{ "bcoid": "GLY_000133", "title": "Human Refseq Protein Function", "description": "The Human NCBI RefSeq Protein Function dataset contains biological function annotaion 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": [ [ "Q9Y5H2-1...", "RefSeq..." ], [ "Q9Y5H2-1...", "RefSeq..." ] ], "headers": [ "uniprotkb_ca...", "database_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_name" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "Q9Y5H2-1", "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", "RefSeq", "NP_061737.1", "15799819", "PCDH-gamma-A11 is silenced epigenetically in astrocytic gliomas" ], [ "Q9BSR8-1", "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", "RefSeq", "NP_115688.1", "26235900", "YIPF4 is a binding partner of the papillomavirus E5 proteins. Publication Status: Online-Only" ], [ "Q9BSR8-1", "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." ], [ "Q96LR9-1", "RefSeq", "NP_001123887.1", "20628086", "Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)" ], [ "Q96LR9-1", "RefSeq", "NP_001123887.1", "19913121", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "Q9UPM8-1", "RefSeq", "NP_031373.2", "26542808", "The bivalency of the interactions contributes to a higher avidity of tepsin for AP-4." ], [ "Q9UPM8-1", "RefSeq", "NP_031373.2", "26544806", "Rare Variants in AP4E1 is associated with deficits in intracellular trafficking, and Persistent Stuttering." ], [ "Q9UPM8-1", "RefSeq", "NP_031373.2", "20972249", "An autosomal recessive form of spastic tetraplegic cerebral palsy with profound intellectual disability, microcephaly, epilepsy and white matter loss in a consanguineous family resulting from a homozygous deletion involving AP4E1." ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "29749460", "Hypoxia induces the expression of TXNDC5 via upregulating HIF-1alpha in colorectal cancer cells." ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "29784879", "The mannose-trimming activity of EDEM3 toward the model misfolded substrate, the glycoprotein T-cell receptor alpha locus (TCRalpha), was reconstituted only when ERp46 had established a covalent interaction with EDEM3" ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "29131315", "TXNDC5 contributes to abnormal rheumatoid arthritis synovial fibroblast-like cells proliferation, migration and IL-6 production by inhibiting IGFBP1 expression." ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "28604976", "TXNDC5 is also closely associated with rheumatoid arthritis, diabetes, hepatic steatosis and vitiligo. [review] Review article" ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "26810069", "High TXNDC5 expression is associated with renal cell carcinoma." ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "17895523", "Upregulation of TXNDC5 are involved in the early development of colorectal cancer" ], [ "Q8NBS9-1", "RefSeq", "NP_110437.2", "12963716", "Member of the protein disulphide isomerase family and highly expressed in endothelial cells. Protects endothelial cells from apoptosis under hypoxia." ], [ "Q9C0K0-1", "RefSeq", "NP_612808.1", "29503088", "BCL11B regulates mammary cell differentiation." ], [ "Q9C0K0-1", "RefSeq", "NP_612808.1", "29203643", "Results confirm the BCL11B dimerization hypothesis and prove its importance for BCL11B function. By mapping the relevant regions to the CCHC domain, authors describe a previously unidentified mechanism of transcription factor homodimerization. Publication Status: Online-Only" ], [ "Q9C0K0-1", "RefSeq", "NP_612808.1", "29039465", "These results suggest that the upregulation of miR-650 contributes to the development of acute renal allograft rejection by suppression of BCL11B, which leads to apoptosis and inflammatory responses. Thus, miR-650 and BCL11B may represent potential therapeutic targets for the prevention of acute renal allograft rejection." ], [ "Q9C0K0-1", "RefSeq", "NP_612808.1", "28794504", "Decreased transcript and increased promoter methylation levels of BCL11B gene were identified in ankylosing spondylitis patients." ], [ "Q9C0K0-1", "RefSeq", "NP_612808.1", "28669733", "Human T-cell leukemia virus type 1 (HTLV-1) Tax directly binds to BCL11B. Tax enhances BCL11B degradation through proteasome pathway. Loss of BCL11B enhances cell growth in HTLV-1-infected cells." ], [ "Q8N475-1", "RefSeq", "NP_064501.2", "26045876", "FSTL5 plays a suppressive role in hepatocellular carcinoma. Down-regulation of FSTL5 could promote growth and survival of HCC cells by activation of