{ "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": [ [ "O75954-1...", "RefSeq..." ], [ "O75954-1...", "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" } ], [ "O75954-1", "RefSeq", "NP_006666.1", "27177197", "The proliferation, migration and invasion of human gastric cancer SGC7901 cells were significantly inhibited by overexpression of Tspan9." ], [ "O75954-1", "RefSeq", "NP_006666.1", "26865714", "TSPAN9 is an endosomal tetraspanin whose depletion has a pronounced effect on the entry of several viruses that fuse in the early endosome. Publication Status: Online-Only" ], [ "O75954-1", "RefSeq", "NP_006666.1", "18799160", "Tetraspanin CD9 has a role in determining vascular smooth muscle cell injury phenotypes" ], [ "O75954-1", "RefSeq", "NP_006666.1", "18795891", "Findings suggest a role for Tspan9 in regulating platelet function in concert with other platelet tetraspanins and their associated proteins." ], [ "Q8WTX9-1", "RefSeq", "NP_037436.1", "25299331", "In an expression screen for proteins that can activate the IFNB1 promoter, authors identified the ER-associated protein ZDHHC1 as a positive regulator of virus-triggered, MITA/STING-dependent immune signaling." ], [ "Q8WTX9-1", "RefSeq", "NP_037436.1", "23687301", "In silico screening for palmitoyl substrates reveals a role for DHHC1/3/10 (zDHHC1/3/11)-mediated neurochondrin palmitoylation in its targeting to Rab5-positive endosomes." ], [ "Q8WTX9-1", "RefSeq", "NP_037436.1", "20549515", "Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)" ], [ "Q86YM7-1", "RefSeq", "NP_004263.1", "30219717", "Study found the common variant rs7713917 in the HOMER1 gene to be significantly associated with suicide attempt in Chinese patient." ], [ "Q86YM7-1", "RefSeq", "NP_004263.1", "29923011", "Monomeric Homer 1a proteins increase activity of Imin channels, but did not modulate their electrophysiological properties. Recombinant Homer 1c protein did not block the induced calcium currents." ], [ "Q86YM7-1", "RefSeq", "NP_004263.1", "29079138", "Homer 1 rs7713917 gene variant associated with brain structure and function, severity of depression, and antidepressant response in patients affected by a major depressive episode in course of bipolar disorder." ], [ "Q86YM7-1", "RefSeq", "NP_004263.1", "28815330", "This study demonstrate that altered Homer1a levels in specific brain regions and cell types of patients suffering from schizophrenia, bipolar disorder and major depression." ], [ "Q9BRX8-1", "RefSeq", "NP_115709.3", "26438880", "Results suggest that adipocyte-derived PAMM may suppress macrophage activation by inhibiting MAPK signalling pathway." ], [ "Q9BRX8-1", "RefSeq", "NP_115709.3", "26402163", "Antioxidant stress induces PAMM mRNA expression in human peripheral blood mononuclear cells ." ], [ "Q9BRX8-1", "RefSeq", "NP_115709.3", "19951071", "The PAMM is a redox regulatory protein that modulates osteoclast differentiation in vitro. PAMM expression may affect bone resorption in vivo and help to maintain bone mass." ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "28441660", "This study describes the cardiac phenotype and outcome of ELAC2 mutation in Infantile Cardiomyopathy" ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "27769300", "A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement Publication Status: Online-Only" ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "27318894", "ELAC2 rs11545302 polymorphism was associated with PSA > 20 and rs4792311 was associated with TNM > 2." ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "16636667", "Candidate prostate cancer susceptibility gene ELAC2 potentiates TGF-beta/Smad-induced transcriptional responses" ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "11254449", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "11254448", "Observational study of gene-disease association. (HuGE Navigator)" ], [ "Q9BQ52-1", "RefSeq", "NP_776065.1", "11175785", "ELAC2 harbors mutations (including a frameshift and a nonconservative missense change) that segregate with prostate cancer in two Utah pedigrees" ], [ "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." ], [ "Q7Z7M0-1", "RefSeq", "NP_001401.2", "23063620", "Mutations in MEGF8 cause a Carpenter syndrome subtype frequently associated with defective left-right patterning, probably through perturbation of signaling by hedgehog and nodal family members." ], [ "Q13049-1", "RefSeq", "NP_036342.2", "28465353", "Data suggest that, in cardiomyocytes, TRIM32 attenuates activation of SRF signaling and hypertrophy due to dysbindin; TRIM24 promotes these effects. TRIM32 promotes dysbindin degradation; TRIM24 protects dysbindin from degradation. (TRIM = tripartite motif-containing protein; SRF = serum response factor)" ], [ "Q13049-1", "RefSeq", "NP_036342.2", "28052117", "HSP70-TRIM32 complex is biochemically distinct from the previously characterized 14-3-3-TRIM32 phospho-complex. Publication Status: Online-Only" ], [ "Q13049-1", "RefSeq", "NP_036342.2", "28954259", "TRIM32 as a crucial positive regulator of Herpes Simplex Virus type 1 (HSV-1) induced IFN-beta production in corneal epithelial cells, and it played a predominant role in clearing HSV-1 from the cornea." ], [ "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." ], [ "P51397-1", "RefSeq", "NP_004385.1", "25530065", "DAP1 may have an important role in cell adhesion, migration and growth in the context of breast cancer and has significant associations with the apoptosis pathway." ], [ "P51397-1", "RefSeq", "NP_004385.1", "24270644", "DAP1 was found to be correlated with disease progression and long-term survival of the colorectal patients. DAP1 is also a pivotal regulator of the growth and apoptosis and cellular response to