{ "bcoid": "GLY_000719", "title": "The Mouse Glycan Interaction data Citations (MatrixDB)", "description": "The Mouse Glycan Interaction data Citations (MatrixDB)] contains details of the publication present in ...", "filename": "mouse_protein_citations_matrixdb.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Protein" ], "tags": [ "Glycan Interaction Data Citations (MatrixDB)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q61001-1...", "Cell type-sp..." ], [ "P37237-1...", "A decorin-de..." ] ], "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" } ], [ "Q61001-1", "Cell type-specific differences in glycosaminoglycans modulate the biological activity of a heparin-binding peptide (RKRLQVQLSIRT) from the G domain of the laminin alpha1 chain.", "The Journal of biological chemistry", "2001 Jun 22", "Hoffman MP, Engbring JA, Nielsen PK, Vargas J, Steinberg Z, Karmand AJ, Nomizu M, Yamada Y, Kleinman HK", "protein_xref_pubmed", "11304538", "glycan_xref_matrixdb", "GAG_1" ], [ "P37237-1", "A decorin-deficient matrix affects skin chondroitin/dermatan sulfate levels and keratinocyte function.", "Matrix biology : journal of the International Society for Matrix Biology", "2014 Apr", "Nikolovska K, Renke JK, Jungmann O, Grobe K, Iozzo RV, Zamfir AD, Seidler DG", "protein_xref_pubmed", "24447999", "glycan_xref_matrixdb", "GAG_6" ], [ "P19137-1", "Cell type-specific differences in glycosaminoglycans modulate the biological activity of a heparin-binding peptide (RKRLQVQLSIRT) from the G domain of the laminin alpha1 chain.", "The Journal of biological chemistry", "2001 Jun 22", "Hoffman MP, Engbring JA, Nielsen PK, Vargas J, Steinberg Z, Karmand AJ, Nomizu M, Yamada Y, Kleinman HK", "protein_xref_pubmed", "11304538", "glycan_xref_matrixdb", "GAG_1" ], [ "P19137-1", "Binding of the G domains of laminin alpha1 and alpha2 chains and perlecan to heparin, sulfatides, alpha-dystroglycan and several extracellular matrix proteins.", "The EMBO journal", "1999 Feb 15", "Talts JF, Andac Z, Gohring W, Brancaccio A, Timpl R", "protein_xref_pubmed", "10022829", "glycan_xref_matrixdb", "GAG_1" ], [ "Q91V88-1", "Nephronectin binds to heparan sulfate proteoglycans via its MAM domain.", "Matrix biology : journal of the International Society for Matrix Biology", "2013 Apr 24", "Sato Y, Shimono C, Li S, Nakano I, Norioka N, Sugiura N, Kimata K, Yamada M, Sekiguchi K", "protein_xref_pubmed", "23357641", "glycan_xref_matrixdb", "GAG_1" ], [ "Q91V88-1", "Nephronectin binds to heparan sulfate proteoglycans via its MAM domain.", "Matrix biology : journal of the International Society for Matrix Biology", "2013 Apr 24", "Sato Y, Shimono C, Li S, Nakano I, Norioka N, Sugiura N, Kimata K, Yamada M, Sekiguchi K", "protein_xref_pubmed", "23357641", "glycan_xref_matrixdb", "GAG_2" ], [ "Q91V88-1", "Nephronectin binds to heparan sulfate proteoglycans via its MAM domain.", "Matrix biology : journal of the International Society for Matrix Biology", "2013 Apr 24", "Sato Y, Shimono C, Li S, Nakano I, Norioka N, Sugiura N, Kimata K, Yamada M, Sekiguchi K", "protein_xref_pubmed", "23357641", "glycan_xref_matrixdb", "GAG_7" ], [ "Q60675-1", "Binding of the G domains of laminin alpha1 and alpha2 chains and perlecan to heparin, sulfatides, alpha-dystroglycan and several extracellular matrix proteins.", "The EMBO journal", "1999 Feb 15", "Talts JF, Andac Z, Gohring W, Brancaccio A, Timpl R", "protein_xref_pubmed", "10022829", "glycan_xref_matrixdb", "GAG_1" ], [ "P39876-1", "TIMP-3 binds to sulfated glycosaminoglycans of the extracellular matrix.", "The Journal of biological chemistry", "2000 Oct 6", "Yu WH, Yu S, Meng Q, Brew K, Woessner JF Jr", "protein_xref_pubmed", "10900194", "glycan_xref_matrixdb", "GAG_1" ], [ "P07214-1", "The first draft of the endostatin interaction network.", "The Journal of biological chemistry", "2009 Aug 14", "Faye C, Chautard E, Olsen BR, Ricard-Blum S", "protein_xref_pubmed", "19542224", "glycan_xref_matrixdb", "GAG_3" ], [ "P07214-1", "The first draft of the endostatin interaction network.", "The Journal of biological chemistry", "2009 Aug 14", "Faye C, Chautard E, Olsen BR, Ricard-Blum S", "protein_xref_pubmed", "19542224", "glycan_xref_matrixdb", "GAG_1" ], [ "P19137-1", "High and low affinity heparin-binding sites in the G domain of the mouse laminin alpha 4 chain.", "The Journal of biological chemistry", "2000 Sep 22", "Yamaguchi H, Yamashita H, Mori H, Okazaki I, Nomizu M, Beck K, Kitagawa Y", "protein_xref_pubmed", "10893232", "glycan_xref_matrixdb", "GAG_1" ], [ "P16092-1", "Fibroblast growth factor receptors 1 and 2 interact differently with heparin/heparan sulfate. Implications for dynamic assembly of a ternary signaling complex.", "The Journal of biological chemistry", "2002 Aug 9", "Powell AK, Fernig DG, Turnbull JE", "protein_xref_pubmed", "12034712", "glycan_xref_matrixdb", "GAG_1" ], [ "P16092-1", "Fibroblast growth factor receptors 1 and 2 interact differently