Wnt/beta-catenin signaling. Publication Status: Online-Only" ], [ "Q8N475-1", "RefSeq", "NP_064501.2", "21911727", "FSTL5 expression denoted a dismal prognosis both within and across medulloblastoma subgroups." ], [ "Q3ZCQ2-1", "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", "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", "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", "RefSeq", "NP_001014301.1", "23640736", "AXIIR acts as a novel inducer of apoptosis in human cells, partially through activating Caspase-8." ], [ "Q3ZCQ2-1", "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", "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", "RefSeq", "NP_001014301.1", "16895901", "Analysis of the annexin II receptor on human marrow stromal cells" ], [ "O96024-1", "RefSeq", "NP_003773.1", "30611881", "B3GALT4 knockdown decreases GM1 ganglioside level and enhances vulnerability for neurodegeneration." ], [ "O96024-1", "RefSeq", "NP_003773.1", "30131660", "Colorectal cancer (CRC) patients expressing both high B7-H3 and high B3GALT4 contributed to a significant decrease in overall survival. The expression of B3GALT4 in CRC is positively correlated with B7-H3 expression in vitro. B7-H3/B3GLAT4 may be used as dual prognostic biomarkers for CRC." ], [ "O96024-1", "RefSeq", "NP_003773.1", "21519903", "Induction of GM1a/GD1b synthase triggers complex ganglioside expression and alters neuroblastoma cell behavior; a new tumor cell model of ganglioside function" ], [ "O96024-1", "RefSeq", "NP_003773.1", "20594196", "Data showed that GM1/GD1b/GA1 synthase transfectant cells had definite reduction in cell growth and invasion." ], [ "O96024-1", "RefSeq", "NP_003773.1", "19851445", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "O14810-1", "RefSeq", "NP_006642.1", "28422131", "Homozygous CPLX1 variants were identified in three patients with severe infantile myoclonic epilepsy and ID." ], [ "O14810-1", "RefSeq", "NP_006642.1", "28108469", "Data define CPLX1 as a PD risk factor and provide functional insights into the role and regulation of blood SNCA levels. The new blood biomarkers of PARK4 in this Turkish family might become useful for PD prediction" ], [ "O14810-1", "RefSeq", "NP_006642.1", "27866231", "This study demonstrated that complexin-I influence cognitive function in early and late stages of Alzheimer's disease." ], [ "O14810-1", "RefSeq", "NP_006642.1", "26577184", "Study showed for the first time that neuro-Behcet's disease and Behcet's disease patients are inclined to display the GG genotype of the CPLX1 rs936551 polymorphism and to exhibit increased CPLX1 expression levels" ], [ "O14810-1", "RefSeq", "NP_006642.1", "26603934", "Collectively these results demonstrate that CPX-1 is a secreted collagen-binding glycoprotein and provide a foundation for future studies investigating the function of CPX-1." ], [ "P46821-1", "RefSeq", "NP_005900.2", "29925525", "MAP1B-LC1 links microtubules and Stx17 in fed cells, and starvation causes the dephosphorylation of MAP1B-LC1 at Thr217, allowing Stx17 to dissociate from MAP1B-LC1 and bind to Atg14L." ], [ "P46821-1", "RefSeq", "NP_005900.2", "29136244", "High MAP1B expression is associated with resistance to mTOR inhibition in glioblastoma." ], [ "P46821-1", "RefSeq", "NP_005900.2", "29738522", "All of the patients with a microtubule associated protein 1B (MAP1B) variant had a similar brain abnormality, and at least one of the parents who transmitted the variant to their child was also similarly affected. Publication Status: Online-Only" ], [ "P46821-1", "RefSeq", "NP_005900.2", "29432744", "MAP1B heavy chain has a unique binding site for a calcium-binding protein ALG-2." ], [ "P46821-1", "RefSeq", "NP_005900.2", "28864773", "These results suggest that a change in the intracellular calcium level plays a role in regulation of the secretory pathway via interaction of ALG-2 with MISSL and MAP1B." ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "28739720", "Our findings expanded the understanding of the role of BATF2 in tumors, and also suggested a potential of using BATF2 as a therapeutic target to hinder bevacizumab induced epithelial-mesenchymal transition in glioblastoma." ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "27785591", "BATF2 gene was modulated after treatment with zebularine and was a poor prognostic marker, since its low levels were correlated with relapse and a poor prognosis for medulloblastoma patients. Erratum:[Invest New Drugs. 