps it to the UniProtKb canonical accessions for a final dataset output in a csv format. \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/pipeline/extractor/extract-from-endpoint.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: mouse_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_refseq.csv\n Name: efseq_protein_all_10090.gpff\n URI: https://data.glygen.org/ln2wwwdata/source/refseq_protein_all_10090.gpff\n Output Subdomain\n Name: mouse_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_function_refseq.csv\n Name: mouse_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_function_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/mouse_protein_function_refseq.csv" }