with heparin/heparan sulfate. Implications for dynamic assembly of a ternary signaling complex.", "The Journal of biological chemistry", "2002 Aug 9", "Powell AK, Fernig DG, Turnbull JE", "protein_xref_pubmed", "12034712", "glycan_xref_matrixdb", "GAG_2" ], [ "Q9Z0E2-1", "Cell-surface heparan sulfate proteoglycans potentiate chordin antagonism of bone morphogenetic protein signaling and are necessary for cellular uptake of chordin.", "The Journal of biological chemistry", "2004 Dec 3", "Jasuja R, Allen BL, Pappano WN, Rapraeger AC, Greenspan DS", "protein_xref_pubmed", "15381701", "glycan_xref_matrixdb", "GAG_1" ], [ "Q05793-1", "The C-terminal domain V of perlecan promotes beta1 integrin-mediated cell adhesion, binds heparin, nidogen and fibulin-2 and can be modified by glycosaminoglycans.", "European journal of biochemistry", "1997 Nov 15", "Brown JC, Sasaki T, Gohring W, Yamada Y, Timpl R", "protein_xref_pubmed", "9431988", "glycan_xref_matrixdb", "GAG_1" ], [ "P61148-1", "A decorin-deficient matrix affects skin chondroitin/dermatan sulfate levels and keratinocyte function.", "Matrix biology : journal of the International Society for Matrix Biology", "2014 Apr", "Nikolovska K, Renke JK, Jungmann O, Grobe K, Iozzo RV, Zamfir AD, Seidler DG", "protein_xref_pubmed", "24447999", "glycan_xref_matrixdb", "GAG_6" ], [ "Q60675-1", "Cell type-specific differences in glycosaminoglycans modulate the biological activity of a heparin-binding peptide (RKRLQVQLSIRT) from the G domain of the laminin alpha1 chain.", "The Journal of biological chemistry", "2001 Jun 22", "Hoffman MP, Engbring JA, Nielsen PK, Vargas J, Steinberg Z, Karmand AJ, Nomizu M, Yamada Y, Kleinman HK", "protein_xref_pubmed", "11304538", "glycan_xref_matrixdb", "GAG_1" ], [ "P97927-1", "High and low affinity heparin-binding sites in the G domain of the mouse laminin alpha 4 chain.", "The Journal of biological chemistry", "2000 Sep 22", "Yamaguchi H, Yamashita H, Mori H, Okazaki I, Nomizu M, Beck K, Kitagawa Y", "protein_xref_pubmed", "10893232", "glycan_xref_matrixdb", "GAG_1" ], [ "P36363-1", "A decorin-deficient matrix affects skin chondroitin/dermatan sulfate levels and keratinocyte function.", "Matrix biology : journal of the International Society for Matrix Biology", "2014 Apr", "Nikolovska K, Renke JK, Jungmann O, Grobe K, Iozzo RV, Zamfir AD, Seidler DG", "protein_xref_pubmed", "24447999", "glycan_xref_matrixdb", "GAG_6" ], [ "P22777-1", "Interleukin-5 binds to heparin/heparan sulfate. A model for an interaction with extracellular matrix.", "Journal of leukocyte biology", "1998 Mar", "Lipscombe RJ, Nakhoul AM, Sanderson CJ, Coombe DR", "protein_xref_pubmed", "9500522", "glycan_xref_matrixdb", "GAG_1" ], [ "P12850-1", "A method for the non-covalent immobilization of heparin to surfaces.", "Analytical biochemistry", "2004 Jul 1", "Mahoney DJ, Whittle JD, Milner CM, Clark SJ, Mulloy B, Buttle DJ, Jones GC, Day AJ, Short RD", "protein_xref_pubmed", "15183770", "glycan_xref_matrixdb", "GAG_1" ], [ "P01587-1", "Heparin-binding sites in granulocyte-macrophage colony-stimulating factor. Localization and regulation by histidine ionization.", "The Journal of biological chemistry", "2005 Sep 9", "Sebollela A, Cagliari TC, Limaverde GS, Chapeaurouge A, Sorgine MH, Coelho-Sampaio T, Ramos CH, Ferreira ST", "protein_xref_pubmed", "16027123", "glycan_xref_matrixdb", "GAG_1" ] ] }, "readme": "Name\n - The Mouse Glycan Interaction data Citations (MatrixDB)\n\nVersion\n - v-2.1.1\n\nCreated on\n - \n\nModified on\n - \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]\n\nAuthors\n - Sylvie Ricard-Blum [sylvie.ricard-blum@univ-lyon1.fr]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Glycan Interaction data Citations (MatrixDB)] contains details of the publication present in the dataset The Mouse Glycan Interaction data Citations (MatrixDB) https://data.glygen.org/GLY_000333.\n\nDescription Domain\n Keywords\n - MatrixDB\n - Glycan Interaction\n - Publications\n - Citations\n - PubMed\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 - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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: mouse_protein_matrixdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_matrixdb.csv\n Output Subdomain\n Name: mouse_protein_citations_matrixdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_citations_matrixdb.csv\n Name: mouse_protein_citations_matrixdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_citations_matrixdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"13\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"6\"\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: \"13\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"13\"\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: \"13\"\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: \"5\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/mouse_protein_citations_matrixdb.csv" }