2017 Feb;35(1):124. PMID: 27900530]" ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "27926863", "Gain- and loss-of-function studies uncovered a role for Batf2 in myeloid differentiation in both murine and human systems. We thus demonstrate that chronic infection can deplete HSPCs and identify BATF2 as a mediator of infection-induced HSPC terminal differentiation" ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "26808579", "Results demonstrate that SARI is a novel target gene of glucocorticoid receptor, and the upregulation of SARI plays an important role in dexamethasone's killing effect on B lymphoma cells." ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "26977016", "BATF2 may exert selective pressure on the recombination machinery via a repetitive motif-based mechanism for the maintenance of heterochromatin stability." ], [ "Q8N1L9-1", "RefSeq", "NP_612465.3", "20473897", "Decreased expression of BATF2 is associated with hepatocellular carcinoma." ], [ "Q15758-1", "RefSeq", "NP_005619.1", "30635397", "The ASCT2 deficiency was compensated by increased levels of sodium neutral amino acid transporter 1 (SNAT1 or SLC38A1) and SNAT2 (SLC38A2) in ASCT2ko 143B cells, mediated by a GCN2 EIF2alpha kinase (GCN2)-dependent pathway, but this compensation was not observed in ASCT2ko HCC1806 cells." ], [ "Q15758-1", "RefSeq", "NP_005619.1", "30272366", "Results demonstrated that ASCT2 and pmTOR protein levels were significantly higher in epithelial ovarian cancer (EOC) tissues and predicting a poor prognosis. The expression levels of ASCT2 and pmTOR in EOC were positively correlated indicating a synergistic effect on the growth and development of early EOC." ], [ "Q15758-1", "RefSeq", "NP_005619.1", "30029480", "These data collectively establish that in an in vitro context, human epithelial and mesenchymal hepatocellular carcinoma cell lines adapt to ASCT2 or LAT1 knockout. Publication Status: Online-Only" ], [ "Q15758-1", "RefSeq", "NP_005619.1", "30071532", "SLC1A5 expression is increased in tumor samples from esophageal cancer patients, and downregulation of SLC1A5 inhibited cell cycle progression and esophageal cancer growth." ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "30535460", "MLK7AS1 has potential as a biomarker and may promote proliferation in CRC partially through downregulating p21 expression." ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "29654619", "The expression of ZAKbeta is dependent on ZAKalpha expression, and ZAKbeta further enhances ZAKalpha expression and results in synergistic enhancement of apoptosis in osteosarcoma cells." ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "29071797", "The ZAK rs3769201 and rs722864 may be functional susceptibility loci for lung cancer risk." ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "27816943", "Recessive mutations in the kinase ZAK - novel cause of congenital myopathy." ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "26755636", "ZAK is a key player in mammalian limb patterning in humans and mice." ], [ "Q86SG6-1", "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", "RefSeq", "NP_835464.1", "26967905", "Our study demonstrates that NEK8 human mutations cause major organ developmental defects due to altered ciliogenesis and cell differentiation/proliferation through deregulation of the Hippo pathway Publication Status: Online-Only" ], [ "Q86SG6-1", "RefSeq", "NP_835464.1", "26697755", "The mutations: c.2069_2070insC variant (p.Ter693LeufsTer86), and a c.1043C>T variant (p.Thr348Met) in RCC1 domain of NEK8 in two brothers with cardiac, renal, and hepatic anomalies" ], [ "Q86SG6-1", "RefSeq", "NP_835464.1", "15872312", "Characterization of the proteome in mice that have a double point mutation in the related gene." ], [ "Q86SG6-1", "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." ], [ "Q9P0P0-1", "RefSeq", "NP_057578.1", "26711259", "RNF181 limits the proliferation of human diffuse large B cell lymphoma cells that depend upon aberrant CARD11 signaling to NF-kappaB for growth and survival in culture. Erratum:[Mol Cell Biol. 2016 Apr;36(8):1322. PMID: 27034408] Publication Status: Online-Only" ], [ "Q9P0P0-1", "RefSeq", "NP_057578.1", "26398855", "The identification and validation of proteins interacting with HSP238 may lead to the discovery of novel mechanisms through which HSPC238 suppresses tumorigenesis in human hepatocellular carcinoma" ], [ "Q9P0P0-1", "RefSeq", "NP_057578.1", "21391225", "RN181 suppresses the tumorigenesis of hepatocellular carcinoma through the inhibition of ERK/MAPK signaling in the liver." ], [ "Q9P0P0-1", "RefSeq", "NP_057578.1", "19426595", "Data show LOC51255 (RNF181) protein located in the cytoplasm of HePG2 cell line." ], [ "Q9P0P0-1", "RefSeq", "NP_057578.1", "18331836", "The presence of RN181 in human platelets was established; RN181 has ubiquitin E3 ligase activity." ], [ "Q63HQ0-1", "RefSeq", "NP_061039.3", "21525240", "Conclude that a specific fraction of the AP2-derived endocytic pathway is dedicated to secretory purposes under the control of AP1 and Gadkin" ], [ "Q63HQ0-1", "RefSeq", "NP_061039.3", "20332099", "Observational study of gene-disease association. (HuGE Navigator) Erratum:[Hum Mol Genet. 