{ "bcoid": "GLY_000802", "title": "Yeast Proteoform Glycosylation Citations (UniProtKB)", "description": "", "filename": "yeast_proteoform_citations_glycosylation_sites_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Proteoform" ], "tag": [ "Protein Citations UniProtKB" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P36081-1...", "Mapping the ..." ], [ "P38993-1...", "The copper-i..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "glytoucan_ac" } ], [ "P36081-1", "Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae.", "Molecular & cellular proteomics : MCP", "2016-04", "Neubert Patrick, Halim Adnan, Zauser Martin, Essig Andreas, Joshi Hiren J, Zatorska Ewa, Larsen Ida Signe Bohse, Loibl Martin, Castells-Ballester Joan, Aebi Markus, Clausen Henrik, Strahl Sabine", "protein_xref_pubmed", "26764011", "protein_xref_uniprotkb_gly", "P36081", "" ], [ "P38993-1", "The copper-iron connection in biology: structure of the metallo-oxidase Fet3p.", "Proceedings of the National Academy of Sciences of the United States of America", "2005-10-25", "Taylor Alexander B, Stoj Christopher S, Ziegler Lynn, Kosman Daniel J, Hart P John", "protein_xref_pubmed", "16230618", "protein_xref_uniprotkb_gly", "P38993", "" ], [ "P00724-1", "Characterization of the glycosylation sites in yeast external invertase. I. N-linked oligosaccharide content of the individual sequons.", "The Journal of biological chemistry", "1988-05-25", "Reddy V A, Johnson R S, Biemann K, Williams R S, Ziegler F D, Trimble R B, Maley F", "protein_xref_pubmed", "3284881", "protein_xref_uniprotkb_gly", "P00724", "" ], [ "P20840-1", "Structure of Saccharomyces cerevisiae alpha-agglutinin. Evidence for a yeast cell wall protein with multiple immunoglobulin-like domains with atypical disulfides.", "The Journal of biological chemistry", "1995-11-03", "Chen M H, Shen Z M, Bobin S, Kahn P C, Lipke P N", "protein_xref_pubmed", "7592821", "protein_xref_uniprotkb_gly", "P20840", "" ], [ "P47001-1", "O-mannosylation precedes and potentially controls the N-glycosylation of a yeast cell wall glycoprotein.", "EMBO reports", "2003-06", "Ecker Margit, Mrsa Vladimir, Hagen Ilja, Deutzmann Rainer, Strahl Sabine, Tanner Widmar", "protein_xref_pubmed", "12776183", "protein_xref_uniprotkb_gly", "P47001", "" ], [ "P00729-1", "N-Glycosylation analysis of yeast Carboxypeptidase Y reveals the ultimate removal of phosphate from glycans at Asn368.", "International journal of biological macromolecules", "2017-05", "B S Gnanesh Kumar, Surolia Avadhesha", "protein_xref_pubmed", "28189789", "protein_xref_uniprotkb_gly", "P00729", "" ], [ "P00729-1", "Structure of the carboxypeptidase Y inhibitor IC in complex with the cognate proteinase reveals a novel mode of the proteinase-protein inhibitor interaction.", "Journal of molecular biology", "2005-03-11", "Mima Joji, Hayashida Minoru, Fujii Tomomi, Narita Yusuke, Hayashi Rikimaru, Ueda Mitsuyoshi, Hata Yasuo", "protein_xref_pubmed", "15713484", "protein_xref_uniprotkb_gly", "P00729", "" ], [ "P00729-1", "2.8-A structure of yeast serine carboxypeptidase.", "Biochemistry", "1994-09-20", "Endrizzi J A, Breddam K, Remington S J", "protein_xref_pubmed", "7727362", "protein_xref_uniprotkb_gly", "P00729", "" ], [ "P09620-1", "Yeast Kex1p is a Golgi-associated membrane protein: deletions in a cytoplasmic targeting domain result in mislocalization