chemotherapy agents." ], [ "P51397-1", "RefSeq", "NP_004385.1", "22798505", "This study demonstrates an inverse association between DAP1 mRNA levels and tumour stage and clinical outcome in breast cancer" ], [ "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", "29535165", "TXNDC5 mRNA and protein were highly upregulated in failing human left ventricles. TXNDC5 mRNA and protein were increased in human cardiac fibroblasts under transforming growth factor beta1 stimulation in vitro.TXNDC5 knockdown attenuated TGFbeta1-induced activation and ECM protein upregulation independent of SMAD3, but increasing expression of TXNDC5 triggered activation and proliferation and increased ECM protein prod..." ], [ "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", "29247155", "These results strongly suggest that high levels of TXNDC5 in Rheumatoid Arthritis synovial tissues suppress CXCL10 and TNFSF10 expression." ], [ "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." ], [ "Q99956-1", "RefSeq", "NP_001386.1", "30835362", "SNP rs5945326 in DUSP9 gene may be not associated with the risk of gestational diabetes mellitus" ], [ "Q99956-1", "RefSeq", "NP_001386.1", "29880481", "Chemotherapy increased DUSP9 expression and decreased DUSP16 expression in a HIF1-dependent manner." ], [ "Q99956-1", "RefSeq", "NP_001386.1", "25998184", "The results of this study, combined with previous studies, suggested that therapeutic intervention to increase the expression or activity of DUSP9 may enable the activation of anti-proliferation signals in malignant cells." ], [ "Q99956-1", "RefSeq", "NP_001386.1", "24838152", "A possible use for DUSP9 as CIMP marker." ], [ "Q99956-1", "RefSeq", "NP_001386.1", "21206059", "2.7 A resolution crystal structure of the catalytic domain of MKP-4 (MKP-4C) is presented" ], [ "Q99956-1", "RefSeq", "NP_001386.1", "18006813", "Microtubule disruption by MKP4 provides a novel mechanism for tumor suppression by a cytosolic MKP" ], [ "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." ], [ "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." ], [ "Q71RC2-1", "RefSeq", "NP_954660.1", "30520539", "The role of circLARP4/miR-761/RUNX3/p53/p21 signaling in HCC progression, providing a potential survival predictor and therapeutic candidate for HCC." ], [ "Q71RC2-1", "RefSeq", "NP_954660.1", "30686809", "LARP4 could suppress motility and metastatic potential of ovarian cancer cells." ], [ "Q71RC2-1", "RefSeq", "NP_954660.1", "21098120", "LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis." ], [ "Q71RC2-1", "RefSeq", "NP_954660.1", "16682284", "FISH study showed no cytogenetic abnormalities in any of the analyzed cases." ], [ "Q71RC2-1", "RefSeq", "NP_954660.1", "15572213", "The c-MPL protein altered expression provide an opportunity to diagnose and identify subpopulations of MPD patients. Review article" ], [ "Q12879-1", "RefSeq", "NP_001127880.1", "30544257", "The phenotypic spectrum in grin2a mutations ranged from normal or near-normal development with mild epilepsy and speech delay/apraxia to severe developmental and epileptic encephalopathy, often within the epilepsy-aphasia spectrum." ], [ "Q12879-1", "RefSeq", "NP_001127880.1", "30260902", "Three single nucleotide polymorphisms (SNPs) (rs1448258, rs194355, and rs168866) of GRIN2A were genotyped. The distribution of GRIN2A polymorphisms of our participants are shown as follows: rs1448258 CC 516:943, CT 38:75; rs194355 AA 209:381, AG 258:470, GG 78:163; and rs168866 CC 9:17, CT 117:252, TT 425:756. There were no significant discrepancies between cases and controls." ], [ "Q12879-1", "RefSeq", "NP_001127880.1", "29958946", "The results of this study provide preliminary evidence relevant to genetic continuity between schizophrenia and schizotypy for effects of the NMDA receptor gene GRIN2A." ], [ "Q12879-1", "RefSeq", "NP_001127880.1", "29896722", "GRIN2A mutation is associated with epilepsy-aphasia spectrum disorders but with a relatively low rate." ], [ "Q12879-1", "RefSeq", "NP_001127880.1", "29358611", "GRIN2A rare deleterious and loss of function variants are specifically associated with typical and atypical Rolandic epilepsy." ], [ "P17858-1", "RefSeq", "NP_002617.3", "30409970", "TAp73 deficiency results in a pronounced reduction in tumorigenic potential, which can be rescued by forced PFKL expression. Publication Status: Online-Only" ], [ "P17858-1", "RefSeq", "NP_002617.3", "28646105", "Liver PFK1 isoform assembles into filaments in a tetramer- and substrate-dependent manner,organizing isoform specific glucose metabolism in cells." ], [ "P17858-1", "RefSeq", "NP_002617.3", "22923583", "Findings showed glycosylation inhibited PFK1 activity and redirected glucose flux through the pentose phosphate pathway, thereby conferring a selective growth advantage on cancer cells" ], [ "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" ], [ "Q5QJ74-1", "RefSeq", "NP_689928.3", "18262179", "Depletion of Op18 by means of RNA interference increased the susceptibility of tubulin to TBCE or E-like mediated disruption, while overexpressed Op18 exerted a tubulin-protective effect." ] ] }, "readme": "Name\n - Human Protein Function (NCBI Refseq)\n\nVersion\n - 1.5.11\n\nCreated on\n - 2019-03-16T15:35:15.248632\n\nModified on\n - 2019-11-27T15:30:45.385729\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/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: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"15101\"\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: \"15101\"\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: \"52581\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"51858\"", "downloadurl": "/ln2data/releases/data/v-1.5.11/reviewed/human_protein_function_refseq.csv" }