{ "bcoid": "GLY_000133", "title": "Human Protein Function (NCBI Refseq)", "description": "The Human Protein Function (NCBI RefSeq) dataset contains biological function annotation of human [taxid:9606] ...", "filename": "human_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P01135-1...", "protein_xref..." ], [ "P01135-1...", "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" } ], [ "P01135-1", "protein_xref_refseq", "NP_001295087.1", "", "This gene encodes a growth factor that is a ligand for the epidermal growth factor receptor, which activates a signaling pathway for cell proliferation, differentiation and development. This protein may act as either a transmembrane-bound ligand or a soluble ligand. This gene has been associated with many types of cancers, and it may also be involved in some cases of cleft lip/palate. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]." ], [ "P01135-1", "protein_xref_refseq", "NP_001295087.1", "32259630", "Loss of circRNA_0084043 depressed HG-induced damage via sponging miR-140-3p and regulating TGFA." ], [ "P01135-1", "protein_xref_refseq", "NP_001295087.1", "31125781", "Our results have shown that high levels of TGF-alpha and Ki-67 are associated with shorter PFS in patients with chordoma. We also identified TGF-alpha as a potential novel biomarker for predicting prognosis for patients with skull base chordoma." ], [ "P01135-1", "protein_xref_refseq", "NP_001295087.1", "30906781", "Our study found that spherical silica nanoparticles (SiNPs) promoted the proliferation and EMT of BEAS-2B cells by inducing the release of TGF-a from THP-1 cells. Publication Status: Online-Only" ], [ "Q9Y5H2-1", "protein_xref_refseq", "NP_061737.1", "", "This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]." ], [ "Q9Y5H2-1", "protein_xref_refseq", "NP_061737.1", "20388442", "The promoter methylation and mRNA expressions of EMP3 and PCDH-gamma-A11 are closely related with the malignant development of glioma." ], [ "Q9Y5H2-1", "protein_xref_refseq", "NP_061737.1", "15799819", "PCDH-gamma-A11 is silenced epigenetically in astrocytic gliomas" ], [ "Q9BSR8-1", "protein_xref_refseq", "NP_115688.1", "27999994", "The significance of YIPF4 protein for the maintenance of the morphology of the Golgi was tested by RNA interference, revealing a number of specific morphological changes to this organelle on their depletion." ], [ "Q9BSR8-1", "protein_xref_refseq", "NP_115688.1", "26235900", "YIPF4 is a binding partner of the papillomavirus E5 proteins. Publication Status: Online-Only" ], [ "Q9BSR8-1", "protein_xref_refseq", "NP_115688.1", "21757827", "YIPF4 was detected as a single mobility form consistent with its predicted molecular weight, three different mobility forms of YIPF3 were detected by western blotting." ], [ "Q86SG6-1", "protein_xref_refseq", "NP_835464.1", "", "This gene encodes a member of the serine/threionine protein kinase family related to NIMA (never in mitosis, gene A) of Aspergillus nidulans. The encoded protein may play a role in cell cycle progression from G2 to M phase. Mutations in the related mouse gene are associated with a disease phenotype that closely parallels the juvenile autosomal recessive form of polycystic kidney disease in humans. [provided by RefSeq, Jul 2008]." ], [ "Q86SG6-1", "protein_xref_refseq", "NP_835464.1", "27892797", "NEK8 plays a critical role in replication fork stability through its regulation of the DNA repair and replication fork protection protein RAD51." ], [ "Q86SG6-1", "protein_xref_refseq", "NP_835464.1", "15872312", "Characterization of the proteome in mice that have a double point mutation in the related gene." ], [ "Q86SG6-1", "protein_xref_refseq", "NP_835464.1", "15019993", "Data demonstrate for the first time that Nek8 is a novel tumor associated gene, and shares considerable sequence homology with the Nek family of protein kinases and may be involved in G(2)/M progression." ], [ "E2RYF6-1", "protein_xref_refseq", "NP_001185744.1", "28262390", "Genes TGFB1, TLE4 and MUC22 are associated with the risk of childhood asthma in Chinese population." ], [ "E2RYF6-1", "protein_xref_refseq", "NP_001185744.1", "20981447", "The mucin-like gene PBMUCL1 is also one of the candidate genes of Diffuse panbronchiolitis susceptibility." ], [ "Q99965-1", "protein_xref_refseq", "NP_001265043.1", "", "This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. The encoded protein is a subunit of an integral sperm membrane glycoprotein called fertilin, which plays an important role in sperm-egg interactions. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]." ], [ "Q99965-1", "protein_xref_refseq", "NP_001265043.1", "26252478", "ADAM2, CALR3 and SAGE1 cancer/testis antigens are not promising targets for immunotherapy of breast and lung cancer. Publication Status: Online-Only" ], [ "Q99965-1", "protein_xref_refseq", "NP_001265043.1", "18292840", "The fertilin beta contributes not only to successful fertilization, but may has an important impact in development of preimplantation embryos." ], [ "P31994-1", "protein_xref_refseq", "NP_001002275.1", "", "The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]." ], [ "P31994-1", "protein_xref_refseq", "NP_001002275.1", "31940267", "The authors identified a subset of effector CD8(+) T cells that expressed the inhibitory fragment crystallizable receptor FcgammaRIIB following activation and multiple rounds of division. these findings demonstrate a cell-intrinsic coinhibitory function of FcgammaRIIB in regulating CD8(+) T cell immunity." ], [ "P31994-1", "protein_xref_refseq", "NP_001002275.1", "31681256", "The Complex Association of FcgammaRIIb With Autoimmune Susceptibility. Review article Publication Status: Online-Only" ], [ "P31994-1", "protein_xref_refseq", "NP_001002275.1", "31560714", "Study in syngeneic mouse glioblastoma (GBM) model, human GBM samples, and cancer-immune cell co-culture revealed that IGFBP2-promoted immunosuppression associated with its induction of the mesenchymal feature of GBM cells and the inhibitory phosphorylated FcgammaRIIB of GBM exposed immune cells. Inhibition of IGFBP2 relieved immunosuppression by increasing CD8+ T and CD19+ B cells and decreasing CD163+ M2 macrophages. Publication Status: Online-Only" ], [ "P31994-1", "protein_xref_refseq", "NP_001002275.1", "31343409", "I232T substitution reduces in situ two-dimensional binding affinities and association rates of FcgammaRIIB to interact with its ligands, IgG1, IgG2 and IgG3 by three to four folds. This allosteric regulation by a single nucleotide polymorphism provides an intrinsic molecular mechanism for the functional loss of FcgammaRIIB-I232T in systemic lupus erythematosus patients. Publication Status: Online-Only" ], [ "Q8N5H3-3", "protein_xref_refseq", "NP_001092254.1", "25107909", "The functional relevance of the LRAP25-MRCK complex in LIMK1-cofilin signaling and the importance of LRAP adaptors as key determinants of MRCK cellular localization and downstream specificities." ], [ "Q8N5H3-3", "protein_xref_refseq", "NP_001092254.1", "11958456", "Identified two human genes, Mtvr1 and Mtvr2, encoding proteins highly related to the Mouse Mammary Tumor Virus receptor [Mtvr1] [Mtvr2]" ], [ "Q96LR9-1", "protein_xref_refseq", "NP_001123887.1", "", "APOLD1 is an endothelial cell early response protein that may play a role in regulation of endothelial cell signaling and vascular function (Regard et al., 2004 [PubMed 15102925]).[supplied by OMIM, Dec 2008]." ], [ "Q96LR9-1", "protein_xref_refseq", "NP_001123887.1", "20628086", "Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)" ], [ "Q96LR9-1", "protein_xref_refseq", "NP_001123887.1", "19913121", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "O75362-1", "protein_xref_refseq", "NP_006517.1", "31454071", "ZNF217 inhibited both COX2 and PGE2 synthesis through estradiol in KGN cells. ZNF217 and aromatase were decreased, whereas COX2 and PGE2 were increased in the GC of women with PCOS" ], [ "O75362-1", "protein_xref_refseq", "NP_006517.1", "30898548", "Indicated ZNF217 could recruit LSD1 to affect CDH1 epigenetic expression from transcription level." ], [ "O75362-1", "protein_xref_refseq", "NP_006517.1", "28607476", "ZNF217 contributed to ovarian hyperstimulation syndrome (OHSS) onset through promoting E2 synthesis and the increase of vascular permeability . Increased ZNF217 and decreased TSP-1 provided new targets for the prevention or treatment of OHSS Publication Status: Online-Only" ], [ "O75362-1", "protein_xref_refseq", "NP_006517.1", "28207159", "The report shows that the ZNF217 oncogene is a crucial mediator and indicator of bone metastasis from breast cancer." ], [ "O75362-1", "protein_xref_refseq", "NP_006517.1", "27768596", "This study underscored that elevated expression of ZNF217 promotes prostate cancer growth by restraining ferroportin -conducted iron egress" ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "", "This gene encodes a protein with sequence similarity to receptor-like protein tyrosine phosphatases. However, tyrosine phosphatase activity has not been experimentally validated for this protein. Studies of the rat ortholog suggest that the encoded protein may instead function as a phosphatidylinositol phosphatase with the ability to dephosphorylate phosphatidylinositol 3-phosphate and phosphatidylinositol 4,5-diphosphate, and this function may be involved in the regulation of insulin secretion. This protein has been identified as an autoantigen in insulin-dependent diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]." ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "30890718", "The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity. Publication Status: Online-Only" ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "27489308", "Copy-number variations are enriched for PTPRN2 and other neurodevelopmental genes in children with developmental coordination disorder." ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "27153397", "Haplotype-dependent allele-specific methylation of PTPRN2 gene is associated with neurological disorders." ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "26620550", "Reduction in plasma membrane PI(4,5)P2 abundance by PTPRN2 and PLCbeta1 releases the PI(4,5)P2-binding protein cofilin from its inactive membrane-associated state into the cytoplasm where it mediates actin turnover dynamics." ], [ "Q92932-1", "protein_xref_refseq", "NP_001295196.1", "20097759", "While PTPRN2 shares sequence similarity with protein tyrosine phosphatases, this study in rat suggests that this protein instead functions as a membrane bound phosphatidylinositol phosphatase." ], [ "Q8NE22-1", "protein_xref_refseq", "NP_001165461.1", "28029147", "SNP variants at the MAP3K1/SETD9 gene boundary associate with somatic PIK3CA variants in breast cancers." ], [ "P15121-1", "protein_xref_refseq", "NP_001619.1", "", "This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. This member catalyzes the reduction of a number of aldehydes, including the aldehyde form of glucose, and is thereby implicated in the development of diabetic complications by catalyzing the reduction of glucose to sorbitol. Multiple pseudogenes have been identified for this gene. The nomenclature system used by the HUGO Gene Nomenclature Committee to define human aldo-keto reductase family members is known to differ from that used by the Mouse Genome Informatics database. [provided by RefSeq, Feb 2009]." ], [ "P15121-1", "protein_xref_refseq", "NP_001619.1", "32412859", "AKR1B1 plays an important role in the occurrence and development of GC" ], [ "P15121-1", "protein_xref_refseq", "NP_001619.1", "31604989", "Vitamin K1 prevents diabetic cataract by inhibiting lens aldose reductase 2 (ALR2) activity. Publication Status: Online-Only" ], [ "P15121-1", "protein_xref_refseq", "NP_001619.1", "31539366", "ALR2 rs759853 and SDH rs2055858 polymorphisms were respectively associated with a higher and lower risk of diabetic retinopathy. Publication Status: Online-Only" ], [ "P15121-1", "protein_xref_refseq", "NP_001619.1", "30816220", "Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation. Publication Status: Online-Only" ], [ "Q9NRY2-1", "protein_xref_refseq", "NP_067041.1", "", "The protein encoded by this gene is a subunit of single-stranded DNA binding complexes that are important for maintaining genome stability. These complexes are involved in G2/M checkpoint control and homologous recombination repair. [provided by RefSeq, Jul 2016]." ], [ "Q9NRY2-1", "protein_xref_refseq", "NP_067041.1", "29150435", "INTS3, but not C9ORF80, affects the nucleic acid-binding ability of hNABP1 and hNABP2, indicating that INTS3 might regulate hNABP1/hNABP2 biological function, while the role of C9ORF80 remains unknown. Publication Status: Online-Only" ], [ "Q9NRY2-1", "protein_xref_refseq", "NP_067041.1", "19786574", "MISE is part of the INTS3/MISE/hSSB1 (IMS1) complex, which controls the DNA damage response" ], [ "Q9NRY2-1", "protein_xref_refseq", "NP_067041.1", "19605351", "HSSBIP1 forms complexes with INTS3/hSSB1 and INTS3/hSSB2 and participates in the DNA damage response" ], [ "Q9NRY2-1", "protein_xref_refseq", "NP_067041.1", "19683501", "SOSS-C is part of an ssDNA-binding heterotrimeric complex, SOSS which is involved in the maintenance of genome stability." ], [ "Q15777-1", "protein_xref_refseq", "NP_001138871.1", "", "This gene likely encodes a metallophosphoesterase. The encoded protein may play a role a brain development. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]." ], [ "Q15777-1", "protein_xref_refseq", "NP_001138871.1", "32040219", "CTN2 (rs6655267) and MPPED2 (rs536007) are not associated with primary dentition caries. MPPED2 (rs11031093, G Allele) is marginally associated." ], [ "Q15777-1", "protein_xref_refseq", "NP_001138871.1", "30846004", "Findings indicate that epigenetic alterations of MPPED2 promoter region appear sequentially during the colorectal neoplastic progression. Publication Status: Online-Only" ], [ "Q15777-1", "protein_xref_refseq", "NP_001138871.1", "21824479", "The structures of MPPED2 and two mutants show that the poor activity of MPPED2 is not only a consequence of the substitution of an active-site histidine residue by glycine but also due to binding of AMP or GMP to the active site." ], [ "Q15777-1", "protein_xref_refseq", "NP_001138871.1", "19240061", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "P40424-1", "protein_xref_refseq", "NP_001191892.1", "", "This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]." ], [ "P40424-1", "protein_xref_refseq", "NP_001191892.1", "31488872", "HNRPDL transforms hematopoietic cells and a novel HNRPDL/PBX1 axis plays an important role in human CML CD34(+) cells" ], [ "P40424-1", "protein_xref_refseq", "NP_001191892.1", "31885790", "Findings show that NANOG delays HF-MSC senescence by upregulating PBX1 and activating AKT signaling and that a feedback loop likely exists between PBX1 and AKT signaling. Publication Status: Online-Only" ], [ "P40424-1", "protein_xref_refseq", "NP_001191892.1", "31684818", "Expression of PBX1 and MMD was higher in the second trimester among lupus patients who experienced a poor pregnancy outcome compared to those who did not. The pilot study identified two candidate genes that are reflective of the platelet function response to aspirin." ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "", "The protein encoded by this gene is highly conserved in human, mouse, and chicken, showing 94% and 79% amino acid identity of human to mouse and chicken sequences, respectively. Hybridization to this gene was detected in spindle-shaped cells located along nerve fibers between the auditory ganglion and sensory epithelium. These cells accompany neurites at the habenula perforata, the opening through which neurites extend to innervate hair cells. This and the pattern of expression of this gene in chicken inner ear paralleled the histologic findings of acidophilic deposits, consistent with mucopolysaccharide ground substance, in temporal bones from DFNA9 (autosomal dominant nonsyndromic sensorineural deafness 9) patients. Mutations that cause DFNA9 have been reported in this gene. Alternative splicing results in multiple transcript variants encoding the same protein. Additional splice variants encoding distinct isoforms have been described but their biological validities have not been demonstrated. [provided by RefSeq, Oct 2008]." ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "32562050", "Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss." ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "30904974", "We selectively filtered out several reports describing DFNA9 patients with MD-like symptoms caused by COCH mutation" ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "30806805", "The aim of this study was to carry out a systematic review of all reported hearing and vestibular function data in P51S COCH mutation carriers and its correlation with age.[review]" ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "31126177", "In 3 families with hearing impairment, whole exome sequencing revealed 3 novel variants in KCNQ4, LHFPL5 and COCH genes. Another variant in a homozygous state (c.116T>A, p.L39X) was identified in the COCH gene which encodes a secretory protein. Publication Status: Online-Only" ], [ "O43405-1", "protein_xref_refseq", "NP_001334649.1", "29449721", "A homozygous nonsense c.292C>T(p.Arg98*) COCH variant was identified in two brothers with prelingual hearing impairment." ], [ "Q9Y294-1", "protein_xref_refseq", "NP_054753.1", "", "This gene encodes a member of the H3/H4 family of histone chaperone proteins and is similar to the anti-silencing function-1 gene in yeast. The protein is a key component of a histone donor complex that functions in nucleosome assembly. It interacts with histones H3 and H4, and functions together with a chromatin assembly factor during DNA replication and repair. [provided by RefSeq, Jul 2008]." ], [ "Q9Y294-1", "protein_xref_refseq", "NP_054753.1", "31286799", "ASF1A regulated H4(Y72ph) and promotes autophagy in colon cancer cells via a kinase activity through regulation of ATG" ], [ "Q9Y294-1", "protein_xref_refseq", "NP_054753.1", "31229404", "We demonstrate that the CIA-targeting complex promotes the ability of FBXL5 to degrade iron regulatory proteins. In addition, the FBXL5-CIA-targeting complex interaction is regulated by oxygen (O2) tension displaying a robust association in 21% O2 that is severely diminished in 1% O2 and contributes to O2-dependent regulation of IRP degradation" ], [ "Q9Y294-1", "protein_xref_refseq", "NP_054753.1", "30093638", "Faithful transmission of histone variants involves ASF1 and can be impacted by replication stress, with ensuing consequences for cell fate and tumorigenesis Publication Status: Online-Only" ], [ "Q9Y294-1", "protein_xref_refseq", "NP_054753.1", "11897662", "Model is proposed in which the synergism between hAsf1 and CAF-1 for nucleosome formation during DNA repair is achieved through a transient physical interaction allowing histone delivery from Asf1 to CAF-1" ], [ "Q9UQF2-1", "protein_xref_refseq", "NP_005447.1", "", "This