2010 Oct 15;19(20):4121. Hesselbrock, Victor [added]; Tischfield, Jay A [added]]" ], [ "Q63HQ0-1", "RefSeq", "NP_061039.3", "19965873", "Studies unravel the molecular basis for Gadkin-mediated AP-1 recruitment to TGN/endosomal membranes and identify a novel subtype of the AP-1-binding motif." ], [ "Q63HQ0-1", "RefSeq", "NP_061039.3", "19706427", "Gadkin (gamma-BAR), a peripheral membrane protein localized to the trans-Golgi network and to endosomal vesicles, directly associates with the clathrin adaptor AP-1 and the motor protein kinesin KIF5, potentially regulating endosomal vesicle dynamics." ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "28255813", "This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in squamous cell carcinoma of the tongue" ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "22949199", "Rab6A'(Q72L) was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 1.9 A from a crystal belonging to space group P22(1)2(1) with unit-cell parameters a = 36.84, b = 96.78, c = 109.99 A" ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "20198315", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "20064528", "RAB6C is a rare example of a recently emerged retrogene that has acquired the status of a new gene, encoding a functional protein with altered characteristics compared to Rab6A'." ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "17426708", "The negative role played by the WTH3 gene in MDR development is through its proapoptotic potential that is regulated by multiple mechanisms at the transcription level, and one of these mechanisms is linked to the p53 gene." ], [ "Q9H0N0-1", "RefSeq", "NP_115520.2", "16267028", "The behavior of WTH3 in primary drug-resistant breast cancer epithelial cells was similar to that in a model system where epigenetic regulation of the WTH3 gene was linked to the MDR phenotype." ], [ "Q8TE73-1", "RefSeq", "NP_001360.1", "28939216", "A novel mutation causing primary ciliary dyskinesia was found in Japanese patients." ], [ "Q8TE73-1", "RefSeq", "NP_001360.1", "27988889", "These findings demonstrated that new DNAH5 mutations could be used for molecular diagnosis of Kartagener syndrome, providing families with genetic counseling and prenatal diagnosis." ], [ "Q8TE73-1", "RefSeq", "NP_001360.1", "27779714", "To the best of our knowledge, the first reported case of PCD caused by the DNAH5 mutation in a Japanese patient." ] ] }, "readme": "Name\n - Human Refseq Protein Function\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-03-16T15:35:15.248632\n\nModified on\n - 2019-09-12T17:35:06.698252\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]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Human NCBI RefSeq Protein Function dataset contains biological function annotaion of human [taxid:9606] genes from GeneRIF section in the NCBI RefSeq database The data is downloaded from NCBI RefSeq and is processed into a dataset by GlyGen. 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 accesion 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/ln2data/releases/data/v-1.4.5/source/source/refseq_protein_all_9606.gpff\n Name: human_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_xref_refseq.csv\n Output Subdomain\n Name: human_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_function_refseq.csv\n Name: human_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/human_protein_function_refseq.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"12317\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"12317\"\n Name: \"database_name\"\n Description: \"The name of the source database\"\n Unique Values: \"1\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"43724\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"43231\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/human_protein_function_refseq.csv" }