to the vacuolar membrane.", "The Journal of cell biology", "1992-12", "Cooper A, Bussey H", "protein_xref_pubmed", "1469044", "protein_xref_uniprotkb_gly", "P09620", "" ], [ "P33767-1", "Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.", "Science (New York, N.Y.)", "2018-02-02", "Wild Rebekka, Kowal Julia, Eyring Jillianne, Ngwa Elsy M, Aebi Markus, Locher Kaspar P", "protein_xref_pubmed", "29301962", "protein_xref_uniprotkb_gly", "P33767", "" ], [ "Q12127-1", "Characterization of Ccw12p, a major key player in cell wall stability of Saccharomyces cerevisiae.", "Yeast (Chichester, England)", "2007-04", "Ragni Enrico, Sipiczki Matthias, Strahl Sabine", "protein_xref_pubmed", "17315267", "protein_xref_uniprotkb_gly", "Q12127", "" ], [ "P47001-1", "Pir proteins of Saccharomyces cerevisiae are attached to beta-1,3-glucan by a new protein-carbohydrate linkage.", "The Journal of biological chemistry", "2006-04-28", "Ecker Margit, Deutzmann Rainer, Lehle Ludwig, Mrsa Vladimir, Tanner Widmar", "protein_xref_pubmed", "16495216", "protein_xref_uniprotkb_gly", "P47001", "" ], [ "P39685-1", "POM152 is an integral protein of the pore membrane domain of the yeast nuclear envelope.", "The Journal of cell biology", "1994-04", "Wozniak R W, Blobel G, Rout M P", "protein_xref_pubmed", "8138573", "protein_xref_uniprotkb_gly", "P39685", "" ], [ "P42838-1", "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "eLife", "2020-12-15", "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "protein_xref_pubmed", "33320091", "protein_xref_uniprotkb_gly", "P42838", "" ], [ "P25656-1", "Structure and autoregulation of a P4-ATPase lipid flippase.", "Nature", "2019-07", "Timcenko Milena, Lyons Joseph A, Januliene Dovile, Ulstrup Jakob J, Dieudonn\u00e9 Thibaud, Montigny C\u00e9dric, Ash Miriam-Rose, Karlsen Jesper Lykkegaard, Boesen Thomas, K\u00fchlbrandt Werner, Lenoir Guillaume, Moeller Arne, Nissen Poul", "protein_xref_pubmed", "31243363", "protein_xref_uniprotkb_gly", "P25656", "" ], [ "P25656-1", "Autoinhibition and activation mechanisms of the eukaryotic lipid flippase Drs2p-Cdc50p.", "Nature communications", "2019 Sep 12", "Bai L, Kovach A, You Q, Hsu HC, Zhao G, Li H", "protein_xref_pubmed", "31515475", "protein_xref_uniprotkb_gly", "P25656", "" ], [ "Q03691-1", "Membrane topology and post-translational modification of the Saccharomyces cerevisiae essential protein Rot1.", "Yeast (Chichester, England)", "2008-02", "Juanes M Angeles, Carlos Igual J, Carmen Ba\u00f1\u00f3 M", "protein_xref_pubmed", "17914748", "protein_xref_uniprotkb_gly", "Q03691", "" ], [ "Q04121-1", "The yeast Na+/H+ exchanger Nhx1 is an N-linked glycoprotein. Topological implications.", "The Journal of biological chemistry", "2001-02-02", "Wells K M, Rao R", "protein_xref_pubmed", "11036065", "protein_xref_uniprotkb_gly", "Q04121", "" ], [ "Q12127-1", "Sed1p and Srl1p are required to compensate for cell wall instability in Saccharomyces cerevisiae mutants defective in multiple GPI-anchored mannoproteins.", "Molecular microbiology", "2004-06", "Hagen Ilja, Ecker Margit, Lagorce Arnaud, Francois Jean M, Sestak Sergej, Rachel Reinhard, Grossmann Guido, Hauser Nicole C, Hoheisel J\u00f6rg D, Tanner Widmar, Strahl Sabine", "protein_xref_pubmed", "15165243", "protein_xref_uniprotkb_gly", "Q12127", "" ], [ "D6VTK4-1", "Mutational analysis of the role of N-glycosylation