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in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation.", "journal": "The Journal of biological chemistry", "date": "2005-01-07", "authors": "Chang Shuang, Pikaard Craig S", "reference": { "type": "PubMed", "id": "15516340", "url": "https://pubmed.ncbi.nlm.nih.gov/15516340" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9XFH4-1", "protein_name": "Chromatin remodeling protein DDM1", "gene_name": "DDM1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9XFH4", "url": "https://www.uniprot.org/uniprotkb/Q9XFH4" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.15516340", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": 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increases throughout Arabidopsis development.", "journal": "Planta", "date": "2005-10", "authors": "Ruiz-Garc\u00eda L, Cervera M T, Mart\u00ednez-Zapater J M", "reference": { "type": "PubMed", "id": "15968513", "url": "https://pubmed.ncbi.nlm.nih.gov/15968513" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9XFH4-1", "protein_name": "Chromatin remodeling protein DDM1", "gene_name": "DDM1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9XFH4", "url": "https://www.uniprot.org/uniprotkb/Q9XFH4" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.15968513", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 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"total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Analysis of Arabidopsis PsbQA gene expression in transgenic tobacco reveals differential role of its promoter and transcribed region in organ-specific and light-mediated regulation.", "journal": "Transgenic Res.", "date": "2004", "authors": "Gaur Tripti, Tyagi Akhilesh K", "reference": { "type": "PubMed", "id": "15198198", "url": "https://pubmed.ncbi.nlm.nih.gov/15198198" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9XFT3-1", "protein_name": "Oxygen-evolving enhancer protein 3-1, chloroplastic", "gene_name": "PSBQ1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9XFT3", "url": "https://www.uniprot.org/uniprotkb/Q9XFT3" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.15198198", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ 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"species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9XGW1", "url": "https://www.uniprot.org/uniprotkb/Q9XGW1" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.12468725", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { 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"count": 0 } ], "sort_fields": [] } ] }, { "title": "VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation.", "journal": "The Plant journal : for cell and molecular biology", "date": "2009-03", "authors": "Ceserani Teresa, Trofka Anna, Gandotra Neeru, Nelson Timothy", "reference": { "type": "PubMed", "id": "19000166", "url": "https://pubmed.ncbi.nlm.nih.gov/19000166" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9XI87-1", "protein_name": "Serine/threonine-protein kinase VIK", "gene_name": "VIK", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9ZPS9-1", "protein_name": "Serine/threonine-protein kinase BRI1-like 2", "gene_name": "BRL2", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9SIN1-1", "protein_name": "Inactive TPR repeat-containing thioredoxin TTL3", "gene_name": "TTL3", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", 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J.", "date": "2009", "authors": "Stanne Tara M, Sj\u00f6gren Lars L E, Koussevitzky Shai, Clarke Adrian K", "reference": { "type": "PubMed", "id": "18754756", "url": "https://pubmed.ncbi.nlm.nih.gov/18754756" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9XJ35-1", "protein_name": "ATP-dependent Clp protease proteolytic subunit-related protein 1, chloroplastic", "gene_name": "CLPR1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9XJ35", "url": "https://www.uniprot.org/uniprotkb/Q9XJ35" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.18754756", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], 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"journal": "The Journal of biological chemistry", "date": "2014-02-21", "authors": "Reyes Francisca C, Buono Rafael A, Roschzttardtz Hannetz, Di Rubbo Simone, Yeun Li Huey, Russinova Eugenia, Otegui Marisa S", "reference": { "type": "PubMed", "id": "24385429", "url": "https://pubmed.ncbi.nlm.nih.gov/24385429" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZNT0-1", "protein_name": "Protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1", "gene_name": "SKD1", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9SZ15-1", "protein_name": "Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5", "gene_name": "LIP5", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZNT0", "url": "https://www.uniprot.org/uniprotkb/Q9ZNT0" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], 