{ "bcoid": "GLY_000133", "title": "Human Protein Function (NCBI Refseq)", "description": "The Human Protein Function (NCBI RefSeq) 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." ], [ "E2RYF6-1", "RefSeq", "NP_001185744.1", "28262390", "Genes TGFB1, TLE4 and MUC22 are associated with the risk of childhood asthma in Chinese population." ], [ "E2RYF6-1", "RefSeq", "NP_001185744.1", "20981447", "The mucin-like gene PBMUCL1 is also one of the candidate genes of Diffuse panbronchiolitis susceptibility." ], [ "Q8N5H3-3", "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", "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", "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)" ], [ "Q92932-1", "RefSeq", "NP_001295196.1", "27489308", "Copy-number variations are enriched for PTPRN2 and other neurodevelopmental genes in children with developmental coordination disorder." ], [ "Q92932-1", "RefSeq", "NP_001295196.1", "27153397", "Haplotype-dependent allele-specific methylation of PTPRN2 gene is associated with neurological disorders." ], [ "Q92932-1", "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", "RefSeq", "NP_001295196.1", "25877877", "ProPTPRN2 elicited these effects through direct interaction with TRAF2." ], [ "Q92932-1", "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", "RefSeq", "NP_001165461.1", "28029147", "SNP variants at the MAP3K1/SETD9 gene boundary associate with somatic PIK3CA variants in breast cancers." ], [ "Q9NRY2-1", "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", "RefSeq", "NP_067041.1", "19786574", "MISE is part of the INTS3/MISE/hSSB1 (IMS1) complex, which controls the DNA damage response" ], [ "Q9NRY2-1", "RefSeq", "NP_067041.1", "19605351", "HSSBIP1 forms complexes with INTS3/hSSB1 and INTS3/hSSB2 and participates in the DNA damage response" ], [ "Q9NRY2-1", "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", "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", "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", "RefSeq", "NP_001138871.1", "19240061", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "P40424-1", "RefSeq", "NP_001191892.1", "31204910", "Most adult ALL patients with t (1; 19) (E2A-PBX1) is Pre B-Adult Acute Lymphoblastic Leukemia by Immunophenotyping" ], [ "P40424-1", "RefSeq", "NP_001191892.1", "30377043", "Our results indicate an important influence of the neurodevelopment genes, PBX1, LMX1A, and SLITRK1 in obsessive-compulsive disorder susceptibility" ], [ "P40424-1", "RefSeq", "NP_001191892.1", "29705861", "B-cell acute lymphoblastic leukemia patients with positive E2A-PBX1 fusion expression after transplant will have a poor prognosis." ], [ "P40424-1", "RefSeq", "NP_001191892.1", "29678569", "PBX1 plays an oncogenic role in clear cell renal carcinoma via JAK2/STAT3 pathway" ], [ "P40424-1", "RefSeq", "NP_001191892.1", "29694893", "An oncogenic role for the protein lysine methyltransferase SETDB2 in leukemia pathogenesis. It is overexpressed in pre-BCR(+) ALL and required for their maintenance in vitro and in vivo. SETDB2 expression is maintained as a direct target gene of the chimeric transcription factor E2A-PBX1 in a subset of ALL and suppresses expression of the cell-cycle inhibitor CDKN2C through histone H3K9 tri-methylation." ], [ "Q9Y294-1", "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", "RefSeq", "NP_054753.1", "29478807", "Uncovered DNA-PKcs-dependent DNA damage-induced ASF1A phosphorylation, which enhances chromatin assembly, promoting MMS22L-TONSL recruitment and, hence, Rad51 loading." ], [ "Q9Y294-1", "RefSeq", "NP_054753.1", "28943310", "ASF1a promotes non-homologous end joining repair by facilitating phosphorylation of MDC1 by ATM at double-strand breaks." ], [ "Q9Y294-1", "RefSeq", "NP_054753.1", "28625518", "ASF1A is aberrantly over-expressed in GIC tumors and plays key roles in GIC development and progression by stimulating the transcription of beta-catenin target genes." ], [ "Q9Y294-1", "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" ], [ "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" ], [ "Q6UXZ0-1", "RefSeq", "NP_001306871.1", "26342724", "Identified TMIGD1 as a novel cell adhesion molecule expressed in kidney epithelial cells that protects kidney epithelial cells from oxidative cell injury to promote cell survival" ], [ "Q9H4G0-1", "RefSeq", "NP_001245258.1", "29428502", "4.1N, betaII spectrin and ankyrin G are structural components of the lateral membrane skeleton and this skeleton plays an essential role in the assembly of a fully functional lateral membrane." ], [ "Q9H4G0-1", "RefSeq", "NP_001245258.1", "27448302", "Data show that overexpression of 4.1N protein decreased expression of flotillin-1, decreased activation of beta-catenin/Wnt pathway in non-small-cell lung cancer (NSCLC) cells." ], [ "Q9H4G0-1", "RefSeq", "NP_001245258.1", "26575790", "Data suggest that repression of JNK-c-Jun signaling through pancreatic polypeptide receptor 1 (PP1) is one of the key anti-tumor mechanisms of neuronal membrane cytoskeletal protein 4.1 (4.1N)." ], [ "Q9H4G0-1", "RefSeq", "NP_001245258.1", "26648170", "The data of the current study identified 4.1N as an inhibitor of hypoxiainduced tumor progression in epithelial ovarian cancer cells." ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "30431081", "Data showed that DOK7 transcript variants 1 (DOK7V1) were decreased in lung cancer, and associated with poor overall survival and progressionfree survival. Its overexpression limited the proliferation and migration, but enhanced the adhesion to the extracellular matrix, of lung cancer cells. Further data indicate that DOK7V1 may inhibit proliferation and migration via negatively regulating the PI3K/AKT/mTOR signaling." ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "30829272", "This study shows hypermethylation of DOK7 gene in DNA from patients affected with breast cancer" ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "29990858", "Repression of Dok7 expression via DNMT1 mediated DNA methylation promotes glioma cell proliferation." ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "29292499", "Data identified MuSK activator Dok-7 as a another ROR1-binding protein independently of MuSK interaction." ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "20603078", "The crystal structure of the Dok7 PH-PTB domains in complex with a phosphopeptide representing the Dok7-binding site on MuSK, is presented." ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "17439981", "Study of patients with congenital myasthenic syndromes with mutations in DOK7; none with DOK7 mutations had tubular aggregates in muscle biopsy, implying 'limb-girdle myasthenia with tubular aggregates' may be distinct from CMS caused by DOK7 mutations" ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "16917026", "Findings showed that recessive inheritance of mutations in Dok-7, which result in a defective structure of the neuromuscular junction, is a cause of congenital myasthenic syndromes with proximal muscle weakness" ], [ "Q18PE1-1", "RefSeq", "NP_001158145.1", "16794080", "Dok-7 is essential for neuromuscular synaptogenesis through its interaction with MuSK" ], [ "O14810-1", "RefSeq", "NP_006642.1", "29118371", "Findings do not support microRNA137 (MIR137) and complexin 1 (CPLX1) conferring susceptibility to schizophrenia in Han Chinese. Publication Status: Online-Only" ], [ "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", "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." ], [ "Q86VF2-1", "RefSeq", "NP_001158058.1", "30335789", "Study results in UOK146 renal cell carcinoma cell line provide evidence of novel splicing in intron 15 of IGFN1 leading to the formation of two more alternative spliced isoforms. Potential G-quadruplex forming sequence (PQS) in this intron forms a stable G-quadruplex which is involved in the alternative splicing and regulates splicing efficiency. Publication Status: Online-Only" ], [ "Q86VF2-1", "RefSeq", "NP_001158058.1", "29323771", "A novel variant, c.6196A>G in the IGFN1 gene, was significantly associated with only Polypoidal choroidal vasculopathy (combined p = 7.1 x 10(-11) , odds ratio = 9.44), but not with neovascular age-related macular degeneration(combined p = 0.683, odds ratio = 1.30)." ], [ "Q86VF2-1", "RefSeq", "NP_001158058.1", "18756455", "A model in which this increased expression of IGFN1 serves to down-regulate protein synthesis via interaction with eEF1A during denervation." ], [ "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." ], [ "Q9Y6N9-1", "RefSeq", "NP_001284693.1", "28653419", "Harmonin can adopt two different structural states, 'open' and 'closed', as a result of the self-interaction between its domains." ], [ "Q9Y6N9-1", "RefSeq", "NP_001284693.1", "28660889", "Crystall structure shows the interactions between harmonin protein domains and its partner Myo7a. Publication Status: Online-Only" ], [ "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", "29396440", "Promoting epithelial mesenchymal transition is the primary role for ZAK in cancer progression. Publication Status: Online-Only" ], [ "Q9NYL2-1", "RefSeq", "NP_057737.2", "29071797", "The ZAK rs3769201 and rs722864 may be functional susceptibility loci for lung cancer risk." ], [ "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." ], [ "Q8TE73-1", "RefSeq", "NP_001360.1", "28939216", "A novel mutation causing primary ciliary dyskinesia was found in Japanese patients." ] ] }, "readme": "Name\n - Human Protein Function (NCBI Refseq)\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-03-16T15:35:15.248632\n\nModified on\n - 2020-04-10T11:41:20.232299\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 Protein Function (NCBI RefSeq) dataset contains biological function annotaion 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 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-1.5.18/source/source/refseq_protein_all_9606.gpff\n Name: human_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/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-1.5.18/reviewed/human_protein_function_refseq.csv\n Name: human_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_protein_function_refseq.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"15115\"\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: \"15115\"\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: \"52695\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"51945\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/human_protein_function_refseq.csv" }