in alpha-factor receptor function.", "Biochemistry", "2001-08-14", "Mentesana P E, Konopka J B", "protein_xref_pubmed", "11583169", "protein_xref_uniprotkb_gly", "D6VTK4", "" ], [ "P40345-1", "Expanding of Phospholipid:Diacylglycerol AcylTransferase (PDAT) from Saccharomyces cerevisiae as Multifunctional Biocatalyst with Broad Acyl Donor/Acceptor Selectivity.", "Applied biochemistry and biotechnology", "2019 Jul", "Feng Y, Zhang Y, Ding W, Wu P, Cao X, Xue S", "protein_xref_pubmed", "30706417", "protein_xref_uniprotkb_gly", "P40345", "" ], [ "P54074-1", "Asi1 is an inner nuclear membrane protein that restricts promoter access of two latent transcription factors.", "The Journal of cell biology", "2006-06-05", "Boban Mirta, Zargari Arezou, Andr\u00e9asson Claes, Heessen Stijn, Thyberg Johan, Ljungdahl Per O", "protein_xref_pubmed", "16735580", "protein_xref_uniprotkb_gly", "P54074", "" ], [ "P54074-1", "Inner nuclear membrane proteins Asi1, Asi2, and Asi3 function in concert to maintain the latent properties of transcription factors Stp1 and Stp2.", "The Journal of biological chemistry", "2007-01-05", "Zargari Arezou, Boban Mirta, Heessen Stijn, Andr\u00e9asson Claes, Thyberg Johan, Ljungdahl Per O", "protein_xref_pubmed", "17085444", "protein_xref_uniprotkb_gly", "P54074", "" ], [ "P47011-1", "Yeast glycogenin (Glg2p) produced in Escherichia coli is simultaneously glucosylated at two vicinal tyrosine residues but results in a reduced bacterial glycogen accumulation.", "European journal of biochemistry", "2004-10", "Albrecht Tanja, Haebel Sophie, Koch Anke, Krause Ulrike, Eckermann Nora, Steup Martin", "protein_xref_pubmed", "15479227", "protein_xref_uniprotkb_gly", "P47011", "" ], [ "P38109-1", "A newly characterized vacuolar serine carboxypeptidase, Atg42/Ybr139w, is required for normal vacuole function and the terminal steps of autophagy in the yeast Saccharomyces cerevisiae.", "Molecular biology of the cell", "2018-05-01", "Parzych Katherine R, Ariosa Aileen, Mari Muriel, Klionsky Daniel J", "protein_xref_pubmed", "29514932", "protein_xref_uniprotkb_gly", "P38109", "" ], [ "Q12355-1", "Reducing haziness in white wine by overexpression of Saccharomyces cerevisiae genes YOL155c and YDR055w.", "Applied microbiology and biotechnology", "2007-01", "Brown Shauna L, Stockdale Vanessa J, Pettolino Filomena, Pocock Kenneth F, de Barros Lopes Miguel, Williams Patrick J, Bacic Antony, Fincher Geoffrey B, H\u00f8j Peter B, Waters Elizabeth J", "protein_xref_pubmed", "17024473", "protein_xref_uniprotkb_gly", "Q12355", "" ], [ "Q08417-1", "Long chain base tolerance in Saccharomyces cerevisiae is induced by retrograde signals from the mitochondria.", "The Journal of biological chemistry", "2006-03-10", "Panwar Sneh Lata, Moye-Rowley W Scott", "protein_xref_pubmed", "16407254", "protein_xref_uniprotkb_gly", "Q08417", "" ], [ "P41543-1", "Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.", "Science (New York, N.Y.)", "2018-02-02", "Wild Rebekka, Kowal Julia, Eyring Jillianne, Ngwa Elsy M, Aebi Markus, Locher Kaspar P", "protein_xref_pubmed", "29301962", "protein_xref_uniprotkb_gly", "P41543", "" ], [ "P38875-1", "The GPI transamidase complex of Saccharomyces cerevisiae contains Gaa1p, Gpi8p, and Gpi16p.", "Molecular biology of the cell", "2001-10", "Fraering P, Imhof I, Meyer U, Strub J M, van Dorsselaer A, Vionnet C, Conzelmann