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"count": 0 } ], "sort_fields": [] } ] }, { "title": "Arabidopsis photorespiratory serine hydroxymethyltransferase activity requires the mitochondrial accumulation of ferredoxin-dependent glutamate synthase.", "journal": "The Plant cell", "date": "2009-02", "authors": "Jamai Aziz, Salom\u00e9 Patrice A, Schilling Stephen H, Weber Andreas P M, McClung C Robertson", "reference": { "type": "PubMed", "id": "19223513", "url": "https://pubmed.ncbi.nlm.nih.gov/19223513" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZNZ7-1", "protein_name": "Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial", "gene_name": "GLU1", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9SZJ5-1", "protein_name": "Serine hydroxymethyltransferase 1, mitochondrial", "gene_name": "SHM1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZNZ7", "url": 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malate dehydrogenase from chloroplasts of Arabidopsis thaliana L.", "journal": "J. Biol. Chem.", "date": "1998", "authors": "Berkemeyer M, Scheibe R, Ocheretina O", "reference": { "type": "PubMed", "id": "9774405", "url": "https://pubmed.ncbi.nlm.nih.gov/9774405" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZP06-1", "protein_name": "Malate dehydrogenase 1, mitochondrial", "gene_name": "F12M16.14", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9SN86-1", "protein_name": "Malate dehydrogenase, chloroplastic", "gene_name": "F1P2.70", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q9ZP05-1", "protein_name": "Malate dehydrogenase 2, peroxisomal", "gene_name": "PMDH2", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZP06", "url": "https://www.uniprot.org/uniprotkb/Q9ZP06" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.9774405", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Ionising radiation induces the expression of PARP-1 and PARP-2 genes in Arabidopsis.", "journal": "Mol. Genet. Genomics", "date": "2001", "authors": "Doucet-Chabeaud G, Godon C, Brutesco C, de Murcia G, Kazmaier M", "reference": { "type": "PubMed", "id": "11523787", "url": "https://pubmed.ncbi.nlm.nih.gov/11523787" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZP54-1", "protein_name": "Poly [ADP-ribose] polymerase 1", "gene_name": "PARP1", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "Q11207-1", "protein_name": "Poly [ADP-ribose] polymerase 2", "gene_name": "PARP2", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZP54", "url": "https://www.uniprot.org/uniprotkb/Q9ZP54" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.11523787", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Analysis of Arabidopsis arginase gene transcription patterns indicates specific biological functions for recently diverged paralogs.", "journal": "Plant Mol. Biol.", "date": "2008", "authors": "Brownfield Disa L, Todd Christopher D, Deyholos Michael K", "reference": { "type": "PubMed", "id": "18425591", "url": "https://pubmed.ncbi.nlm.nih.gov/18425591" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZPF5-1", "protein_name": "Arginase 2, chloroplastic/mitochondrial", "gene_name": "ARGAH2", "tax_name": "Mouse-ear cress" }, { "uniprot_canonical_ac": "P46637-1", "protein_name": "Arginase 1, mitochondrial", "gene_name": "ARGAH1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZPF5", "url": "https://www.uniprot.org/uniprotkb/Q9ZPF5" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.18425591", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { 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Heynh.", "journal": "Biochem. Soc. 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"journal": "Biotechnology journal", "date": "2006-03", "authors": "Froissard Marine, Belgareh-Touz\u00e9 Na\u00efma, Buisson Nicole, Desimone Marcelo, Frommer Wolf B, Haguenauer-Tsapis Rosine", "reference": { "type": "PubMed", "id": "16897711", "url": "https://pubmed.ncbi.nlm.nih.gov/16897711" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "Q9ZPR7-1", "protein_name": "Ureide permease 1", "gene_name": "UPS1", "tax_name": "Mouse-ear cress" } ], "species": [ { "name": "Arabidopsis thaliana", "taxid": 3702, "evidence": [ { "database": "UniProtKB", "id": "Q9ZPR7", "url": "https://www.uniprot.org/uniprotkb/Q9ZPR7" } ], "common_name": "Mouse-ear cress", "glygen_name": "Arabidopsis", "reference_species": "Arabidopsis thaliana [3702]" } ], "record_id": "pubmed.16897711", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": 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