gene encodes a regulator of the pancreatic beta-cell function. It is highly similar to JIP-1, a mouse protein known to be a regulator of c-Jun amino-terminal kinase (Mapk8). This protein has been shown to prevent MAPK8 mediated activation of transcription factors, and to decrease IL-1 beta and MAP kinase kinase 1 (MEKK1) induced apoptosis in pancreatic beta cells. This protein also functions as a DNA-binding transactivator of the glucose transporter GLUT2. RE1-silencing transcription factor (REST) is reported to repress the expression of this gene in insulin-secreting beta cells. This gene is found to be mutated in a type 2 diabetes family, and thus is thought to be a susceptibility gene for type 2 diabetes. [provided by RefSeq, May 2011]." ], [ "Q9UQF2-1", "protein_xref_refseq", "NP_005447.1", "30026235", "Extensive biochemical characterization of the KLC:JIP1 interaction, as well as identification of potential KLC1-binding partners, improves the understanding of how this growing family of cargos is recruited to kinesin1 by KLC1." ], [ "Q9UQF2-1", "protein_xref_refseq", "NP_005447.1", "27891669", "All binary complexes (KLC1:APP, KLC1:JIP1, and APP:JIP1) contain conformations with favorable binding free energies indicating that KLC1 and JIP1 may take part in APP transport in Alzheimer's disease patients." ], [ "Q9UQF2-1", "protein_xref_refseq", "NP_005447.1", "23825109", "Analysis of the role of JIP1 in APP transport; knockdown of JIP1 did not affect either amyloid precursor protein transport or amyloid-beta peptide production" ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "29694949", "Overexpression of AX2R significantly inhibited cell proliferation, migration and tube formation in both types of endothelial cells and increased the expression of KLF2, mediating VEGF and VEGFR2." ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "27183438", "Data highlighted the crucial role of AXIIR in reducing Mum2C cell viability through inducing apoptosis, while autophagy played a protective role in this process." ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "25633185", "These subsequent effects might be via suppressing the expression of matrix metalloproteinase 2 and matrix metalloproteinase 9. ... AXIIR participates in angiogenesis, and may be a potential therapeutic target for angiogenesis related diseases" ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "23640736", "AXIIR acts as a novel inducer of apoptosis in human cells, partially through activating Caspase-8." ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "22223826", "Results show that AXII and AXIIR play important roles in multiple myeloma (MM) and that targeting the AXII/AXIIR axis may be a novel therapeutic approach for MM." ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "18636554", "Annexin II and its receptor axis play a central role in prostate cancer metastasis, and prostate cancer utilizes the hematopoietic stem cell homing mechanisms to gain access to the niche." ], [ "Q3ZCQ2-1", "protein_xref_refseq", "NP_001014301.1", "16895901", "Analysis of the annexin II receptor on human marrow stromal cells" ], [ "Q6UXZ0-1", "protein_xref_refseq", "NP_001306871.1", "32508154", "Transcriptomic identification of TMIGD1 and its relationship with the ileal epithelial cell differentiation in Crohn's disease." ], [ "Q6UXZ0-1", "protein_xref_refseq", "NP_001306871.1", "32303178", "The mitochondrial outer membrane protein SYNJ2BP interacts with the cell adhesion molecule TMIGD1 and can recruit it to mitochondria. Publication Status: Online-Only" ] ] }, "readme": "Name\n - Human Protein Function (NCBI Refseq)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-03-16T15:35:15.248632\n\nModified on\n - 2022-01-19T11:15:01.844413\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 Human Protein Function (NCBI RefSeq) dataset contains biological function annotation of human [taxid:9606] genes from GeneRIF section in the NCBI RefSeq database. The dataset is downloaded 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 parses the NCBI RefSeq gpff files to extract the geneRIFs that contain protein function. The script also maps RefSeq accession to the UniProtKB Canonical accessions. \n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.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: refseq_protein_all_9606.gpff\n URI: https://data.glygen.org/ln2wwwdata/source/source/refseq_protein_all_9606.gpff\n Name: human_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_xref_refseq.csv\n Output Subdomain\n Name: human_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_function_refseq.csv\n Name: human_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_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/human_protein_function_refseq.csv" }