A", "protein_xref_pubmed", "11598210", "protein_xref_uniprotkb_gly", "P38875", "" ], [ "P41948-1", "In vivo N-glycosylation of the mep2 high-affinity ammonium transporter of Saccharomyces cerevisiae reveals an extracytosolic N-terminus.", "Molecular microbiology", "2000-11", "Marini A M, Andr\u00e9 B", "protein_xref_pubmed", "11069679", "protein_xref_uniprotkb_gly", "P41948", "" ], [ "P23776-1", "The ER protein folding sensor UDP-glucose glycoprotein-glucosyltransferase modifies substrates distant to local changes in glycoprotein conformation.", "Nature structural & molecular biology", "2004 Feb", "Taylor SC, Ferguson AD, Bergeron JJ, Thomas DY", "protein_xref_pubmed", "14730348", "protein_xref_uniprotkb_gly", "P23776", "" ], [ "P47033-1", "Analysis of congenital disorder of glycosylation-Id in a yeast model system shows diverse site-specific under-glycosylation of glycoproteins.", "Journal of proteome research", "2012-11-02", "Bailey Ulla-Maja, Jamaluddin Muhammad Fairuz, Schulz Benjamin L", "protein_xref_pubmed", "23038983", "protein_xref_uniprotkb_gly", "P47033", "" ], [ "P27809-1", "Glycosylation in Saccharomyces cerevisiae: cloning and characterization of an alpha-1,2-mannosyltransferase structural gene.", "Glycobiology", "1992-02", "H\u00e4usler A, Robbins P W", "protein_xref_pubmed", "1550992", "protein_xref_uniprotkb_gly", "P27809", "" ], [ "P39007-1", "Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.", "Science (New York, N.Y.)", "2018-02-02", "Wild Rebekka, Kowal Julia, Eyring Jillianne, Ngwa Elsy M, Aebi Markus, Locher Kaspar P", "protein_xref_pubmed", "29301962", "protein_xref_uniprotkb_gly", "P39007", "" ], [ "P39006-1", "Lipid Homeostasis Is Maintained by Dual Targeting of the Mitochondrial PE Biosynthesis Enzyme to the ER.", "Developmental cell", "2018-01-22", "Friedman Jonathan R, Kannan Muthukumar, Toulmay Alexandre, Jan Calvin H, Weissman Jonathan S, Prinz William A, Nunnari Jodi", "protein_xref_pubmed", "29290583", "protein_xref_uniprotkb_gly", "P39006", "" ] ] }, "readme": "Name\n - Yeast Proteoform Glycosylation Citations (UniProtKB)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2022-09-02T10:55:15.390409\n\nModified on\n - 2023-09-11T20:40:10\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n - Glycosylation\n\n Pipeline Steps\n - Step-1: The script extracts the PMID from the dataset and uses the Entrez API to retrieve the publication details and extracts in a csv dataset. \n\nExecution Domain\n Scripts\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: yeast_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_uniprotkb.csv\n Output Subdomain\n Name: yeast_proteoform_citations_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_glycosylation_sites_uniprotkb.csv\n Name: yeast_proteoform_citations_glycosylation_sites_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_glycosylation_sites_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"29\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"33\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"22\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"33\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"33\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"33\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"29\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_glycosylation_sites_uniprotkb.csv" }